Starting phenix.real_space_refine on Mon Nov 18 16:46:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3t_17394/11_2024/8p3t_17394_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3t_17394/11_2024/8p3t_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3t_17394/11_2024/8p3t_17394.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3t_17394/11_2024/8p3t_17394.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3t_17394/11_2024/8p3t_17394_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3t_17394/11_2024/8p3t_17394_neut.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 14, 'ARG:plan': 6} 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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 9, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 9, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 13, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 7, '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: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 7, '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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 1, 'ARG: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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG: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: {'GLU:plan': 1, 'ARG: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: 12.47, per 1000 atoms: 0.74 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: 4.51 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 1.86 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: 6.02 Time building geometry restraints manager: 5.23 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 42.830 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.690 ------------------------------------------------------------------------------- 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 17252 Z= 0.752 Angle : 1.402 23.589 23419 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 : 11.91 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (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 TRP 0.016 0.003 TRP D 456 HIS 0.006 0.001 HIS G 128 PHE 0.028 0.003 PHE D 542 TYR 0.026 0.004 TYR C 391 ARG 0.019 0.001 ARG A 624 *********************** 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 : 1.803 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: 0.3613 time to fit residues: 143.4141 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 : 2.005 ------------------------------------------------------------------------------- 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 184 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 198 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17252 Z= 0.176 Angle : 0.544 7.407 23419 Z= 0.289 Chirality : 0.039 0.206 2704 Planarity : 0.004 0.046 2877 Dihedral : 5.982 58.557 2488 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.02 % Favored : 98.89 % Rotamer: Outliers : 2.81 % Allowed : 18.53 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.18), residues: 2183 helix: 2.40 (0.14), residues: 1333 sheet: -1.69 (0.38), residues: 150 loop : -0.73 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 667 HIS 0.006 0.001 HIS E 82 PHE 0.011 0.001 PHE A 619 TYR 0.016 0.001 TYR D 669 ARG 0.007 0.001 ARG B 657 *********************** 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 222 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 1.901 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 520 GLU cc_start: 0.8879 (mp0) cc_final: 0.8549 (mp0) REVERT: A 637 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7904 (ptmt) REVERT: A 656 ARG cc_start: 0.8056 (mtt90) cc_final: 0.7765 (mtt180) REVERT: B 666 MET cc_start: 0.7754 (mtp) cc_final: 0.7496 (mtt) REVERT: C 403 MET cc_start: 0.2902 (OUTLIER) cc_final: 0.1834 (pmm) REVERT: C 637 LYS cc_start: 0.6616 (mmtt) cc_final: 0.6372 (ptmm) REVERT: E 6 ARG cc_start: 0.6729 (ttt-90) cc_final: 0.5879 (tmm160) REVERT: E 56 GLU cc_start: 0.9200 (tp30) cc_final: 0.8666 (tp30) REVERT: E 70 GLU cc_start: 0.9107 (pt0) cc_final: 0.8891 (pm20) REVERT: E 81 ASP cc_start: 0.8935 (t0) cc_final: 0.8613 (t0) REVERT: F 81 ASP cc_start: 0.9151 (t0) cc_final: 0.8714 (t0) REVERT: F 95 GLU cc_start: 0.8996 (tp30) cc_final: 0.8717 (tp30) REVERT: F 206 GLN cc_start: 0.8688 (tt0) cc_final: 0.8287 (tm-30) REVERT: G 58 MET cc_start: 0.8962 (tpp) cc_final: 0.8710 (tpp) REVERT: G 99 ARG cc_start: 0.9174 (ptm160) cc_final: 0.8920 (ptm160) REVERT: H 81 ASP cc_start: 0.8425 (t0) cc_final: 0.8152 (t70) REVERT: H 149 ASN cc_start: 0.9380 (t0) cc_final: 0.9118 (t0) REVERT: H 190 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8889 (mm-30) REVERT: H 202 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8536 (mp0) REVERT: H 204 HIS cc_start: 0.6278 (OUTLIER) cc_final: 0.5848 (m-70) outliers start: 46 outliers final: 25 residues processed: 217 average time/residue: 0.3383 time to fit residues: 109.2917 Evaluate side-chains 172 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.836 ------------------------------------------------------------------------------- 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 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 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 110 optimal weight: 0.7980 chunk 61 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 GLN A ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17252 Z= 0.319 Angle : 0.577 12.848 23419 Z= 0.308 Chirality : 0.040 0.175 2704 Planarity : 0.004 0.064 2877 Dihedral : 4.507 57.641 2424 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.29 % Favored : 98.61 % Rotamer: Outliers : 3.71 % Allowed : 19.67 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.18), residues: 2183 helix: 2.70 (0.14), residues: 1333 sheet: -1.87 (0.34), residues: 205 loop : -0.48 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 667 HIS 0.005 0.001 HIS C 431 PHE 0.011 0.001 PHE D 604 TYR 0.012 0.001 TYR D 669 ARG 0.007 0.001 ARG A 656 *********************** 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 205 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 145 time to evaluate : 1.921 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: 0.8873 (mp0) cc_final: 0.8536 (mp0) REVERT: C 403 MET cc_start: 0.3968 (OUTLIER) cc_final: 0.1841 (mtm) REVERT: C 416 ARG cc_start: 0.5016 (tpt90) cc_final: 0.3591 (tmt170) REVERT: C 637 LYS cc_start: 0.6616 (mmtt) cc_final: 0.6415 (ptmm) REVERT: D 403 MET cc_start: 0.5374 (mpp) cc_final: 0.4822 (mpp) REVERT: E 56 GLU cc_start: 0.9134 (tp30) cc_final: 0.8739 (tp30) REVERT: E 70 GLU cc_start: 0.9113 (pt0) cc_final: 0.8833 (pm20) REVERT: E 81 ASP cc_start: 0.8933 (t0) cc_final: 0.8626 (t70) REVERT: E 99 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8100 (mtp-110) REVERT: E 128 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.7124 (t-90) REVERT: F 37 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7713 (ttm-80) REVERT: F 81 ASP cc_start: 0.9111 (t0) cc_final: 0.8714 (t0) REVERT: F 95 GLU cc_start: 0.8978 (tp30) cc_final: 0.8773 (tp30) REVERT: F 102 ARG cc_start: 0.9403 (OUTLIER) cc_final: 0.8257 (tpt-90) REVERT: F 206 GLN cc_start: 0.8753 (tt0) cc_final: 0.8357 (tm-30) REVERT: H 8 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8805 (tt) REVERT: H 10 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8038 (tmm) REVERT: H 81 ASP cc_start: 0.8436 (t0) cc_final: 0.8123 (t70) REVERT: H 149 ASN cc_start: 0.9530 (t0) cc_final: 0.9237 (t0) REVERT: H 190 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8807 (mm-30) REVERT: H 202 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: H 204 HIS cc_start: 0.6534 (OUTLIER) cc_final: 0.6116 (m-70) outliers start: 60 outliers final: 40 residues processed: 196 average time/residue: 0.3201 time to fit residues: 93.0380 Evaluate side-chains 180 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 2.019 ------------------------------------------------------------------------------- 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 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 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 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 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 67 CYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 ARG 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 12 ILE 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 8 ILE Chi-restraints excluded: chain H residue 10 MET Chi-restraints excluded: chain H residue 25 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 Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 189 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17252 Z= 0.164 Angle : 0.500 11.443 23419 Z= 0.260 Chirality : 0.038 0.183 2704 Planarity : 0.003 0.041 2877 Dihedral : 4.199 59.358 2421 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.88 % Favored : 99.03 % Rotamer: Outliers : 3.29 % Allowed : 20.02 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.18), residues: 2183 helix: 2.92 (0.14), residues: 1335 sheet: -1.53 (0.39), residues: 154 loop : -0.54 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 456 HIS 0.004 0.001 HIS G 82 PHE 0.009 0.001 PHE D 604 TYR 0.010 0.001 TYR D 669 ARG 0.004 0.000 ARG D 711 *********************** 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 209 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 156 time to evaluate : 1.937 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: 0.8735 (mp0) cc_final: 0.8380 (mp0) REVERT: A 657 ARG cc_start: 0.8109 (mmt180) cc_final: 0.7204 (ptt180) REVERT: B 459 MET cc_start: 0.6237 (mmm) cc_final: 0.6035 (mmm) REVERT: B 666 MET cc_start: 0.7117 (mtt) cc_final: 0.6787 (mtm) REVERT: C 403 MET cc_start: 0.3807 (OUTLIER) cc_final: 0.1625 (mtm) REVERT: D 403 MET cc_start: 0.5217 (mpp) cc_final: 0.4655 (mpp) REVERT: D 541 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7318 (mmm160) REVERT: D 542 PHE cc_start: 0.7767 (p90) cc_final: 0.7481 (p90) REVERT: D 761 LYS cc_start: 0.3545 (pttt) cc_final: 0.3246 (mmmt) REVERT: E 56 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8679 (tp30) REVERT: E 70 GLU cc_start: 0.9171 (pt0) cc_final: 0.8878 (pm20) REVERT: E 81 ASP cc_start: 0.8911 (t0) cc_final: 0.8614 (t70) REVERT: F 78 LYS cc_start: 0.8533 (ptmm) cc_final: 0.8250 (pttt) REVERT: F 81 ASP cc_start: 0.9115 (t0) cc_final: 0.8669 (t0) REVERT: F 95 GLU cc_start: 0.8995 (tp30) cc_final: 0.8411 (tp30) REVERT: F 102 ARG cc_start: 0.9300 (OUTLIER) cc_final: 0.8141 (tpt-90) REVERT: F 160 ASN cc_start: 0.8184 (m-40) cc_final: 0.7719 (m110) REVERT: F 206 GLN cc_start: 0.8774 (tt0) cc_final: 0.8371 (tm-30) REVERT: G 58 MET cc_start: 0.9022 (tpp) cc_final: 0.8811 (tpp) REVERT: H 8 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8848 (tt) REVERT: H 10 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8025 (tmm) REVERT: H 32 TYR cc_start: 0.9026 (m-80) cc_final: 0.8815 (m-10) REVERT: H 81 ASP cc_start: 0.8404 (t0) cc_final: 0.8097 (t70) REVERT: H 149 ASN cc_start: 0.9471 (t0) cc_final: 0.9077 (t0) REVERT: H 202 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8488 (mp0) REVERT: H 204 HIS cc_start: 0.6391 (OUTLIER) cc_final: 0.6095 (m-70) outliers start: 53 outliers final: 32 residues processed: 196 average time/residue: 0.3075 time to fit residues: 91.5604 Evaluate side-chains 189 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR 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 637 LYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 803 MET 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 423 GLU Chi-restraints excluded: chain D residue 498 ILE 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 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 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 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 150 ILE Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 10 MET Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 87 optimal weight: 0.1980 chunk 180 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 108 optimal weight: 20.0000 chunk 190 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 431 HIS ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17252 Z= 0.215 Angle : 0.503 9.824 23419 Z= 0.264 Chirality : 0.038 0.226 2704 Planarity : 0.003 0.041 2877 Dihedral : 4.136 59.402 2421 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.25 % Favored : 98.71 % Rotamer: Outliers : 4.06 % Allowed : 19.31 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.18), residues: 2183 helix: 2.90 (0.14), residues: 1341 sheet: -1.43 (0.40), residues: 153 loop : -0.49 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 456 HIS 0.004 0.001 HIS G 82 PHE 0.010 0.001 PHE D 604 TYR 0.014 0.001 TYR A 728 ARG 0.005 0.000 ARG C 416 *********************** 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 212 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 146 time to evaluate : 1.748 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 520 GLU cc_start: 0.8732 (mp0) cc_final: 0.8348 (mp0) REVERT: A 657 ARG cc_start: 0.8258 (mmt180) cc_final: 0.6939 (ttm170) REVERT: B 666 MET cc_start: 0.7340 (mtt) cc_final: 0.7123 (mtm) REVERT: C 403 MET cc_start: 0.4090 (OUTLIER) cc_final: 0.1424 (mtm) REVERT: C 416 ARG cc_start: 0.5300 (tpt90) cc_final: 0.4200 (ttp-170) REVERT: D 403 MET cc_start: 0.5436 (mpp) cc_final: 0.4933 (mpp) REVERT: D 492 MET cc_start: -0.1216 (ptt) cc_final: -0.4284 (ttp) REVERT: D 541 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7221 (mmm160) REVERT: E 56 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8704 (tp30) REVERT: E 70 GLU cc_start: 0.9137 (pt0) cc_final: 0.8841 (pm20) REVERT: E 81 ASP cc_start: 0.8909 (t0) cc_final: 0.8595 (t70) REVERT: E 99 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8142 (mtp-110) REVERT: E 128 HIS cc_start: 0.7539 (OUTLIER) cc_final: 0.7236 (t70) REVERT: F 81 ASP cc_start: 0.9100 (t0) cc_final: 0.8639 (t0) REVERT: F 95 GLU cc_start: 0.8996 (tp30) cc_final: 0.8416 (tp30) REVERT: F 102 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.8276 (tpt-90) REVERT: F 206 GLN cc_start: 0.8818 (tt0) cc_final: 0.8404 (tm-30) REVERT: H 10 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8020 (tmm) REVERT: H 32 TYR cc_start: 0.9066 (m-80) cc_final: 0.8863 (m-10) REVERT: H 81 ASP cc_start: 0.8416 (t0) cc_final: 0.8087 (t70) REVERT: H 149 ASN cc_start: 0.9529 (t0) cc_final: 0.9165 (t0) REVERT: H 202 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: H 204 HIS cc_start: 0.6349 (OUTLIER) cc_final: 0.6086 (m-70) outliers start: 66 outliers final: 37 residues processed: 200 average time/residue: 0.2953 time to fit residues: 89.1492 Evaluate side-chains 187 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 538 LEU 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 B residue 510 VAL Chi-restraints excluded: chain B residue 803 MET 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 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 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 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 150 ILE Chi-restraints excluded: chain F residue 204 HIS 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 10 MET Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 202 GLU 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 71 optimal weight: 8.9990 chunk 190 optimal weight: 0.0370 chunk 41 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 52 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 743 ASN F 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17252 Z= 0.247 Angle : 0.522 9.153 23419 Z= 0.274 Chirality : 0.039 0.217 2704 Planarity : 0.003 0.041 2877 Dihedral : 4.114 59.446 2421 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 0.97 % Favored : 98.98 % Rotamer: Outliers : 3.77 % Allowed : 19.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.18), residues: 2183 helix: 2.94 (0.14), residues: 1335 sheet: -1.33 (0.43), residues: 141 loop : -0.38 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 762 HIS 0.011 0.001 HIS C 431 PHE 0.010 0.001 PHE D 604 TYR 0.015 0.001 TYR A 728 ARG 0.003 0.000 ARG B 657 *********************** 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 207 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 146 time to evaluate : 1.909 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: 0.8745 (mp0) cc_final: 0.8352 (mp0) REVERT: A 657 ARG cc_start: 0.8358 (mmt180) cc_final: 0.7064 (ttm170) REVERT: C 403 MET cc_start: 0.4220 (OUTLIER) cc_final: 0.2963 (mtm) REVERT: D 492 MET cc_start: -0.1109 (ptt) cc_final: -0.4069 (ttp) REVERT: D 541 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7144 (mmm160) REVERT: D 761 LYS cc_start: 0.4027 (mmmt) cc_final: 0.3492 (pptt) REVERT: E 56 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8738 (tp30) REVERT: E 70 GLU cc_start: 0.9148 (pt0) cc_final: 0.8842 (pm20) REVERT: E 81 ASP cc_start: 0.8918 (t0) cc_final: 0.8590 (t70) REVERT: E 99 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8161 (mtp-110) REVERT: E 128 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.7237 (t70) REVERT: F 81 ASP cc_start: 0.9095 (t0) cc_final: 0.8715 (t0) REVERT: F 95 GLU cc_start: 0.8982 (tp30) cc_final: 0.8424 (tp30) REVERT: F 102 ARG cc_start: 0.9359 (OUTLIER) cc_final: 0.8335 (tpt-90) REVERT: F 206 GLN cc_start: 0.8862 (tt0) cc_final: 0.8444 (tm-30) REVERT: G 58 MET cc_start: 0.9027 (tpp) cc_final: 0.8809 (tpp) REVERT: H 10 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8048 (tmm) REVERT: H 81 ASP cc_start: 0.8356 (t0) cc_final: 0.8022 (t70) REVERT: H 149 ASN cc_start: 0.9554 (t0) cc_final: 0.9251 (t0) REVERT: H 190 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8963 (mm-30) REVERT: H 202 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8407 (mp0) REVERT: H 204 HIS cc_start: 0.6523 (OUTLIER) cc_final: 0.6230 (m-70) outliers start: 61 outliers final: 46 residues processed: 195 average time/residue: 0.2918 time to fit residues: 87.9078 Evaluate side-chains 195 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 140 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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 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 B residue 510 VAL Chi-restraints excluded: chain B residue 803 MET 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 459 MET 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 532 VAL 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 185 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 12 ILE 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 148 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 10 MET Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 120 optimal weight: 0.0670 chunk 154 optimal weight: 10.0000 chunk 119 optimal weight: 40.0000 chunk 178 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17252 Z= 0.199 Angle : 0.507 8.516 23419 Z= 0.265 Chirality : 0.039 0.235 2704 Planarity : 0.003 0.043 2877 Dihedral : 4.096 58.571 2421 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.29 % Favored : 98.66 % Rotamer: Outliers : 3.95 % Allowed : 19.78 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.18), residues: 2183 helix: 2.92 (0.14), residues: 1341 sheet: -1.18 (0.45), residues: 131 loop : -0.34 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 456 HIS 0.011 0.001 HIS C 431 PHE 0.012 0.001 PHE A 491 TYR 0.021 0.001 TYR A 728 ARG 0.004 0.000 ARG C 416 *********************** 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: 64 poor density : 149 time to evaluate : 1.745 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: A 520 GLU cc_start: 0.8723 (mp0) cc_final: 0.8302 (mp0) REVERT: A 637 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8563 (ptmt) REVERT: A 657 ARG cc_start: 0.8363 (mmt180) cc_final: 0.7180 (ttm170) REVERT: B 666 MET cc_start: 0.7260 (mtt) cc_final: 0.6908 (mtt) REVERT: C 403 MET cc_start: 0.3765 (OUTLIER) cc_final: 0.2637 (mtm) REVERT: C 416 ARG cc_start: 0.5231 (tpt90) cc_final: 0.4007 (ttp-170) REVERT: C 515 ASP cc_start: 0.9228 (m-30) cc_final: 0.8942 (m-30) REVERT: C 666 MET cc_start: 0.7738 (mmt) cc_final: 0.7419 (mmp) REVERT: D 492 MET cc_start: -0.0856 (ptt) cc_final: -0.3597 (ttp) REVERT: D 541 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7151 (mmm160) REVERT: E 56 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8726 (tp30) REVERT: E 70 GLU cc_start: 0.9156 (pt0) cc_final: 0.8845 (pm20) REVERT: E 81 ASP cc_start: 0.8915 (t0) cc_final: 0.8580 (t70) REVERT: E 99 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8164 (mtp-110) REVERT: E 128 HIS cc_start: 0.7509 (OUTLIER) cc_final: 0.7221 (t70) REVERT: F 81 ASP cc_start: 0.9089 (t0) cc_final: 0.8725 (t0) REVERT: F 95 GLU cc_start: 0.8984 (tp30) cc_final: 0.8404 (tp30) REVERT: F 102 ARG cc_start: 0.9330 (OUTLIER) cc_final: 0.8300 (tpt-90) REVERT: F 206 GLN cc_start: 0.8883 (tt0) cc_final: 0.8484 (tm-30) REVERT: H 10 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8038 (tmm) REVERT: H 32 TYR cc_start: 0.9051 (m-80) cc_final: 0.8837 (m-10) REVERT: H 70 GLU cc_start: 0.8973 (tp30) cc_final: 0.8673 (tp30) REVERT: H 74 ARG cc_start: 0.8749 (ttp80) cc_final: 0.8391 (ttm-80) REVERT: H 81 ASP cc_start: 0.8375 (t0) cc_final: 0.8039 (t70) REVERT: H 149 ASN cc_start: 0.9516 (t0) cc_final: 0.9207 (t0) REVERT: H 190 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8889 (mm-30) REVERT: H 202 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8374 (mp0) outliers start: 64 outliers final: 47 residues processed: 197 average time/residue: 0.2895 time to fit residues: 87.0490 Evaluate side-chains 200 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 144 time to evaluate : 1.861 ------------------------------------------------------------------------------- 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 526 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 538 LEU 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 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 459 MET 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 532 VAL 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 D residue 808 ILE 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 158 SER Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 204 HIS 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 148 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 10 MET Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 202 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 126 optimal weight: 0.4980 chunk 63 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 40 optimal weight: 50.0000 chunk 134 optimal weight: 0.8980 chunk 143 optimal weight: 8.9990 chunk 104 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 743 ASN F 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17252 Z= 0.257 Angle : 0.543 10.021 23419 Z= 0.284 Chirality : 0.039 0.252 2704 Planarity : 0.003 0.042 2877 Dihedral : 4.158 59.149 2421 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.39 % Favored : 98.57 % Rotamer: Outliers : 4.12 % Allowed : 20.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.18), residues: 2183 helix: 2.87 (0.14), residues: 1342 sheet: -1.14 (0.45), residues: 131 loop : -0.31 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 667 HIS 0.010 0.001 HIS C 431 PHE 0.010 0.001 PHE D 491 TYR 0.016 0.001 TYR A 728 ARG 0.003 0.000 ARG B 657 *********************** 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 211 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 144 time to evaluate : 1.985 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: A 520 GLU cc_start: 0.8666 (mp0) cc_final: 0.8288 (mp0) REVERT: A 657 ARG cc_start: 0.8398 (mmt180) cc_final: 0.7223 (ttm170) REVERT: B 666 MET cc_start: 0.7224 (mtt) cc_final: 0.6906 (mtt) REVERT: C 403 MET cc_start: 0.3961 (OUTLIER) cc_final: 0.3229 (mtm) REVERT: C 499 MET cc_start: 0.5653 (ppp) cc_final: 0.5372 (ppp) REVERT: C 666 MET cc_start: 0.7979 (mmt) cc_final: 0.7727 (mmt) REVERT: D 492 MET cc_start: -0.1001 (ptt) cc_final: -0.3885 (ttp) REVERT: D 541 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7137 (mmm160) REVERT: E 56 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8695 (tp30) REVERT: E 70 GLU cc_start: 0.9139 (pt0) cc_final: 0.8821 (pm20) REVERT: E 81 ASP cc_start: 0.8920 (t0) cc_final: 0.8590 (t70) REVERT: E 97 LEU cc_start: 0.8962 (mt) cc_final: 0.8735 (mt) REVERT: E 99 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8164 (mtp-110) REVERT: E 128 HIS cc_start: 0.7539 (OUTLIER) cc_final: 0.7240 (t70) REVERT: F 78 LYS cc_start: 0.8500 (ptmm) cc_final: 0.8206 (ptpp) REVERT: F 81 ASP cc_start: 0.9088 (t0) cc_final: 0.8759 (t0) REVERT: F 95 GLU cc_start: 0.8991 (tp30) cc_final: 0.8482 (tp30) REVERT: F 102 ARG cc_start: 0.9368 (OUTLIER) cc_final: 0.8718 (tpt-90) REVERT: F 206 GLN cc_start: 0.8900 (tt0) cc_final: 0.8490 (tm-30) REVERT: G 58 MET cc_start: 0.9075 (tpp) cc_final: 0.8788 (tpp) REVERT: H 10 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8042 (tmm) REVERT: H 81 ASP cc_start: 0.8387 (t0) cc_final: 0.8044 (t70) REVERT: H 149 ASN cc_start: 0.9552 (t0) cc_final: 0.9232 (t0) REVERT: H 190 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8818 (mm-30) REVERT: H 202 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8391 (mp0) REVERT: H 204 HIS cc_start: 0.6527 (OUTLIER) cc_final: 0.6289 (m-70) outliers start: 67 outliers final: 48 residues processed: 198 average time/residue: 0.2909 time to fit residues: 87.8489 Evaluate side-chains 197 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 140 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 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 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 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 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 532 VAL 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 808 ILE 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 158 SER Chi-restraints excluded: chain F residue 185 SER 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 78 LYS 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 10 MET Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 0.9980 chunk 202 optimal weight: 0.3980 chunk 184 optimal weight: 3.9990 chunk 196 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17252 Z= 0.221 Angle : 0.546 8.378 23419 Z= 0.286 Chirality : 0.039 0.286 2704 Planarity : 0.003 0.042 2877 Dihedral : 4.108 58.706 2417 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.34 % Favored : 98.61 % Rotamer: Outliers : 3.89 % Allowed : 20.20 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.18), residues: 2183 helix: 2.85 (0.14), residues: 1342 sheet: -0.96 (0.47), residues: 127 loop : -0.29 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 667 HIS 0.010 0.001 HIS C 431 PHE 0.012 0.001 PHE D 663 TYR 0.014 0.001 TYR A 728 ARG 0.005 0.000 ARG A 449 *********************** 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 210 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 147 time to evaluate : 1.930 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 520 GLU cc_start: 0.8645 (mp0) cc_final: 0.8235 (mp0) REVERT: A 657 ARG cc_start: 0.8499 (mmt180) cc_final: 0.7347 (ttm170) REVERT: B 666 MET cc_start: 0.7222 (mtt) cc_final: 0.6917 (mtm) REVERT: C 403 MET cc_start: 0.4014 (OUTLIER) cc_final: 0.3287 (mtm) REVERT: D 492 MET cc_start: -0.1039 (ptt) cc_final: -0.3882 (ttp) REVERT: D 541 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7160 (mmm160) REVERT: E 56 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8686 (tp30) REVERT: E 70 GLU cc_start: 0.9145 (pt0) cc_final: 0.8814 (pm20) REVERT: E 81 ASP cc_start: 0.8908 (t0) cc_final: 0.8512 (t70) REVERT: E 97 LEU cc_start: 0.8960 (mt) cc_final: 0.8732 (mt) REVERT: E 99 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8165 (mtp-110) REVERT: E 128 HIS cc_start: 0.7516 (OUTLIER) cc_final: 0.7232 (t70) REVERT: F 58 MET cc_start: 0.8380 (tpp) cc_final: 0.8137 (tpt) REVERT: F 81 ASP cc_start: 0.9092 (t0) cc_final: 0.8751 (t0) REVERT: F 95 GLU cc_start: 0.8982 (tp30) cc_final: 0.8473 (tp30) REVERT: F 102 ARG cc_start: 0.9344 (OUTLIER) cc_final: 0.8398 (tpt-90) REVERT: F 206 GLN cc_start: 0.8898 (tt0) cc_final: 0.8485 (tm-30) REVERT: G 58 MET cc_start: 0.9039 (tpp) cc_final: 0.8744 (tpp) REVERT: H 10 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.7992 (tmm) REVERT: H 74 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8525 (ttp-110) REVERT: H 81 ASP cc_start: 0.8377 (t0) cc_final: 0.8037 (t70) REVERT: H 149 ASN cc_start: 0.9523 (t0) cc_final: 0.9205 (t0) REVERT: H 190 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8835 (mm-30) outliers start: 63 outliers final: 50 residues processed: 197 average time/residue: 0.2752 time to fit residues: 85.4791 Evaluate side-chains 201 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 144 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 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 662 VAL Chi-restraints excluded: chain A residue 805 VAL 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 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 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 532 VAL 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 808 ILE 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 158 SER Chi-restraints excluded: chain F residue 185 SER 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 78 LYS 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 10 MET 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 207 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 106 optimal weight: 30.0000 chunk 138 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17252 Z= 0.225 Angle : 0.582 12.655 23419 Z= 0.301 Chirality : 0.040 0.265 2704 Planarity : 0.003 0.042 2877 Dihedral : 3.950 58.564 2414 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.53 % Allowed : 20.92 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.18), residues: 2183 helix: 2.80 (0.14), residues: 1343 sheet: -0.82 (0.51), residues: 114 loop : -0.33 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 667 HIS 0.010 0.001 HIS C 431 PHE 0.011 0.001 PHE D 580 TYR 0.013 0.001 TYR A 728 ARG 0.003 0.000 ARG B 657 ********************** 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 204 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 147 time to evaluate : 1.972 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 520 GLU cc_start: 0.8644 (mp0) cc_final: 0.8244 (mp0) REVERT: A 657 ARG cc_start: 0.8524 (mmt180) cc_final: 0.7459 (ttm170) REVERT: B 666 MET cc_start: 0.7326 (mtt) cc_final: 0.6962 (mtm) REVERT: C 403 MET cc_start: 0.3818 (OUTLIER) cc_final: 0.3274 (mtm) REVERT: C 515 ASP cc_start: 0.9231 (m-30) cc_final: 0.8945 (m-30) REVERT: D 492 MET cc_start: -0.0716 (ptt) cc_final: -0.3584 (ttp) REVERT: D 541 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7184 (mmm160) REVERT: E 56 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8685 (tp30) REVERT: E 70 GLU cc_start: 0.9145 (pt0) cc_final: 0.8813 (pm20) REVERT: E 81 ASP cc_start: 0.8899 (t0) cc_final: 0.8495 (t70) REVERT: E 97 LEU cc_start: 0.8959 (mt) cc_final: 0.8731 (mt) REVERT: E 99 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8160 (mtp-110) REVERT: E 128 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.7220 (t70) REVERT: F 81 ASP cc_start: 0.9091 (t0) cc_final: 0.8762 (t0) REVERT: F 95 GLU cc_start: 0.8980 (tp30) cc_final: 0.8471 (tp30) REVERT: F 102 ARG cc_start: 0.9343 (OUTLIER) cc_final: 0.8332 (tpt-90) REVERT: F 206 GLN cc_start: 0.8897 (tt0) cc_final: 0.8484 (tm-30) REVERT: G 58 MET cc_start: 0.9044 (tpp) cc_final: 0.8791 (tpp) REVERT: H 10 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.7962 (tmm) REVERT: H 74 ARG cc_start: 0.8755 (ttp80) cc_final: 0.8534 (ttp-110) REVERT: H 81 ASP cc_start: 0.8378 (t0) cc_final: 0.8036 (t70) REVERT: H 149 ASN cc_start: 0.9522 (t0) cc_final: 0.9200 (t0) REVERT: H 190 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8825 (mm-30) outliers start: 57 outliers final: 48 residues processed: 191 average time/residue: 0.2896 time to fit residues: 84.9063 Evaluate side-chains 199 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 144 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 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 662 VAL Chi-restraints excluded: chain A residue 805 VAL 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 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 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 523 MET Chi-restraints excluded: chain D residue 532 VAL 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 808 ILE 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 158 SER Chi-restraints excluded: chain F residue 185 SER 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 10 MET 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 185 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 48 optimal weight: 0.4980 chunk 174 optimal weight: 0.0980 chunk 72 optimal weight: 8.9990 chunk 178 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 160 ASN H 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.124226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.078943 restraints weight = 152034.633| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 8.48 r_work: 0.2860 rms_B_bonded: 6.22 restraints_weight: 2.0000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 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 = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17252 Z= 0.211 Angle : 0.574 12.647 23419 Z= 0.295 Chirality : 0.039 0.279 2704 Planarity : 0.003 0.042 2877 Dihedral : 3.849 58.284 2412 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.47 % Allowed : 21.10 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.18), residues: 2183 helix: 2.82 (0.14), residues: 1342 sheet: -0.91 (0.49), residues: 114 loop : -0.33 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 667 HIS 0.009 0.001 HIS C 431 PHE 0.009 0.001 PHE D 491 TYR 0.013 0.001 TYR A 728 ARG 0.003 0.000 ARG B 657 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3543.87 seconds wall clock time: 65 minutes 29.67 seconds (3929.67 seconds total)