Starting phenix.real_space_refine on Sat Oct 11 19:05:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3v_17396/10_2025/8p3v_17396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3v_17396/10_2025/8p3v_17396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p3v_17396/10_2025/8p3v_17396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3v_17396/10_2025/8p3v_17396.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p3v_17396/10_2025/8p3v_17396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3v_17396/10_2025/8p3v_17396.map" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.044 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 97 5.16 5 C 11085 2.51 5 N 2747 2.21 5 O 2985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16914 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2862 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 377} Chain breaks: 3 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 2, 'GLU:plan': 14, 'ARG:plan': 6, 'TYR:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 148 Chain: "B" Number of atoms: 2912 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 2881 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 6, 'ARG:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 90 Conformer: "B" Number of residues, atoms: 384, 2881 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 6, 'ARG:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 90 bond proxies already assigned to first conformer: 2909 Chain: "C" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2859 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 373} Chain breaks: 4 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 13, 'ASP:plan': 5, 'ARG:plan': 3, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 115 Chain: "D" Number of atoms: 2859 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 381, 2828 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 368} Chain breaks: 4 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'ASP:plan': 7, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 112 Conformer: "B" Number of residues, atoms: 381, 2828 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 368} Chain breaks: 4 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'ASP:plan': 7, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 112 bond proxies already assigned to first conformer: 2855 Chain: "E" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1357 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1357 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1351 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1357 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N APHE B 570 " occ=0.48 ... (20 atoms not shown) pdb=" CZ BPHE B 570 " occ=0.52 residue: pdb=" N AGLN B 582 " occ=0.35 ... (16 atoms not shown) pdb=" NE2BGLN B 582 " occ=0.65 residue: pdb=" N APHE B 619 " occ=0.34 ... (20 atoms not shown) pdb=" CZ BPHE B 619 " occ=0.66 residue: pdb=" N APHE D 570 " occ=0.63 ... (20 atoms not shown) pdb=" CZ BPHE D 570 " occ=0.37 residue: pdb=" N AGLN D 582 " occ=0.46 ... (16 atoms not shown) pdb=" NE2BGLN D 582 " occ=0.54 residue: pdb=" N APHE D 619 " occ=0.43 ... (20 atoms not shown) pdb=" CZ BPHE D 619 " occ=0.57 Time building chain proxies: 5.23, per 1000 atoms: 0.31 Number of scatterers: 16914 At special positions: 0 Unit cell: (117.925, 112.625, 137.8, 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 97 16.00 O 2985 8.00 N 2747 7.00 C 11085 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=2.01 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.04 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4114 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 27 sheets defined 61.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.540A pdb=" N GLN A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 removed outlier: 4.087A 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 511 through 515 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 623 removed outlier: 3.562A pdb=" N VAL A 597 " --> pdb=" O SER A 593 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 623 " --> pdb=" O PHE A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 636 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 764 Processing helix chain 'A' and resid 788 through 815 removed outlier: 3.803A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.629A 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 511 through 515 Processing helix chain 'B' and resid 518 through 542 Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 591 through 625 removed outlier: 3.910A pdb=" N GLU B 623 " --> pdb=" O APHE B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 638 Processing helix chain 'B' and resid 649 through 657 Processing helix chain 'B' and resid 660 through 673 removed outlier: 3.532A 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: 3.648A pdb=" N PHE B 792 " --> pdb=" O VAL B 788 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 815 " --> pdb=" O CYS B 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.539A pdb=" N GLN C 410 " --> pdb=" O ASN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 removed outlier: 4.290A 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 511 through 515 removed outlier: 3.854A pdb=" N LEU C 514 " --> pdb=" O PHE C 511 " (cutoff:3.500A) 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 623 removed outlier: 3.743A pdb=" N GLU C 623 " --> pdb=" O PHE C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 638 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 788 through 814 removed outlier: 3.742A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 411 removed outlier: 3.564A pdb=" N GLN D 410 " --> pdb=" O ASN D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 415 removed outlier: 4.238A 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 Processing helix chain 'D' and resid 568 through 581 Processing helix chain 'D' and resid 591 through 622 removed outlier: 3.543A pdb=" N VAL D 597 " --> pdb=" O SER D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 638 Processing helix chain 'D' and resid 649 through 657 Processing helix chain 'D' and resid 660 through 673 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 785 through 787 No H-bonds generated for 'chain 'D' and resid 785 through 787' Processing helix chain 'D' and resid 788 through 815 removed outlier: 3.735A 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: 4.184A pdb=" N GLU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 162 removed outlier: 3.702A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 209 Processing helix chain 'F' and resid 6 through 30 removed outlier: 3.524A pdb=" N MET F 10 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU F 11 " --> pdb=" O GLY F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 removed outlier: 3.608A pdb=" N LEU F 97 " --> pdb=" O THR F 93 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 125 Processing helix chain 'F' and resid 133 through 162 Processing helix chain 'F' and resid 176 through 209 removed outlier: 3.986A pdb=" N LEU F 207 " --> pdb=" O LYS F 203 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 209 " --> pdb=" O GLN F 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 removed outlier: 3.765A pdb=" N THR G 13 " --> pdb=" O GLN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 105 Processing helix chain 'G' and resid 105 through 128 removed outlier: 3.889A pdb=" N GLU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 162 removed outlier: 3.888A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 209 removed outlier: 3.614A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (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: 3.790A pdb=" N GLU H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.871A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 209 Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 440 removed outlier: 6.618A pdb=" N TYR A 391 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU A 439 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 470 " --> pdb=" O ILE A 392 " (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: 3.675A 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: 4.054A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 700 through 701 removed outlier: 4.169A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 643 through 644 Processing sheet with id=AA8, first strand: chain 'B' and resid 436 through 440 removed outlier: 6.699A pdb=" N TYR B 391 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLU B 439 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL B 393 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 470 " --> pdb=" O ILE B 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 403 through 404 Processing sheet with id=AB1, first strand: chain 'B' and resid 485 through 487 Processing sheet with id=AB2, first strand: chain 'B' and resid 492 through 494 removed outlier: 3.904A pdb=" N MET B 492 " --> pdb=" O TYR B 728 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 644 removed outlier: 6.470A pdb=" N ALA B 642 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LEU B 699 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLY B 644 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N GLU B 701 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE B 498 " --> pdb=" O VAL B 719 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 436 through 440 removed outlier: 6.566A pdb=" N TYR C 391 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU C 439 " --> pdb=" O TYR C 391 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL C 393 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB6, first strand: chain 'C' and resid 447 through 450 removed outlier: 3.780A pdb=" N ALA C 448 " --> pdb=" O ASN C 457 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA C 455 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AB8, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.870A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.553A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR C 698 " --> pdb=" O MET C 499 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 436 through 440 removed outlier: 6.367A pdb=" N TYR D 391 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLU D 439 " --> pdb=" O TYR D 391 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL D 393 " --> pdb=" O GLU D 439 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 470 " --> pdb=" O ILE D 392 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 403 through 404 Processing sheet with id=AC3, first strand: chain 'D' and resid 485 through 487 Processing sheet with id=AC4, first strand: chain 'D' and resid 492 through 494 removed outlier: 3.828A pdb=" N MET D 492 " --> pdb=" O TYR D 728 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 642 through 644 removed outlier: 6.597A pdb=" N ALA D 642 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU D 699 " --> pdb=" O ALA D 642 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY D 644 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N GLU D 701 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE D 498 " --> pdb=" O VAL D 719 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 77 through 79 removed outlier: 3.637A pdb=" N LYS E 78 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AC8, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AC9, first strand: chain 'H' and resid 77 through 79 removed outlier: 4.057A pdb=" N LYS H 78 " --> pdb=" O THR H 66 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR H 66 " --> pdb=" O LYS H 78 " (cutoff:3.500A) 1126 hydrogen bonds defined for protein. 3266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.07 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3330 1.32 - 1.45: 4294 1.45 - 1.58: 9526 1.58 - 1.70: 0 1.70 - 1.83: 158 Bond restraints: 17308 Sorted by residual: bond pdb=" C ILE D 641 " pdb=" O ILE D 641 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.17e-02 7.31e+03 2.32e+01 bond pdb=" C TYR D 391 " pdb=" O TYR D 391 " ideal model delta sigma weight residual 1.234 1.293 -0.060 1.34e-02 5.57e+03 1.98e+01 bond pdb=" N VAL C 484 " pdb=" CA VAL C 484 " ideal model delta sigma weight residual 1.456 1.498 -0.041 9.50e-03 1.11e+04 1.88e+01 bond pdb=" N VAL A 484 " pdb=" CA VAL A 484 " ideal model delta sigma weight residual 1.456 1.497 -0.040 9.50e-03 1.11e+04 1.80e+01 bond pdb=" C SER D 631 " pdb=" O SER D 631 " ideal model delta sigma weight residual 1.235 1.275 -0.040 1.00e-02 1.00e+04 1.59e+01 ... (remaining 17303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 23060 3.46 - 6.92: 420 6.92 - 10.37: 15 10.37 - 13.83: 6 13.83 - 17.29: 3 Bond angle restraints: 23504 Sorted by residual: angle pdb=" O GLU C 623 " pdb=" C GLU C 623 " pdb=" N ARG C 624 " ideal model delta sigma weight residual 122.59 136.56 -13.97 1.33e+00 5.65e-01 1.10e+02 angle pdb=" CA PRO D 508 " pdb=" N PRO D 508 " pdb=" CD PRO D 508 " ideal model delta sigma weight residual 112.00 99.47 12.53 1.40e+00 5.10e-01 8.01e+01 angle pdb=" C GLU C 630 " pdb=" CA GLU C 630 " pdb=" CB GLU C 630 " ideal model delta sigma weight residual 110.42 93.13 17.29 1.99e+00 2.53e-01 7.55e+01 angle pdb=" C GLU C 623 " pdb=" N ARG C 624 " pdb=" CA ARG C 624 " ideal model delta sigma weight residual 121.70 107.20 14.50 1.80e+00 3.09e-01 6.49e+01 angle pdb=" C ILE D 498 " pdb=" CA ILE D 498 " pdb=" CB ILE D 498 " ideal model delta sigma weight residual 110.82 100.36 10.46 1.54e+00 4.22e-01 4.61e+01 ... (remaining 23499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8752 17.96 - 35.93: 909 35.93 - 53.89: 211 53.89 - 71.85: 45 71.85 - 89.82: 11 Dihedral angle restraints: 9928 sinusoidal: 3484 harmonic: 6444 Sorted by residual: 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 -105.64 -16.96 0 2.50e+00 1.60e-01 4.60e+01 dihedral pdb=" CB CYS E 67 " pdb=" SG CYS E 67 " pdb=" SG CYS E 77 " pdb=" CB CYS E 77 " ideal model delta sinusoidal sigma weight residual 93.00 36.71 56.29 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CB CYS H 67 " pdb=" SG CYS H 67 " pdb=" SG CYS H 77 " pdb=" CB CYS H 77 " ideal model delta sinusoidal sigma weight residual 93.00 46.49 46.51 1 1.00e+01 1.00e-02 2.99e+01 ... (remaining 9925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1570 0.084 - 0.169: 998 0.169 - 0.253: 132 0.253 - 0.338: 11 0.338 - 0.422: 4 Chirality restraints: 2715 Sorted by residual: chirality pdb=" CG LEU D 635 " pdb=" CB LEU D 635 " pdb=" CD1 LEU D 635 " pdb=" CD2 LEU D 635 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CB VAL A 742 " pdb=" CA VAL A 742 " pdb=" CG1 VAL A 742 " pdb=" CG2 VAL A 742 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.76e+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 2.82 -0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 2712 not shown) Planarity restraints: 2893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 624 " -0.562 9.50e-02 1.11e+02 2.52e-01 3.87e+01 pdb=" NE ARG A 624 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 624 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 624 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 624 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 711 " 0.416 9.50e-02 1.11e+02 1.87e-01 2.14e+01 pdb=" NE ARG A 711 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 711 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 711 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 711 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 657 " -0.370 9.50e-02 1.11e+02 1.66e-01 1.69e+01 pdb=" NE ARG A 657 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 657 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 657 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 657 " -0.015 2.00e-02 2.50e+03 ... (remaining 2890 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4066 2.79 - 3.32: 17054 3.32 - 3.84: 27979 3.84 - 4.37: 32523 4.37 - 4.90: 56144 Nonbonded interactions: 137766 Sorted by model distance: nonbonded pdb=" OG1 THR F 30 " pdb=" OG SER F 178 " model vdw 2.259 3.040 nonbonded pdb=" O SER C 631 " pdb=" OD1 ASP C 634 " model vdw 2.302 3.040 nonbonded pdb=" O ILE E 154 " pdb=" OG SER E 158 " model vdw 2.304 3.040 nonbonded pdb=" O SER E 36 " pdb=" OG1 THR E 59 " model vdw 2.305 3.040 nonbonded pdb=" OG SER G 125 " pdb=" OE2 GLU G 126 " model vdw 2.309 3.040 ... (remaining 137761 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 623 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 502 or resid 509 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 622 or (resid 623 and (name N or name CA or name C or name O or name CB \ )) or resid 631 through 632 or (resid 633 through 638 and (name N or name CA or \ name C or name O or name CB )) or resid 639 through 640 or (resid 641 through 6 \ 43 and (name N or name CA or name C or name O or name CB )) or resid 644 through \ 658 or (resid 659 and (name N or name CA or name C or name O or name CB )) or r \ esid 660 through 664 or (resid 665 and (name N or name CA or name C or name O or \ name CB )) or resid 666 through 683 or (resid 684 and (name N or name CA or nam \ e C or name O or name CB )) or resid 685 through 687 or (resid 688 and (name N o \ r name CA or name C or name O or name CB )) or resid 689 through 690 or (resid 6 \ 91 through 693 and (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 nam \ e 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 623 or resid 631 t \ hrough 633 or (resid 634 through 638 and (name N or name CA or name C or name O \ or name CB )) or resid 639 through 640 or (resid 641 through 643 and (name N or \ name CA or name C or name O or name CB )) or resid 644 through 687 or (resid 688 \ and (name N or name CA or name C or name O or name CB )) or resid 689 through 6 \ 91 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 through 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 50 \ 2 or resid 509 through 545 or (resid 566 and (name N or name CA or name C or nam \ e O or name CB )) or resid 567 through 569 or resid 571 through 581 or resid 583 \ through 618 or resid 620 through 634 or (resid 635 through 638 and (name N or n \ ame CA or name C or name O or name CB )) or resid 639 through 640 or (resid 641 \ through 643 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 4 through 658 or (resid 659 and (name N or name CA or name C or name O or name C \ B )) or resid 660 through 664 or (resid 665 and (name N or name CA or name C or \ name O or name CB )) or resid 666 through 687 or (resid 688 and (name N or name \ CA or name C or name O or name CB )) or resid 689 through 691 or (resid 692 thro \ ugh 693 and (name N or name CA or name C or name O or name CB )) or resid 694 th \ rough 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=0.34 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.200 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 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 : 0.011 0.075 17316 Z= 0.832 Angle : 1.330 17.288 23520 Z= 0.963 Chirality : 0.096 0.422 2715 Planarity : 0.012 0.252 2893 Dihedral : 15.532 89.818 5790 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.55 % Allowed : 2.89 % Favored : 96.55 % Rotamer: Outliers : 5.25 % Allowed : 17.29 % Favored : 77.46 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.17), residues: 2195 helix: 1.09 (0.13), residues: 1317 sheet: -2.24 (0.38), residues: 137 loop : -1.16 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 690 TYR 0.021 0.004 TYR D 669 PHE 0.022 0.002 PHE B 678 TRP 0.020 0.003 TRP D 456 HIS 0.008 0.002 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.01130 (17308) covalent geometry : angle 1.33056 (23504) SS BOND : bond 0.00698 ( 8) SS BOND : angle 0.86800 ( 16) hydrogen bonds : bond 0.20444 ( 1126) hydrogen bonds : angle 6.01017 ( 3266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 209 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 ASP cc_start: 0.9275 (m-30) cc_final: 0.8846 (m-30) REVERT: B 443 ASP cc_start: 0.4226 (m-30) cc_final: 0.3962 (t0) REVERT: B 525 ILE cc_start: 0.9515 (mt) cc_final: 0.9251 (mp) REVERT: B 787 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8417 (p0) REVERT: C 515 ASP cc_start: 0.9238 (m-30) cc_final: 0.9014 (m-30) REVERT: C 605 THR cc_start: 0.9675 (m) cc_final: 0.9442 (m) REVERT: C 657 ARG cc_start: 0.7326 (ptp-110) cc_final: 0.7075 (ptt-90) REVERT: D 670 MET cc_start: 0.2708 (mtt) cc_final: 0.1308 (mtm) REVERT: E 10 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.8184 (tmm) REVERT: E 39 VAL cc_start: 0.9219 (OUTLIER) cc_final: 0.8942 (t) REVERT: E 58 MET cc_start: 0.8660 (tpt) cc_final: 0.8165 (tpt) REVERT: E 78 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8802 (ptpp) REVERT: F 203 LYS cc_start: 0.8957 (tppt) cc_final: 0.8735 (tppt) REVERT: F 204 HIS cc_start: 0.6899 (OUTLIER) cc_final: 0.5495 (m-70) REVERT: F 205 GLN cc_start: 0.9097 (tp40) cc_final: 0.8751 (pp30) REVERT: G 9 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8114 (tm130) REVERT: G 79 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7973 (mmtp) REVERT: G 102 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.8127 (tpt-90) REVERT: G 205 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8123 (tm-30) REVERT: H 9 GLN cc_start: 0.9281 (mt0) cc_final: 0.8858 (mt0) REVERT: H 13 THR cc_start: 0.9548 (m) cc_final: 0.9300 (p) REVERT: H 24 MET cc_start: 0.8901 (tpp) cc_final: 0.8440 (tpp) REVERT: H 200 TYR cc_start: 0.9082 (t80) cc_final: 0.8876 (t80) outliers start: 87 outliers final: 49 residues processed: 280 average time/residue: 0.1507 time to fit residues: 61.5914 Evaluate side-chains 211 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 154 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 625 MET Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 637 LYS Chi-restraints excluded: chain C residue 734 LYS Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 781 SER Chi-restraints excluded: chain D residue 812 TYR Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 201 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.0170 chunk 212 optimal weight: 0.9980 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 743 ASN ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN F 160 ASN G 204 HIS H 9 GLN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.132913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.082491 restraints weight = 129074.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.085249 restraints weight = 35363.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.085912 restraints weight = 16173.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.086082 restraints weight = 13990.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.086176 restraints weight = 12648.814| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17316 Z= 0.130 Angle : 0.578 10.073 23520 Z= 0.304 Chirality : 0.039 0.151 2715 Planarity : 0.004 0.039 2893 Dihedral : 6.283 76.130 2525 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.06 % Favored : 98.85 % Rotamer: Outliers : 2.80 % Allowed : 19.32 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.18), residues: 2195 helix: 2.31 (0.14), residues: 1365 sheet: -1.46 (0.40), residues: 147 loop : -0.97 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 65 TYR 0.018 0.001 TYR C 698 PHE 0.019 0.001 PHE D 655 TRP 0.011 0.001 TRP C 574 HIS 0.004 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00279 (17308) covalent geometry : angle 0.57768 (23504) SS BOND : bond 0.00190 ( 8) SS BOND : angle 0.49452 ( 16) hydrogen bonds : bond 0.04398 ( 1126) hydrogen bonds : angle 4.04738 ( 3266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 0.651 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 403 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7412 (pmm) REVERT: A 498 ILE cc_start: 0.9331 (mt) cc_final: 0.9084 (mt) REVERT: A 515 ASP cc_start: 0.8634 (m-30) cc_final: 0.8192 (m-30) REVERT: A 581 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8526 (mpt) REVERT: A 587 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8587 (pp) REVERT: A 717 MET cc_start: 0.8272 (ppp) cc_final: 0.7985 (ppp) REVERT: B 403 MET cc_start: 0.5923 (mpp) cc_final: 0.5200 (mpp) REVERT: B 443 ASP cc_start: 0.4908 (m-30) cc_final: 0.4276 (t0) REVERT: B 459 MET cc_start: 0.4880 (mpp) cc_final: 0.3423 (ttp) REVERT: B 659 LYS cc_start: 0.7669 (mmtt) cc_final: 0.7046 (mmtt) REVERT: B 717 MET cc_start: 0.7680 (mmt) cc_final: 0.7477 (mmt) REVERT: C 500 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6814 (tp) REVERT: C 657 ARG cc_start: 0.8011 (ptp-110) cc_final: 0.7270 (ptt90) REVERT: C 686 MET cc_start: 0.8727 (tmm) cc_final: 0.8346 (ppp) REVERT: C 687 ILE cc_start: 0.8809 (pt) cc_final: 0.8531 (pt) REVERT: D 499 MET cc_start: -0.0863 (ppp) cc_final: -0.1572 (ppp) REVERT: D 670 MET cc_start: 0.2045 (mtt) cc_final: 0.1712 (mtt) REVERT: G 205 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8407 (tm-30) REVERT: H 24 MET cc_start: 0.8959 (tpp) cc_final: 0.8308 (tpp) outliers start: 46 outliers final: 15 residues processed: 211 average time/residue: 0.1427 time to fit residues: 45.4608 Evaluate side-chains 163 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 173 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 180 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 157 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 40.0000 chunk 165 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 42 optimal weight: 50.0000 chunk 130 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 144 optimal weight: 0.4980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 710 GLN E 205 GLN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN H 149 ASN H 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.128788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.079311 restraints weight = 172453.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.081323 restraints weight = 41726.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.080754 restraints weight = 24056.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.080882 restraints weight = 22890.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.080843 restraints weight = 17948.025| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17316 Z= 0.194 Angle : 0.568 9.403 23520 Z= 0.301 Chirality : 0.040 0.179 2715 Planarity : 0.004 0.039 2893 Dihedral : 4.233 57.161 2432 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.16 % Allowed : 19.80 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.18), residues: 2195 helix: 2.57 (0.14), residues: 1371 sheet: -1.30 (0.41), residues: 156 loop : -0.74 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 37 TYR 0.015 0.001 TYR H 200 PHE 0.017 0.001 PHE C 580 TRP 0.013 0.001 TRP A 762 HIS 0.004 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00441 (17308) covalent geometry : angle 0.56801 (23504) SS BOND : bond 0.00320 ( 8) SS BOND : angle 0.60360 ( 16) hydrogen bonds : bond 0.04650 ( 1126) hydrogen bonds : angle 3.98918 ( 3266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 0.658 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 515 ASP cc_start: 0.8629 (m-30) cc_final: 0.8252 (m-30) REVERT: A 581 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8556 (mpt) REVERT: A 587 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8589 (pp) REVERT: A 666 MET cc_start: 0.8340 (tpp) cc_final: 0.8032 (tpt) REVERT: A 717 MET cc_start: 0.8580 (ppp) cc_final: 0.8010 (ppp) REVERT: B 403 MET cc_start: 0.5802 (mpp) cc_final: 0.5589 (mpp) REVERT: B 443 ASP cc_start: 0.5229 (m-30) cc_final: 0.4535 (t70) REVERT: B 459 MET cc_start: 0.5016 (mpp) cc_final: 0.3456 (ttp) REVERT: C 657 ARG cc_start: 0.8189 (ptp-110) cc_final: 0.7413 (ptt90) REVERT: C 801 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9294 (tm) REVERT: D 492 MET cc_start: 0.3651 (ptt) cc_final: 0.3119 (ptt) REVERT: F 149 ASN cc_start: 0.9225 (t0) cc_final: 0.8752 (t0) REVERT: F 204 HIS cc_start: 0.7145 (OUTLIER) cc_final: 0.5999 (m-70) REVERT: G 153 ILE cc_start: 0.9621 (OUTLIER) cc_final: 0.9326 (mp) REVERT: G 202 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8663 (tm-30) REVERT: G 205 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8517 (tm-30) outliers start: 52 outliers final: 22 residues processed: 185 average time/residue: 0.1326 time to fit residues: 37.6342 Evaluate side-chains 169 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 13 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 219 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 150 optimal weight: 0.0570 chunk 1 optimal weight: 6.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.131735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.083503 restraints weight = 178469.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.085129 restraints weight = 41244.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.085230 restraints weight = 23984.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.085197 restraints weight = 18932.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.085352 restraints weight = 15944.777| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17316 Z= 0.112 Angle : 0.519 10.468 23520 Z= 0.267 Chirality : 0.038 0.184 2715 Planarity : 0.003 0.041 2893 Dihedral : 3.871 54.636 2427 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.62 % Allowed : 19.20 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.18), residues: 2195 helix: 2.75 (0.14), residues: 1370 sheet: -1.30 (0.41), residues: 147 loop : -0.58 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 37 TYR 0.020 0.001 TYR H 200 PHE 0.012 0.001 PHE C 580 TRP 0.011 0.001 TRP A 762 HIS 0.002 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00245 (17308) covalent geometry : angle 0.51853 (23504) SS BOND : bond 0.00217 ( 8) SS BOND : angle 0.48516 ( 16) hydrogen bonds : bond 0.03718 ( 1126) hydrogen bonds : angle 3.74454 ( 3266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.603 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 459 MET cc_start: 0.6054 (mmm) cc_final: 0.5409 (tpp) REVERT: A 499 MET cc_start: 0.8041 (tmm) cc_final: 0.7646 (tmm) REVERT: A 515 ASP cc_start: 0.8605 (m-30) cc_final: 0.8202 (m-30) REVERT: A 581 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8507 (mpt) REVERT: A 587 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8562 (pp) REVERT: A 666 MET cc_start: 0.8489 (tpp) cc_final: 0.8134 (tpp) REVERT: A 717 MET cc_start: 0.8624 (ppp) cc_final: 0.8251 (ppp) REVERT: B 403 MET cc_start: 0.5902 (mpp) cc_final: 0.5672 (mpp) REVERT: B 443 ASP cc_start: 0.5087 (m-30) cc_final: 0.4512 (t0) REVERT: B 459 MET cc_start: 0.4922 (mpp) cc_final: 0.3642 (ttp) REVERT: B 492 MET cc_start: 0.3629 (OUTLIER) cc_final: 0.2320 (mpp) REVERT: B 704 MET cc_start: 0.8985 (ttp) cc_final: 0.8505 (mtp) REVERT: C 492 MET cc_start: 0.5066 (mmm) cc_final: 0.4864 (mmm) REVERT: C 499 MET cc_start: 0.5977 (tpp) cc_final: 0.4661 (tpp) REVERT: C 657 ARG cc_start: 0.8341 (ptp-110) cc_final: 0.7553 (ptt90) REVERT: C 704 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7117 (mpp) REVERT: C 801 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9225 (tm) REVERT: D 492 MET cc_start: 0.3284 (ptt) cc_final: 0.2621 (ptt) REVERT: F 149 ASN cc_start: 0.9248 (t0) cc_final: 0.8927 (t0) REVERT: F 204 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.6219 (m-70) REVERT: G 153 ILE cc_start: 0.9587 (OUTLIER) cc_final: 0.9263 (mp) REVERT: G 202 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8606 (tm-30) REVERT: G 205 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8512 (tm-30) outliers start: 43 outliers final: 24 residues processed: 193 average time/residue: 0.1324 time to fit residues: 39.2175 Evaluate side-chains 177 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 15 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 65 optimal weight: 30.0000 chunk 121 optimal weight: 40.0000 chunk 141 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN B 582 GLN A C 752 GLN D 710 GLN E 204 HIS F 160 ASN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS H 204 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.124913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.076161 restraints weight = 121950.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.077409 restraints weight = 42293.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.076463 restraints weight = 24534.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.076712 restraints weight = 24780.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.077867 restraints weight = 18662.982| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 17316 Z= 0.342 Angle : 0.676 13.056 23520 Z= 0.360 Chirality : 0.043 0.193 2715 Planarity : 0.004 0.041 2893 Dihedral : 4.312 56.691 2427 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.17 % Allowed : 19.14 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.18), residues: 2195 helix: 2.36 (0.14), residues: 1368 sheet: -1.06 (0.45), residues: 140 loop : -0.38 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 657 TYR 0.021 0.002 TYR H 200 PHE 0.027 0.002 PHE F 179 TRP 0.010 0.002 TRP C 574 HIS 0.007 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00779 (17308) covalent geometry : angle 0.67605 (23504) SS BOND : bond 0.00456 ( 8) SS BOND : angle 0.82181 ( 16) hydrogen bonds : bond 0.05277 ( 1126) hydrogen bonds : angle 4.35965 ( 3266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 138 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 MET cc_start: 0.8314 (ttp) cc_final: 0.7992 (mmm) REVERT: A 515 ASP cc_start: 0.8631 (m-30) cc_final: 0.8188 (m-30) REVERT: A 581 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8515 (mpt) REVERT: A 587 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8612 (pp) REVERT: A 666 MET cc_start: 0.8352 (tpp) cc_final: 0.7918 (tpp) REVERT: A 670 MET cc_start: 0.6411 (ptt) cc_final: 0.6047 (ptt) REVERT: A 717 MET cc_start: 0.8728 (ppp) cc_final: 0.8258 (ppp) REVERT: B 443 ASP cc_start: 0.5826 (m-30) cc_final: 0.5023 (t0) REVERT: B 459 MET cc_start: 0.5209 (mpp) cc_final: 0.4067 (ttp) REVERT: B 492 MET cc_start: 0.4118 (OUTLIER) cc_final: 0.2972 (mpp) REVERT: C 499 MET cc_start: 0.5786 (tpp) cc_final: 0.5526 (tpp) REVERT: C 582 GLN cc_start: 0.8846 (mt0) cc_final: 0.8599 (mt0) REVERT: C 657 ARG cc_start: 0.8617 (ptp-110) cc_final: 0.7865 (ptt90) REVERT: C 686 MET cc_start: 0.9046 (tmm) cc_final: 0.8743 (tmm) REVERT: C 704 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7307 (mpp) REVERT: C 801 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9319 (tm) REVERT: D 581 MET cc_start: 0.8552 (mmm) cc_final: 0.8140 (ttm) REVERT: E 9 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8909 (tt0) REVERT: F 149 ASN cc_start: 0.9329 (t0) cc_final: 0.8902 (t0) REVERT: G 153 ILE cc_start: 0.9638 (OUTLIER) cc_final: 0.9362 (mp) REVERT: G 204 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.6505 (t-90) REVERT: G 205 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8512 (tm-30) outliers start: 68 outliers final: 42 residues processed: 187 average time/residue: 0.1294 time to fit residues: 36.8691 Evaluate side-chains 181 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 131 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 690 ARG Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 704 MET Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 13 THR Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 172 optimal weight: 0.0980 chunk 185 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 213 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.130664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.082833 restraints weight = 160180.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083482 restraints weight = 45429.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.083704 restraints weight = 22040.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.084058 restraints weight = 18697.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.083956 restraints weight = 15231.309| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17316 Z= 0.109 Angle : 0.531 8.981 23520 Z= 0.273 Chirality : 0.038 0.167 2715 Planarity : 0.003 0.040 2893 Dihedral : 3.945 58.511 2427 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.74 % Allowed : 20.99 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.18), residues: 2195 helix: 2.75 (0.14), residues: 1367 sheet: -0.91 (0.45), residues: 141 loop : -0.32 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 74 TYR 0.020 0.001 TYR H 200 PHE 0.022 0.001 PHE F 179 TRP 0.013 0.001 TRP H 177 HIS 0.016 0.001 HIS H 204 Details of bonding type rmsd covalent geometry : bond 0.00236 (17308) covalent geometry : angle 0.53079 (23504) SS BOND : bond 0.00222 ( 8) SS BOND : angle 0.58455 ( 16) hydrogen bonds : bond 0.03703 ( 1126) hydrogen bonds : angle 3.74902 ( 3266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 ASP cc_start: 0.8578 (m-30) cc_final: 0.8188 (m-30) REVERT: A 581 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8565 (mpt) REVERT: A 587 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8563 (pp) REVERT: A 666 MET cc_start: 0.8298 (tpp) cc_final: 0.7929 (tpp) REVERT: A 717 MET cc_start: 0.8658 (ppp) cc_final: 0.8392 (ppp) REVERT: B 443 ASP cc_start: 0.5303 (m-30) cc_final: 0.4718 (t0) REVERT: B 459 MET cc_start: 0.5258 (mpp) cc_final: 0.4223 (ttp) REVERT: B 492 MET cc_start: 0.3273 (OUTLIER) cc_final: 0.2135 (mpp) REVERT: C 657 ARG cc_start: 0.8346 (ptp-110) cc_final: 0.7667 (ptt90) REVERT: C 686 MET cc_start: 0.9058 (tmm) cc_final: 0.8710 (tmm) REVERT: C 704 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.7074 (mpp) REVERT: C 801 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9269 (tm) REVERT: F 149 ASN cc_start: 0.9299 (t0) cc_final: 0.9015 (t0) REVERT: F 204 HIS cc_start: 0.6999 (OUTLIER) cc_final: 0.6047 (m-70) REVERT: G 57 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8602 (p) REVERT: G 153 ILE cc_start: 0.9573 (OUTLIER) cc_final: 0.9253 (mp) REVERT: G 204 HIS cc_start: 0.7822 (OUTLIER) cc_final: 0.6974 (t-90) REVERT: G 205 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8531 (tm-30) outliers start: 44 outliers final: 26 residues processed: 179 average time/residue: 0.1223 time to fit residues: 34.8863 Evaluate side-chains 174 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 704 MET Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 5 optimal weight: 0.0000 chunk 206 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 146 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 205 optimal weight: 3.9990 chunk 170 optimal weight: 0.0670 chunk 160 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 150 optimal weight: 0.0770 overall best weight: 0.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.132054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.084836 restraints weight = 153252.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.085271 restraints weight = 44193.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.086704 restraints weight = 21567.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.086375 restraints weight = 16109.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.086524 restraints weight = 14948.298| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17316 Z= 0.101 Angle : 0.512 8.570 23520 Z= 0.261 Chirality : 0.038 0.160 2715 Planarity : 0.003 0.042 2893 Dihedral : 3.780 59.399 2427 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.86 % Allowed : 21.17 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.18), residues: 2195 helix: 2.84 (0.14), residues: 1372 sheet: -0.69 (0.45), residues: 137 loop : -0.28 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 690 TYR 0.009 0.001 TYR D 728 PHE 0.026 0.001 PHE F 179 TRP 0.011 0.001 TRP H 177 HIS 0.017 0.001 HIS H 204 Details of bonding type rmsd covalent geometry : bond 0.00216 (17308) covalent geometry : angle 0.51195 (23504) SS BOND : bond 0.00193 ( 8) SS BOND : angle 0.49671 ( 16) hydrogen bonds : bond 0.03325 ( 1126) hydrogen bonds : angle 3.56536 ( 3266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7163 (pmm) REVERT: A 499 MET cc_start: 0.7994 (tmm) cc_final: 0.7374 (tmm) REVERT: A 515 ASP cc_start: 0.8594 (m-30) cc_final: 0.8162 (m-30) REVERT: A 587 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8581 (pp) REVERT: A 717 MET cc_start: 0.8687 (ppp) cc_final: 0.8466 (ppp) REVERT: B 403 MET cc_start: 0.5979 (OUTLIER) cc_final: 0.5725 (mpp) REVERT: B 443 ASP cc_start: 0.5061 (m-30) cc_final: 0.4662 (t70) REVERT: B 459 MET cc_start: 0.5354 (mpp) cc_final: 0.4213 (ttp) REVERT: B 492 MET cc_start: 0.3569 (OUTLIER) cc_final: 0.2272 (mpp) REVERT: C 657 ARG cc_start: 0.8445 (ptp-110) cc_final: 0.7628 (ptt90) REVERT: C 670 MET cc_start: 0.4303 (tmm) cc_final: 0.4078 (tmm) REVERT: C 686 MET cc_start: 0.9016 (tmm) cc_final: 0.8661 (tmm) REVERT: C 704 MET cc_start: 0.7468 (mpp) cc_final: 0.7177 (mpp) REVERT: D 492 MET cc_start: 0.3786 (ptt) cc_final: 0.3183 (ptt) REVERT: E 30 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8983 (p) REVERT: F 149 ASN cc_start: 0.9329 (t0) cc_final: 0.8992 (t0) REVERT: G 153 ILE cc_start: 0.9529 (OUTLIER) cc_final: 0.9263 (mp) REVERT: G 204 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.7136 (t-90) REVERT: G 205 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8542 (tm-30) outliers start: 46 outliers final: 26 residues processed: 199 average time/residue: 0.1196 time to fit residues: 37.6432 Evaluate side-chains 185 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 472 VAL 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 587 ILE Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 704 MET Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 182 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 161 optimal weight: 0.8980 chunk 109 optimal weight: 30.0000 chunk 130 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.130732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.082528 restraints weight = 190223.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.083452 restraints weight = 47954.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.084187 restraints weight = 22982.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083813 restraints weight = 20869.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.084076 restraints weight = 16113.686| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17316 Z= 0.126 Angle : 0.545 9.809 23520 Z= 0.275 Chirality : 0.038 0.155 2715 Planarity : 0.003 0.044 2893 Dihedral : 3.741 59.626 2427 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.39 % Allowed : 21.53 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.18), residues: 2195 helix: 2.85 (0.14), residues: 1370 sheet: -0.53 (0.48), residues: 127 loop : -0.15 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 129 TYR 0.017 0.001 TYR E 156 PHE 0.029 0.001 PHE F 179 TRP 0.009 0.001 TRP B 667 HIS 0.003 0.001 HIS C 431 Details of bonding type rmsd covalent geometry : bond 0.00287 (17308) covalent geometry : angle 0.54502 (23504) SS BOND : bond 0.00198 ( 8) SS BOND : angle 0.43328 ( 16) hydrogen bonds : bond 0.03588 ( 1126) hydrogen bonds : angle 3.66154 ( 3266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.663 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 515 ASP cc_start: 0.8560 (m-30) cc_final: 0.8161 (m-30) REVERT: A 587 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8622 (pp) REVERT: A 666 MET cc_start: 0.9355 (mtm) cc_final: 0.8413 (tpp) REVERT: A 670 MET cc_start: 0.6667 (ppp) cc_final: 0.6140 (ppp) REVERT: A 717 MET cc_start: 0.8699 (ppp) cc_final: 0.8411 (ppp) REVERT: B 443 ASP cc_start: 0.5194 (m-30) cc_final: 0.4785 (t70) REVERT: B 459 MET cc_start: 0.5348 (mpp) cc_final: 0.3962 (ttp) REVERT: B 492 MET cc_start: 0.4027 (OUTLIER) cc_final: 0.2725 (mpp) REVERT: C 657 ARG cc_start: 0.8550 (ptp-110) cc_final: 0.7785 (ptt90) REVERT: C 686 MET cc_start: 0.9045 (tmm) cc_final: 0.8717 (tmm) REVERT: C 704 MET cc_start: 0.7300 (mpp) cc_final: 0.7027 (mpp) REVERT: D 492 MET cc_start: 0.3857 (ptt) cc_final: 0.3251 (ptt) REVERT: D 686 MET cc_start: 0.6103 (mtp) cc_final: 0.5457 (mtp) REVERT: E 30 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8962 (p) REVERT: F 149 ASN cc_start: 0.9373 (t0) cc_final: 0.9073 (t0) REVERT: G 153 ILE cc_start: 0.9567 (OUTLIER) cc_final: 0.9274 (mp) REVERT: G 205 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8516 (tm-30) outliers start: 38 outliers final: 32 residues processed: 179 average time/residue: 0.1233 time to fit residues: 34.5550 Evaluate side-chains 180 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 472 VAL 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 587 ILE Chi-restraints excluded: chain A residue 690 ARG Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 704 MET Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 182 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 90 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.129548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.080977 restraints weight = 169168.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.082344 restraints weight = 46527.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082658 restraints weight = 23486.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.082555 restraints weight = 21029.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082371 restraints weight = 18314.008| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17316 Z= 0.148 Angle : 0.565 9.435 23520 Z= 0.286 Chirality : 0.038 0.162 2715 Planarity : 0.003 0.044 2893 Dihedral : 3.779 58.117 2427 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.68 % Allowed : 21.47 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.59 (0.18), residues: 2195 helix: 2.81 (0.14), residues: 1371 sheet: -0.58 (0.46), residues: 137 loop : -0.08 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.013 0.001 TYR C 793 PHE 0.031 0.001 PHE F 179 TRP 0.007 0.001 TRP C 574 HIS 0.013 0.001 HIS H 204 Details of bonding type rmsd covalent geometry : bond 0.00340 (17308) covalent geometry : angle 0.56487 (23504) SS BOND : bond 0.00233 ( 8) SS BOND : angle 0.47631 ( 16) hydrogen bonds : bond 0.03836 ( 1126) hydrogen bonds : angle 3.71825 ( 3266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.559 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 403 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.6979 (pmm) REVERT: A 515 ASP cc_start: 0.8576 (m-30) cc_final: 0.8179 (m-30) REVERT: A 587 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8581 (pp) REVERT: A 666 MET cc_start: 0.9363 (mtm) cc_final: 0.8345 (tpp) REVERT: A 670 MET cc_start: 0.6728 (ppp) cc_final: 0.6233 (ppp) REVERT: A 717 MET cc_start: 0.8793 (ppp) cc_final: 0.8543 (ppp) REVERT: B 443 ASP cc_start: 0.5446 (m-30) cc_final: 0.4965 (t70) REVERT: B 459 MET cc_start: 0.5382 (mpp) cc_final: 0.3988 (ttp) REVERT: B 492 MET cc_start: 0.3925 (OUTLIER) cc_final: 0.2908 (mpp) REVERT: B 704 MET cc_start: 0.9039 (ttp) cc_final: 0.8537 (tpp) REVERT: C 657 ARG cc_start: 0.8577 (ptp-110) cc_final: 0.7864 (ptt90) REVERT: C 670 MET cc_start: 0.4226 (tmm) cc_final: 0.3996 (tmm) REVERT: C 686 MET cc_start: 0.9137 (tmm) cc_final: 0.8829 (tmm) REVERT: C 704 MET cc_start: 0.7039 (OUTLIER) cc_final: 0.6806 (mpp) REVERT: D 492 MET cc_start: 0.3873 (ptt) cc_final: 0.3242 (ptt) REVERT: F 149 ASN cc_start: 0.9359 (t0) cc_final: 0.9045 (t0) REVERT: G 153 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9267 (mp) REVERT: G 204 HIS cc_start: 0.7787 (OUTLIER) cc_final: 0.6355 (m-70) REVERT: G 205 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8521 (tm-30) outliers start: 43 outliers final: 32 residues processed: 172 average time/residue: 0.1247 time to fit residues: 33.9041 Evaluate side-chains 176 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 403 MET 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 587 ILE Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 704 MET Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 6 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 112 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 178 optimal weight: 0.8980 chunk 115 optimal weight: 50.0000 chunk 177 optimal weight: 1.9990 chunk 78 optimal weight: 40.0000 chunk 134 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 chunk 114 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 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 = 0.4272 r_free = 0.4272 target = 0.130731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.081410 restraints weight = 147324.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.084337 restraints weight = 39133.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084032 restraints weight = 18455.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.084225 restraints weight = 16952.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.084356 restraints weight = 14550.006| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17316 Z= 0.114 Angle : 0.551 10.188 23520 Z= 0.277 Chirality : 0.038 0.157 2715 Planarity : 0.003 0.044 2893 Dihedral : 3.751 57.950 2427 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.44 % Allowed : 21.59 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.18), residues: 2195 helix: 2.83 (0.14), residues: 1372 sheet: -0.64 (0.44), residues: 147 loop : -0.02 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 129 TYR 0.012 0.001 TYR C 793 PHE 0.029 0.001 PHE F 179 TRP 0.009 0.001 TRP H 177 HIS 0.003 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00258 (17308) covalent geometry : angle 0.55124 (23504) SS BOND : bond 0.00192 ( 8) SS BOND : angle 0.44101 ( 16) hydrogen bonds : bond 0.03580 ( 1126) hydrogen bonds : angle 3.63353 ( 3266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7257 (pmm) REVERT: A 515 ASP cc_start: 0.8597 (m-30) cc_final: 0.8164 (m-30) REVERT: A 587 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8609 (pp) REVERT: A 666 MET cc_start: 0.9370 (mtm) cc_final: 0.8346 (tpp) REVERT: A 670 MET cc_start: 0.6719 (ppp) cc_final: 0.6241 (ppp) REVERT: B 403 MET cc_start: 0.5695 (OUTLIER) cc_final: 0.5447 (mpp) REVERT: B 443 ASP cc_start: 0.5403 (m-30) cc_final: 0.4995 (t0) REVERT: B 459 MET cc_start: 0.5374 (mpp) cc_final: 0.4037 (ttp) REVERT: B 492 MET cc_start: 0.4284 (OUTLIER) cc_final: 0.3198 (mpp) REVERT: B 704 MET cc_start: 0.9012 (ttp) cc_final: 0.8507 (tpp) REVERT: C 657 ARG cc_start: 0.8584 (ptp-110) cc_final: 0.7875 (ptt90) REVERT: C 670 MET cc_start: 0.4208 (tmm) cc_final: 0.3941 (tmm) REVERT: C 686 MET cc_start: 0.9117 (tmm) cc_final: 0.8805 (tmm) REVERT: C 704 MET cc_start: 0.7025 (mpp) cc_final: 0.6775 (mpp) REVERT: D 492 MET cc_start: 0.3788 (ptt) cc_final: 0.3213 (ptt) REVERT: E 30 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8969 (p) REVERT: F 149 ASN cc_start: 0.9361 (t0) cc_final: 0.9059 (t0) REVERT: G 149 ASN cc_start: 0.9058 (OUTLIER) cc_final: 0.8681 (t160) REVERT: G 153 ILE cc_start: 0.9566 (OUTLIER) cc_final: 0.9149 (mp) REVERT: G 204 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.6339 (m-70) REVERT: G 205 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8520 (tm-30) outliers start: 39 outliers final: 27 residues processed: 176 average time/residue: 0.1257 time to fit residues: 34.7801 Evaluate side-chains 180 residues out of total 1857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 472 VAL 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 587 ILE Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 704 MET Chi-restraints excluded: chain D residue 808 ILE Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 173 TYR Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 6 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 165 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 78 optimal weight: 40.0000 chunk 67 optimal weight: 20.0000 chunk 96 optimal weight: 0.6980 chunk 216 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.130251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.082530 restraints weight = 168430.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.083535 restraints weight = 45235.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.083451 restraints weight = 22730.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.083737 restraints weight = 22320.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083779 restraints weight = 16619.092| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17316 Z= 0.172 Angle : 0.753 59.187 23520 Z= 0.412 Chirality : 0.041 0.439 2715 Planarity : 0.003 0.044 2893 Dihedral : 3.735 58.029 2427 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.33 % Allowed : 21.71 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.58 (0.18), residues: 2195 helix: 2.79 (0.14), residues: 1372 sheet: -0.59 (0.46), residues: 137 loop : -0.03 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 690 TYR 0.012 0.001 TYR C 793 PHE 0.030 0.001 PHE F 179 TRP 0.010 0.001 TRP C 574 HIS 0.003 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00400 (17308) covalent geometry : angle 0.75330 (23504) SS BOND : bond 0.00232 ( 8) SS BOND : angle 0.47354 ( 16) hydrogen bonds : bond 0.03646 ( 1126) hydrogen bonds : angle 3.65491 ( 3266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3671.70 seconds wall clock time: 63 minutes 46.34 seconds (3826.34 seconds total)