Starting phenix.real_space_refine on Sun Aug 24 07:32:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3w_17397/08_2025/8p3w_17397_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3w_17397/08_2025/8p3w_17397.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8p3w_17397/08_2025/8p3w_17397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3w_17397/08_2025/8p3w_17397.map" model { file = "/net/cci-nas-00/data/ceres_data/8p3w_17397/08_2025/8p3w_17397_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3w_17397/08_2025/8p3w_17397_neut.cif" } 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= 0.042 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 104 5.16 5 C 11462 2.51 5 N 2778 2.21 5 O 3135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17485 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2894 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 393, 2876 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 379} Chain breaks: 3 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 8, 'ASP:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 14, 'TYR:plan': 2, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 150 Conformer: "B" Number of residues, atoms: 393, 2876 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 379} Chain breaks: 3 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 8, 'ASP:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 14, 'TYR:plan': 2, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 150 bond proxies already assigned to first conformer: 2922 Chain: "B" Number of atoms: 2933 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 385, 2886 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 372} Chain breaks: 4 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 9, 'ASP:plan': 5, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 100 Conformer: "B" Number of residues, atoms: 385, 2886 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 372} Chain breaks: 4 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 9, 'ASP:plan': 5, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 100 bond proxies already assigned to first conformer: 2900 Chain: "C" Number of atoms: 2868 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 385, 2850 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 372} Chain breaks: 4 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 12, 'ASP:plan': 4, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 113 Conformer: "B" Number of residues, atoms: 385, 2850 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 372} Chain breaks: 4 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 12, 'ASP:plan': 4, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 113 bond proxies already assigned to first conformer: 2895 Chain: "D" Number of atoms: 2899 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 384, 2852 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 5, 'TYR:plan': 3, 'ASP:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 10, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 120 Conformer: "B" Number of residues, atoms: 384, 2852 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 5, 'TYR:plan': 3, 'ASP:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 10, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 120 bond proxies already assigned to first conformer: 2864 Chain: "E" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "F" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "G" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 82 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 82 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N AGLY A 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 584 " occ=0.50 residue: pdb=" N ACYS A 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 585 " occ=0.50 residue: pdb=" N AASP A 586 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A 586 " occ=0.50 residue: pdb=" N APHE B 570 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 570 " occ=0.50 residue: pdb=" N AGLN B 582 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 582 " occ=0.50 residue: pdb=" N AGLN B 583 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 583 " occ=0.50 residue: pdb=" N AGLY B 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 584 " occ=0.50 residue: pdb=" N ACYS B 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 585 " occ=0.50 residue: pdb=" N AASP B 586 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP B 586 " occ=0.50 residue: pdb=" N AGLY C 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY C 584 " occ=0.50 residue: pdb=" N ACYS C 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 585 " occ=0.50 residue: pdb=" N AASP C 586 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP C 586 " occ=0.50 ... (remaining 6 not shown) Time building chain proxies: 6.21, per 1000 atoms: 0.36 Number of scatterers: 17485 At special positions: 0 Unit cell: (111.3, 107.325, 136.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 6 15.00 O 3135 8.00 N 2778 7.00 C 11462 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=2.05 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=2.02 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.05 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: 1.41 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4138 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 28 sheets defined 62.3% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.584A pdb=" N GLN A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 removed outlier: 4.185A 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 626 removed outlier: 4.864A pdb=" N GLU A 623 " --> pdb=" O PHE A 619 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.680A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 638 " --> pdb=" O ASP A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 660 through 673 Processing helix chain 'A' and resid 681 through 691 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 784 through 787 Processing helix chain 'A' and resid 788 through 814 removed outlier: 3.510A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.604A 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 623 Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 649 through 657 Processing helix chain 'B' and resid 660 through 673 removed outlier: 3.618A 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 784 through 787 Processing helix chain 'B' and resid 788 through 815 removed outlier: 3.585A pdb=" N PHE B 792 " --> pdb=" O VAL B 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.586A pdb=" N GLN C 410 " --> pdb=" O ASN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 removed outlier: 4.195A 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 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 622 Processing helix chain 'C' and resid 631 through 638 removed outlier: 3.618A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 681 through 691 Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 788 through 814 removed outlier: 3.563A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 415 removed outlier: 4.247A 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 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 removed outlier: 3.599A pdb=" N SER D 672 " --> pdb=" O THR D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 692 Processing helix chain 'D' and resid 702 through 711 Processing helix chain 'D' and resid 738 through 752 Processing helix chain 'D' and resid 753 through 764 Processing helix chain 'D' and resid 784 through 787 Processing helix chain 'D' and resid 788 through 815 removed outlier: 3.589A 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: 4.254A pdb=" N GLU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 162 removed outlier: 3.924A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 209 removed outlier: 3.583A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 105 through 126 removed outlier: 3.811A pdb=" N GLU F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.757A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 209 removed outlier: 3.550A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG F 208 " --> pdb=" O HIS F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 93 through 105 Processing helix chain 'G' and resid 105 through 128 removed outlier: 4.193A pdb=" N GLU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 162 removed outlier: 3.872A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 209 removed outlier: 3.592A 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: 3.759A pdb=" N GLU H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.800A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 209 removed outlier: 3.545A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG H 208 " --> pdb=" O HIS H 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 440 removed outlier: 3.523A 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: 3.702A 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: 4.090A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 642 through 644 removed outlier: 6.596A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 436 through 440 removed outlier: 6.701A 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: 5.917A 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=AA8, first strand: chain 'B' and resid 403 through 404 Processing sheet with id=AA9, first strand: chain 'B' and resid 485 through 487 Processing sheet with id=AB1, first strand: chain 'B' and resid 492 through 494 removed outlier: 3.923A pdb=" N MET B 492 " --> pdb=" O TYR B 728 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 642 through 644 removed outlier: 6.494A pdb=" N ALA B 642 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU B 699 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY B 644 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N GLU B 701 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TYR B 696 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS B 501 " --> pdb=" O TYR B 696 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE B 498 " --> pdb=" O VAL B 719 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 435 through 440 Processing sheet with id=AB4, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB5, first strand: chain 'C' and resid 447 through 449 removed outlier: 3.806A pdb=" N ALA C 448 " --> pdb=" O ASN C 457 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AB7, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.917A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.575A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 436 through 440 removed outlier: 6.335A pdb=" N TYR D 391 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU D 439 " --> pdb=" O TYR D 391 " (cutoff:3.500A) removed outlier: 5.920A 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=AC1, first strand: chain 'D' and resid 403 through 404 Processing sheet with id=AC2, first strand: chain 'D' and resid 485 through 487 Processing sheet with id=AC3, first strand: chain 'D' and resid 492 through 494 removed outlier: 3.887A pdb=" N MET D 492 " --> pdb=" O TYR D 728 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 642 through 644 removed outlier: 6.574A pdb=" N ALA D 642 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU D 699 " --> pdb=" O ALA D 642 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY D 644 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N GLU D 701 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N TYR D 696 " --> pdb=" O LYS D 501 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS D 501 " --> pdb=" O TYR D 696 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE D 498 " --> pdb=" O VAL D 719 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AC6, first strand: chain 'E' and resid 37 through 38 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 34 through 35 Processing sheet with id=AC9, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AD1, first strand: chain 'H' and resid 77 through 79 1135 hydrogen bonds defined for protein. 3306 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: 3.19 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 2642 1.27 - 1.42: 4780 1.42 - 1.56: 10224 1.56 - 1.70: 19 1.70 - 1.85: 164 Bond restraints: 17829 Sorted by residual: bond pdb=" C BGLY A 584 " pdb=" O BGLY A 584 " ideal model delta sigma weight residual 1.230 1.403 -0.173 1.58e-02 4.01e+03 1.19e+02 bond pdb=" C BGLY C 584 " pdb=" O BGLY C 584 " ideal model delta sigma weight residual 1.232 1.396 -0.165 1.81e-02 3.05e+03 8.27e+01 bond pdb=" C ACYS B 585 " pdb=" O ACYS B 585 " ideal model delta sigma weight residual 1.234 1.330 -0.096 1.20e-02 6.94e+03 6.36e+01 bond pdb=" C AGLN B 583 " pdb=" O AGLN B 583 " ideal model delta sigma weight residual 1.237 1.129 0.108 1.36e-02 5.41e+03 6.26e+01 bond pdb=" C ACYS A 585 " pdb=" O ACYS A 585 " ideal model delta sigma weight residual 1.234 1.312 -0.077 1.20e-02 6.94e+03 4.17e+01 ... (remaining 17824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.12: 24049 7.12 - 14.25: 52 14.25 - 21.37: 7 21.37 - 28.50: 2 28.50 - 35.62: 1 Bond angle restraints: 24111 Sorted by residual: angle pdb=" N ALA D 661 " pdb=" CA ALA D 661 " pdb=" CB ALA D 661 " ideal model delta sigma weight residual 110.49 74.87 35.62 1.69e+00 3.50e-01 4.44e+02 angle pdb=" N ACYS B 585 " pdb=" CA ACYS B 585 " pdb=" CB ACYS B 585 " ideal model delta sigma weight residual 111.21 87.24 23.97 1.67e+00 3.59e-01 2.06e+02 angle pdb=" N BCYS D 585 " pdb=" CA BCYS D 585 " pdb=" CB BCYS D 585 " ideal model delta sigma weight residual 110.49 134.47 -23.98 1.69e+00 3.50e-01 2.01e+02 angle pdb=" N ACYS D 585 " pdb=" CA ACYS D 585 " pdb=" CB ACYS D 585 " ideal model delta sigma weight residual 110.97 90.21 20.76 1.56e+00 4.11e-01 1.77e+02 angle pdb=" N BCYS C 585 " pdb=" CA BCYS C 585 " pdb=" CB BCYS C 585 " ideal model delta sigma weight residual 110.97 129.20 -18.23 1.56e+00 4.11e-01 1.36e+02 ... (remaining 24106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.00: 9540 23.00 - 46.01: 644 46.01 - 69.01: 134 69.01 - 92.01: 24 92.01 - 115.02: 1 Dihedral angle restraints: 10343 sinusoidal: 3858 harmonic: 6485 Sorted by residual: dihedral pdb=" N BCYS C 585 " pdb=" C BCYS C 585 " pdb=" CA BCYS C 585 " pdb=" CB BCYS C 585 " ideal model delta harmonic sigma weight residual 122.80 171.94 -49.14 0 2.50e+00 1.60e-01 3.86e+02 dihedral pdb=" N BCYS A 585 " pdb=" C BCYS A 585 " pdb=" CA BCYS A 585 " pdb=" CB BCYS A 585 " ideal model delta harmonic sigma weight residual 122.80 171.20 -48.40 0 2.50e+00 1.60e-01 3.75e+02 dihedral pdb=" C BCYS C 585 " pdb=" N BCYS C 585 " pdb=" CA BCYS C 585 " pdb=" CB BCYS C 585 " ideal model delta harmonic sigma weight residual -122.60 -170.09 47.49 0 2.50e+00 1.60e-01 3.61e+02 ... (remaining 10340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.425: 2730 0.425 - 0.851: 4 0.851 - 1.276: 0 1.276 - 1.702: 2 1.702 - 2.127: 2 Chirality restraints: 2738 Sorted by residual: chirality pdb=" CA BCYS C 585 " pdb=" N BCYS C 585 " pdb=" C BCYS C 585 " pdb=" CB BCYS C 585 " both_signs ideal model delta sigma weight residual False 2.51 0.38 2.13 2.00e-01 2.50e+01 1.13e+02 chirality pdb=" CA BCYS A 585 " pdb=" N BCYS A 585 " pdb=" C BCYS A 585 " pdb=" CB BCYS A 585 " both_signs ideal model delta sigma weight residual False 2.51 0.43 2.08 2.00e-01 2.50e+01 1.08e+02 chirality pdb=" CA BCYS D 585 " pdb=" N BCYS D 585 " pdb=" C BCYS D 585 " pdb=" CB BCYS D 585 " both_signs ideal model delta sigma weight residual False 2.51 1.09 1.42 2.00e-01 2.50e+01 5.06e+01 ... (remaining 2735 not shown) Planarity restraints: 2952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV F1301 " -0.072 2.00e-02 2.50e+03 1.43e-01 2.05e+02 pdb=" C29 POV F1301 " 0.188 2.00e-02 2.50e+03 pdb="C210 POV F1301 " -0.190 2.00e-02 2.50e+03 pdb="C211 POV F1301 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV H1301 " 0.063 2.00e-02 2.50e+03 1.22e-01 1.49e+02 pdb=" C29 POV H1301 " -0.160 2.00e-02 2.50e+03 pdb="C210 POV H1301 " 0.161 2.00e-02 2.50e+03 pdb="C211 POV H1301 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLC D1002 " -0.152 2.00e-02 2.50e+03 1.14e-01 1.31e+02 pdb=" C11 OLC D1002 " 0.058 2.00e-02 2.50e+03 pdb=" C8 OLC D1002 " -0.057 2.00e-02 2.50e+03 pdb=" C9 OLC D1002 " 0.151 2.00e-02 2.50e+03 ... (remaining 2949 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 83 2.57 - 3.15: 14893 3.15 - 3.74: 26900 3.74 - 4.32: 38729 4.32 - 4.90: 63449 Nonbonded interactions: 144054 Sorted by model distance: nonbonded pdb=" N SER A 725 " pdb=" O LYS D 659 " model vdw 1.988 3.120 nonbonded pdb=" O GLY A 720 " pdb=" NZ LYS D 665 " model vdw 2.051 3.120 nonbonded pdb=" CB ALA D 661 " pdb=" N VAL D 662 " model vdw 2.218 2.832 nonbonded pdb=" N GLU G 55 " pdb=" OE1 GLU G 55 " model vdw 2.304 3.120 nonbonded pdb=" N GLU E 55 " pdb=" OE1 GLU E 55 " model vdw 2.304 3.120 ... (remaining 144049 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 389 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 508 through 546 or resid 567 through 569 or resid \ 571 through 581 or resid 587 through 622 or resid 630 through 664 or (resid 665 \ and (name N or name CA or name C or name O or name CB )) or resid 666 through 10 \ 02)) selection = (chain 'B' and ((resid 389 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 398 or (resid 399 and (name N or name CA or \ name C or name O or name CB )) or resid 400 through 403 or (resid 404 and (name \ N or name CA or name C or name O or name CB )) or resid 405 through 415 or (res \ id 416 and (name N or name CA or name C or name O or name CB )) or resid 417 thr \ ough 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) \ or resid 431 through 444 or (resid 445 and (name N or name CA or name C or name \ O or name CB )) or resid 446 through 461 or (resid 462 and (name N or name CA or \ name C or name O or name CB )) or resid 463 through 500 or (resid 501 through 5 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 508 through \ 545 or (resid 566 and (name N or name CA or name C or name O or name CB )) or r \ esid 567 through 569 or resid 571 through 581 or resid 587 through 618 or (resid \ 619 and (name N or name CA or name C or name O or name CB )) or resid 620 throu \ gh 622 or resid 630 through 632 or (resid 633 through 634 and (name N or name CA \ or name C or name O or name CB )) or resid 635 through 658 or (resid 659 and (n \ ame N or name CA or name C or name O or name CB )) or resid 660 through 664 or ( \ resid 665 and (name N or name CA or name C or name O or name CB )) or resid 666 \ through 683 or (resid 684 and (name N or name CA or name C or name O or name CB \ )) or resid 685 through 687 or (resid 688 and (name N or name CA or name C or na \ me O or name CB )) or resid 689 through 690 or (resid 691 through 693 and (name \ N or name CA or name C or name O or name CB )) or resid 694 through 705 or (resi \ d 706 and (name N or name CA or name C or name O or name CB )) or resid 707 thro \ ugh 813 or (resid 814 through 815 and (name N or name CA or name C or name O or \ name CB )) or resid 1001 through 1002)) selection = (chain 'C' and ((resid 389 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 546 or resid 567 through 569 or resid 571 through 581 or resid \ 587 through 618 or (resid 619 and (name N or name CA or name C or name O or name \ CB )) or resid 620 through 622 or resid 630 through 633 or (resid 634 and (name \ N or name CA or name C or name O or name CB )) or resid 635 through 687 or (res \ id 688 and (name N or name CA or name C or name O or name CB )) or resid 689 thr \ ough 691 or (resid 692 through 693 and (name N or name CA or name C or name O or \ name CB )) or resid 694 through 708 or (resid 709 and (name N or name CA or nam \ e C or name O or name CB )) or resid 710 through 1002)) selection = (chain 'D' and (resid 389 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 \ 0 or (resid 501 through 502 and (name N or name CA or name C or name O or name C \ B )) or resid 508 through 545 or (resid 566 and (name N or name CA or name C or \ name O or name CB )) or resid 567 through 569 or resid 571 through 581 or resid \ 587 through 622 or resid 630 through 658 or (resid 659 and (name N or name CA or \ name C or name O or name CB )) or resid 660 through 664 or (resid 665 and (name \ N or name CA or name C or name O or name CB )) or resid 666 through 687 or (res \ id 688 and (name N or name CA or name C or name O or name CB )) or resid 689 thr \ ough 691 or (resid 692 through 693 and (name N or name CA or name C or name O or \ name CB )) or resid 694 through 705 or (resid 706 and (name N or name CA or nam \ e C or name O or name CB )) or resid 707 through 708 or (resid 709 and (name N o \ r name CA or name C or name O or name CB )) or resid 710 through 813 or (resid 8 \ 14 through 815 and (name N or name CA or name C or name O or name CB )) or resid \ 1001 through 1002)) } ncs_group { reference = (chain 'E' and (resid 5 through 209 or (resid 1201 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211))) \ ) selection = (chain 'F' and (resid 5 through 209 or (resid 1301 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211))) \ ) selection = (chain 'G' and (resid 5 through 209 or (resid 1201 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211))) \ ) selection = (chain 'H' and (resid 5 through 209 or (resid 1301 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211))) \ ) } 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=0.50 max=1.00 mean=0.99 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: 1.360 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.700 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.173 17837 Z= 0.885 Angle : 1.631 35.619 24127 Z= 1.158 Chirality : 0.127 2.127 2738 Planarity : 0.021 0.387 2952 Dihedral : 15.873 115.017 6181 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.03 % Favored : 96.88 % Rotamer: Outliers : 3.17 % Allowed : 4.63 % Favored : 92.20 % Cbeta Deviations : 0.92 % 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: -0.44 (0.17), residues: 2211 helix: 0.68 (0.13), residues: 1356 sheet: -2.06 (0.35), residues: 167 loop : -1.69 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.002 ARG B 595 TYR 0.030 0.006 TYR F 180 PHE 0.045 0.005 PHE B 567 TRP 0.049 0.007 TRP D 602 HIS 0.015 0.004 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.01237 (17829) covalent geometry : angle 1.63055 (24111) SS BOND : bond 0.01378 ( 8) SS BOND : angle 2.55807 ( 16) hydrogen bonds : bond 0.13269 ( 1135) hydrogen bonds : angle 5.59580 ( 3306) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 302 time to evaluate : 0.517 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 788 VAL cc_start: 0.9138 (m) cc_final: 0.8928 (m) REVERT: D 398 GLU cc_start: -0.3761 (OUTLIER) cc_final: -0.4427 (mm-30) REVERT: D 781 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.7929 (p) REVERT: F 70 GLU cc_start: 0.8742 (pt0) cc_final: 0.8514 (pp20) REVERT: F 128 HIS cc_start: 0.7736 (m-70) cc_final: 0.7398 (t-90) REVERT: G 10 MET cc_start: 0.9119 (tpp) cc_final: 0.8896 (tpp) REVERT: G 205 GLN cc_start: 0.9256 (tt0) cc_final: 0.8875 (tp40) REVERT: H 137 SER cc_start: 0.9307 (m) cc_final: 0.8839 (p) REVERT: H 184 PHE cc_start: 0.9127 (m-80) cc_final: 0.8908 (m-10) outliers start: 40 outliers final: 8 residues processed: 337 average time/residue: 0.1717 time to fit residues: 81.0585 Evaluate side-chains 165 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain C residue 734 LYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 502 LYS Chi-restraints excluded: chain D residue 659 LYS Chi-restraints excluded: chain D residue 781 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 74 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN A 752 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 HIS C 582 GLN E 204 HIS ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN H 204 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.130647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.082583 restraints weight = 158849.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.084974 restraints weight = 50869.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.085575 restraints weight = 28972.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.086027 restraints weight = 18142.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.086224 restraints weight = 17625.488| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17837 Z= 0.147 Angle : 0.577 10.223 24127 Z= 0.304 Chirality : 0.041 0.150 2738 Planarity : 0.004 0.045 2952 Dihedral : 10.757 117.151 2770 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.40 % Allowed : 11.67 % Favored : 85.92 % 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: 1.26 (0.18), residues: 2211 helix: 2.09 (0.14), residues: 1361 sheet: -1.60 (0.37), residues: 165 loop : -1.11 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 74 TYR 0.015 0.001 TYR B 436 PHE 0.027 0.001 PHE C 542 TRP 0.024 0.002 TRP D 667 HIS 0.003 0.001 HIS H 132 Details of bonding type rmsd covalent geometry : bond 0.00323 (17829) covalent geometry : angle 0.57715 (24111) SS BOND : bond 0.01064 ( 8) SS BOND : angle 0.81350 ( 16) hydrogen bonds : bond 0.04203 ( 1135) hydrogen bonds : angle 3.99797 ( 3306) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 GLU cc_start: 0.8343 (mp0) cc_final: 0.8080 (mp0) REVERT: A 717 MET cc_start: 0.8994 (ppp) cc_final: 0.8768 (ppp) REVERT: B 803 MET cc_start: 0.8600 (mtm) cc_final: 0.8305 (mtm) REVERT: C 704 MET cc_start: 0.6852 (tpp) cc_final: 0.6358 (ptm) REVERT: C 717 MET cc_start: 0.7762 (pmm) cc_final: 0.7294 (pmm) REVERT: D 459 MET cc_start: 0.4268 (mtp) cc_final: 0.4000 (mtp) REVERT: D 499 MET cc_start: 0.1845 (tpp) cc_final: 0.0787 (tpt) REVERT: D 717 MET cc_start: 0.8861 (mmm) cc_final: 0.8505 (mmm) REVERT: E 190 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8711 (mm-30) REVERT: F 9 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7392 (mm-40) REVERT: F 58 MET cc_start: 0.8537 (tpp) cc_final: 0.8310 (tpt) REVERT: G 129 ARG cc_start: 0.6056 (OUTLIER) cc_final: 0.5475 (mtm180) REVERT: G 205 GLN cc_start: 0.8707 (tt0) cc_final: 0.8429 (tp40) REVERT: H 56 GLU cc_start: 0.8418 (pm20) cc_final: 0.8145 (mp0) REVERT: H 149 ASN cc_start: 0.9284 (t0) cc_final: 0.8952 (m-40) REVERT: H 184 PHE cc_start: 0.8151 (m-80) cc_final: 0.7938 (m-10) REVERT: H 204 HIS cc_start: 0.8263 (OUTLIER) cc_final: 0.7603 (m90) outliers start: 31 outliers final: 12 residues processed: 208 average time/residue: 0.1237 time to fit residues: 38.2040 Evaluate side-chains 157 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain C residue 734 LYS Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 189 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS B 414 ASN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 160 ASN F 9 GLN F 160 ASN ** G 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.127425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080240 restraints weight = 156274.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.081823 restraints weight = 56402.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.082086 restraints weight = 31649.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.081875 restraints weight = 26432.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.081924 restraints weight = 25007.233| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17837 Z= 0.195 Angle : 0.580 9.676 24127 Z= 0.307 Chirality : 0.041 0.163 2738 Planarity : 0.004 0.041 2952 Dihedral : 10.156 97.733 2755 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.35 % Allowed : 12.79 % Favored : 84.87 % 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: 1.63 (0.18), residues: 2211 helix: 2.32 (0.14), residues: 1365 sheet: -1.81 (0.37), residues: 165 loop : -0.72 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 690 TYR 0.013 0.001 TYR A 519 PHE 0.023 0.002 PHE C 542 TRP 0.025 0.001 TRP D 667 HIS 0.023 0.002 HIS E 204 Details of bonding type rmsd covalent geometry : bond 0.00442 (17829) covalent geometry : angle 0.57990 (24111) SS BOND : bond 0.00383 ( 8) SS BOND : angle 0.68034 ( 16) hydrogen bonds : bond 0.04330 ( 1135) hydrogen bonds : angle 3.98527 ( 3306) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 ASP cc_start: 0.8496 (m-30) cc_final: 0.7885 (m-30) REVERT: A 520 GLU cc_start: 0.8456 (mp0) cc_final: 0.8041 (mm-30) REVERT: A 581 MET cc_start: 0.9243 (mmt) cc_final: 0.8912 (mmm) REVERT: B 686 MET cc_start: 0.8270 (ppp) cc_final: 0.8013 (ppp) REVERT: B 803 MET cc_start: 0.8554 (mtm) cc_final: 0.8300 (mtm) REVERT: C 459 MET cc_start: 0.4886 (mtm) cc_final: 0.4309 (ttm) REVERT: C 704 MET cc_start: 0.6793 (tpp) cc_final: 0.6497 (ptm) REVERT: C 717 MET cc_start: 0.7713 (pmm) cc_final: 0.7325 (pmm) REVERT: C 761 LYS cc_start: 0.8016 (mmtt) cc_final: 0.7650 (tptt) REVERT: D 446 TYR cc_start: 0.4237 (OUTLIER) cc_final: 0.3719 (t80) REVERT: D 459 MET cc_start: 0.3554 (mtp) cc_final: 0.2855 (mtp) REVERT: D 499 MET cc_start: 0.1514 (tpp) cc_final: 0.0479 (tpt) REVERT: D 665 LYS cc_start: 0.4960 (tttt) cc_final: 0.4588 (tmtt) REVERT: D 717 MET cc_start: 0.9004 (mmm) cc_final: 0.8704 (mmm) REVERT: E 206 GLN cc_start: 0.8980 (pt0) cc_final: 0.8691 (pp30) REVERT: F 9 GLN cc_start: 0.8446 (mm110) cc_final: 0.8131 (mm-40) REVERT: F 95 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7849 (tp30) REVERT: F 204 HIS cc_start: 0.6194 (OUTLIER) cc_final: 0.5226 (m170) REVERT: G 56 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7570 (mm-30) REVERT: G 74 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7741 (ttp-170) REVERT: G 160 ASN cc_start: 0.8374 (m-40) cc_final: 0.8050 (m110) REVERT: G 205 GLN cc_start: 0.8775 (tt0) cc_final: 0.8413 (tp40) REVERT: H 9 GLN cc_start: 0.8829 (mt0) cc_final: 0.8614 (mm-40) REVERT: H 56 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: H 137 SER cc_start: 0.8990 (m) cc_final: 0.8612 (p) REVERT: H 149 ASN cc_start: 0.9334 (t0) cc_final: 0.9087 (t0) outliers start: 31 outliers final: 18 residues processed: 175 average time/residue: 0.1168 time to fit residues: 31.8174 Evaluate side-chains 166 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 2 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 chunk 109 optimal weight: 40.0000 chunk 75 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS H 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.121964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.075267 restraints weight = 172721.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.077011 restraints weight = 55323.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.076214 restraints weight = 35324.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.076488 restraints weight = 31507.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.076479 restraints weight = 25683.958| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 17837 Z= 0.349 Angle : 0.719 9.276 24127 Z= 0.381 Chirality : 0.044 0.171 2738 Planarity : 0.005 0.047 2952 Dihedral : 11.158 80.058 2750 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.23 % Allowed : 14.02 % Favored : 82.76 % 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: 1.35 (0.18), residues: 2211 helix: 1.91 (0.14), residues: 1354 sheet: -1.67 (0.44), residues: 126 loop : -0.52 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 690 TYR 0.021 0.002 TYR A 728 PHE 0.027 0.002 PHE A 663 TRP 0.024 0.002 TRP D 667 HIS 0.009 0.002 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00789 (17829) covalent geometry : angle 0.71869 (24111) SS BOND : bond 0.00540 ( 8) SS BOND : angle 0.91329 ( 16) hydrogen bonds : bond 0.05312 ( 1135) hydrogen bonds : angle 4.56881 ( 3306) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 GLU cc_start: 0.8440 (mp0) cc_final: 0.8110 (mm-30) REVERT: A 581 MET cc_start: 0.9241 (mmt) cc_final: 0.8831 (mmm) REVERT: B 515 ASP cc_start: 0.8389 (m-30) cc_final: 0.8074 (m-30) REVERT: B 803 MET cc_start: 0.8487 (mtm) cc_final: 0.8238 (mtm) REVERT: C 459 MET cc_start: 0.5010 (mtm) cc_final: 0.4425 (ttm) REVERT: C 670 MET cc_start: -0.1598 (ttt) cc_final: -0.1945 (ttt) REVERT: C 704 MET cc_start: 0.6841 (tpp) cc_final: 0.6623 (ptm) REVERT: C 717 MET cc_start: 0.7509 (pmm) cc_final: 0.7066 (pmm) REVERT: C 734 LYS cc_start: 0.5116 (tptt) cc_final: 0.4670 (pttm) REVERT: D 492 MET cc_start: 0.6594 (ttm) cc_final: 0.6326 (ttm) REVERT: D 499 MET cc_start: 0.1847 (tpp) cc_final: 0.0478 (tpt) REVERT: D 665 LYS cc_start: 0.5431 (tttt) cc_final: 0.4987 (tptp) REVERT: E 58 MET cc_start: 0.8179 (mmm) cc_final: 0.7969 (tpt) REVERT: F 160 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8738 (m110) REVERT: F 204 HIS cc_start: 0.6541 (OUTLIER) cc_final: 0.5555 (m170) REVERT: G 41 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8343 (ptm-80) REVERT: G 56 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7526 (mm-30) REVERT: G 205 GLN cc_start: 0.8784 (tt0) cc_final: 0.8263 (tm-30) REVERT: H 56 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: H 137 SER cc_start: 0.9284 (m) cc_final: 0.8833 (p) REVERT: H 149 ASN cc_start: 0.9426 (t0) cc_final: 0.9026 (t0) outliers start: 48 outliers final: 30 residues processed: 175 average time/residue: 0.1338 time to fit residues: 35.6450 Evaluate side-chains 154 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 686 MET Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 129 ARG Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 160 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 194 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 118 optimal weight: 40.0000 chunk 128 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 705 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.125053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.076983 restraints weight = 130845.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.079527 restraints weight = 43382.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.079999 restraints weight = 26582.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.080351 restraints weight = 16914.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.080688 restraints weight = 15886.420| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17837 Z= 0.173 Angle : 0.574 12.180 24127 Z= 0.299 Chirality : 0.040 0.164 2738 Planarity : 0.004 0.040 2952 Dihedral : 10.323 86.973 2746 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.40 % Allowed : 15.84 % Favored : 81.76 % 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: 1.76 (0.18), residues: 2211 helix: 2.30 (0.14), residues: 1358 sheet: -1.57 (0.41), residues: 138 loop : -0.47 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 99 TYR 0.017 0.001 TYR B 519 PHE 0.021 0.001 PHE C 542 TRP 0.033 0.001 TRP D 667 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00395 (17829) covalent geometry : angle 0.57398 (24111) SS BOND : bond 0.00266 ( 8) SS BOND : angle 0.69327 ( 16) hydrogen bonds : bond 0.04196 ( 1135) hydrogen bonds : angle 4.05680 ( 3306) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 MET cc_start: 0.8853 (ttt) cc_final: 0.8499 (tpp) REVERT: A 520 GLU cc_start: 0.8331 (mp0) cc_final: 0.7941 (mm-30) REVERT: A 581 MET cc_start: 0.9280 (mmt) cc_final: 0.8902 (mmm) REVERT: B 803 MET cc_start: 0.8618 (mtm) cc_final: 0.8369 (mtm) REVERT: C 459 MET cc_start: 0.4906 (mtm) cc_final: 0.4315 (ttm) REVERT: C 670 MET cc_start: -0.1728 (ttt) cc_final: -0.2072 (ttt) REVERT: C 704 MET cc_start: 0.6857 (tpp) cc_final: 0.6584 (ptm) REVERT: C 734 LYS cc_start: 0.4827 (tptt) cc_final: 0.4594 (pttm) REVERT: C 761 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7828 (tptt) REVERT: D 446 TYR cc_start: 0.3536 (t80) cc_final: 0.2831 (t80) REVERT: D 499 MET cc_start: 0.1777 (tpp) cc_final: 0.0869 (tpt) REVERT: D 581 MET cc_start: 0.9404 (mmm) cc_final: 0.8703 (mmm) REVERT: D 665 LYS cc_start: 0.5421 (tttt) cc_final: 0.4973 (tptp) REVERT: F 95 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7681 (tp30) REVERT: F 99 ARG cc_start: 0.8620 (ttm-80) cc_final: 0.8129 (ttm-80) REVERT: F 204 HIS cc_start: 0.6633 (OUTLIER) cc_final: 0.5473 (m170) REVERT: G 56 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7643 (mm-30) REVERT: G 160 ASN cc_start: 0.8431 (m-40) cc_final: 0.8115 (m110) REVERT: G 205 GLN cc_start: 0.8801 (tt0) cc_final: 0.8429 (tp40) REVERT: H 137 SER cc_start: 0.9078 (m) cc_final: 0.8719 (p) REVERT: H 149 ASN cc_start: 0.9350 (t0) cc_final: 0.9015 (t0) outliers start: 34 outliers final: 21 residues processed: 170 average time/residue: 0.1310 time to fit residues: 33.8284 Evaluate side-chains 156 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain D residue 686 MET Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 160 ASN 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 31 optimal weight: 0.0370 chunk 91 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.123522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.076455 restraints weight = 137549.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.078852 restraints weight = 51285.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.078024 restraints weight = 26389.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.078544 restraints weight = 28882.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.078590 restraints weight = 21435.186| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17837 Z= 0.232 Angle : 0.625 11.757 24127 Z= 0.325 Chirality : 0.041 0.215 2738 Planarity : 0.004 0.067 2952 Dihedral : 10.065 77.949 2746 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.23 % Allowed : 16.36 % Favored : 80.41 % 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: 1.75 (0.18), residues: 2211 helix: 2.22 (0.14), residues: 1359 sheet: -1.46 (0.40), residues: 145 loop : -0.34 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 99 TYR 0.018 0.002 TYR A 420 PHE 0.022 0.002 PHE C 542 TRP 0.034 0.002 TRP D 667 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00530 (17829) covalent geometry : angle 0.62447 (24111) SS BOND : bond 0.00328 ( 8) SS BOND : angle 0.79711 ( 16) hydrogen bonds : bond 0.04529 ( 1135) hydrogen bonds : angle 4.17830 ( 3306) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 GLU cc_start: 0.8464 (mp0) cc_final: 0.8111 (mm-30) REVERT: A 581 MET cc_start: 0.9273 (mmt) cc_final: 0.8836 (mmm) REVERT: B 803 MET cc_start: 0.8505 (mtm) cc_final: 0.8244 (mtm) REVERT: C 459 MET cc_start: 0.4918 (mtm) cc_final: 0.4298 (ttm) REVERT: C 670 MET cc_start: -0.1075 (ttt) cc_final: -0.1377 (ttt) REVERT: C 704 MET cc_start: 0.6834 (tpp) cc_final: 0.6577 (ptm) REVERT: C 717 MET cc_start: 0.7200 (pmm) cc_final: 0.6656 (pmm) REVERT: C 734 LYS cc_start: 0.4891 (tptt) cc_final: 0.4655 (pttm) REVERT: D 446 TYR cc_start: 0.3553 (OUTLIER) cc_final: 0.2897 (t80) REVERT: D 499 MET cc_start: 0.1723 (tpp) cc_final: 0.0699 (tpt) REVERT: F 99 ARG cc_start: 0.8623 (ttm-80) cc_final: 0.8229 (ttm110) REVERT: F 160 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8669 (m110) REVERT: F 204 HIS cc_start: 0.6417 (OUTLIER) cc_final: 0.5318 (m170) REVERT: G 160 ASN cc_start: 0.8427 (m-40) cc_final: 0.8047 (m110) REVERT: G 205 GLN cc_start: 0.8859 (tt0) cc_final: 0.8467 (tp40) REVERT: H 137 SER cc_start: 0.9158 (m) cc_final: 0.8775 (p) REVERT: H 149 ASN cc_start: 0.9415 (t0) cc_final: 0.9133 (t0) outliers start: 48 outliers final: 35 residues processed: 170 average time/residue: 0.1305 time to fit residues: 34.5232 Evaluate side-chains 166 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 759 LYS Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 686 MET Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 803 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 198 HIS 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 45 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 118 optimal weight: 40.0000 chunk 31 optimal weight: 0.5980 chunk 179 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.125030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.078707 restraints weight = 163209.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.080207 restraints weight = 56654.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.080590 restraints weight = 29687.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.080451 restraints weight = 24847.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.080553 restraints weight = 21119.916| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17837 Z= 0.167 Angle : 0.577 10.425 24127 Z= 0.300 Chirality : 0.040 0.196 2738 Planarity : 0.004 0.073 2952 Dihedral : 9.470 68.193 2746 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.64 % Allowed : 17.18 % Favored : 80.18 % 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: 2.02 (0.18), residues: 2211 helix: 2.46 (0.14), residues: 1360 sheet: -1.45 (0.40), residues: 145 loop : -0.25 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 99 TYR 0.016 0.001 TYR B 519 PHE 0.021 0.001 PHE C 542 TRP 0.044 0.001 TRP D 667 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00383 (17829) covalent geometry : angle 0.57649 (24111) SS BOND : bond 0.00259 ( 8) SS BOND : angle 0.61469 ( 16) hydrogen bonds : bond 0.04056 ( 1135) hydrogen bonds : angle 3.98602 ( 3306) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 GLU cc_start: 0.8386 (mp0) cc_final: 0.7978 (mm-30) REVERT: A 581 MET cc_start: 0.9250 (mmt) cc_final: 0.8922 (mmm) REVERT: B 803 MET cc_start: 0.8588 (mtm) cc_final: 0.8345 (mtm) REVERT: C 459 MET cc_start: 0.4846 (mtm) cc_final: 0.4221 (ttm) REVERT: C 670 MET cc_start: -0.1113 (ttt) cc_final: -0.1434 (ttt) REVERT: C 704 MET cc_start: 0.6833 (tpp) cc_final: 0.6504 (ptm) REVERT: C 734 LYS cc_start: 0.5016 (tptt) cc_final: 0.4785 (pttm) REVERT: C 761 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7393 (tppt) REVERT: D 446 TYR cc_start: 0.3432 (t80) cc_final: 0.2748 (t80) REVERT: D 499 MET cc_start: 0.1561 (tpp) cc_final: 0.0641 (tpt) REVERT: D 581 MET cc_start: 0.8957 (mmm) cc_final: 0.7954 (mmm) REVERT: D 666 MET cc_start: 0.2600 (tpp) cc_final: 0.1914 (tpp) REVERT: E 206 GLN cc_start: 0.8994 (pt0) cc_final: 0.8770 (pp30) REVERT: F 95 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7771 (tp30) REVERT: F 99 ARG cc_start: 0.8666 (ttm-80) cc_final: 0.8211 (ttm-80) REVERT: F 204 HIS cc_start: 0.5791 (OUTLIER) cc_final: 0.4903 (m170) REVERT: G 160 ASN cc_start: 0.8427 (m-40) cc_final: 0.8072 (m110) REVERT: G 205 GLN cc_start: 0.8884 (tt0) cc_final: 0.8489 (tp40) REVERT: H 24 MET cc_start: 0.9444 (tpt) cc_final: 0.9052 (tpp) REVERT: H 137 SER cc_start: 0.9007 (m) cc_final: 0.8649 (p) REVERT: H 149 ASN cc_start: 0.9331 (t0) cc_final: 0.8516 (t0) outliers start: 38 outliers final: 32 residues processed: 171 average time/residue: 0.1353 time to fit residues: 35.7709 Evaluate side-chains 172 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 759 LYS Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 686 MET Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 198 HIS 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 94 optimal weight: 0.4980 chunk 156 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 87 optimal weight: 40.0000 chunk 203 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.125158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.078046 restraints weight = 147122.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.080673 restraints weight = 51300.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.080109 restraints weight = 26834.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.080419 restraints weight = 25761.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.080528 restraints weight = 22486.245| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17837 Z= 0.158 Angle : 0.582 11.239 24127 Z= 0.299 Chirality : 0.040 0.172 2738 Planarity : 0.004 0.060 2952 Dihedral : 9.101 60.394 2746 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.70 % Allowed : 17.54 % Favored : 79.77 % 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: 2.10 (0.18), residues: 2211 helix: 2.50 (0.14), residues: 1359 sheet: -1.36 (0.41), residues: 138 loop : -0.19 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 99 TYR 0.015 0.001 TYR B 420 PHE 0.020 0.001 PHE C 542 TRP 0.043 0.001 TRP D 667 HIS 0.003 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00361 (17829) covalent geometry : angle 0.58242 (24111) SS BOND : bond 0.00215 ( 8) SS BOND : angle 0.61014 ( 16) hydrogen bonds : bond 0.04005 ( 1135) hydrogen bonds : angle 3.94199 ( 3306) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 1.048 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 459 MET cc_start: 0.4243 (mmp) cc_final: 0.2204 (mmt) REVERT: A 520 GLU cc_start: 0.8388 (mp0) cc_final: 0.7977 (mm-30) REVERT: B 803 MET cc_start: 0.8606 (mtm) cc_final: 0.8335 (mtm) REVERT: C 459 MET cc_start: 0.4831 (mtm) cc_final: 0.4191 (ttm) REVERT: C 670 MET cc_start: -0.1266 (ttt) cc_final: -0.1578 (ttt) REVERT: C 704 MET cc_start: 0.6702 (tpp) cc_final: 0.6426 (ptm) REVERT: C 734 LYS cc_start: 0.5050 (tptt) cc_final: 0.4715 (pttm) REVERT: C 761 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7453 (tptt) REVERT: D 446 TYR cc_start: 0.3251 (OUTLIER) cc_final: 0.2590 (t80) REVERT: D 499 MET cc_start: 0.1508 (tpp) cc_final: 0.0516 (tpt) REVERT: D 686 MET cc_start: 0.3654 (OUTLIER) cc_final: 0.3356 (tpt) REVERT: E 37 ARG cc_start: 0.8725 (mtp-110) cc_final: 0.8458 (mmt90) REVERT: F 9 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7750 (mm-40) REVERT: F 95 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7783 (tp30) REVERT: F 99 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8263 (ttm-80) REVERT: F 204 HIS cc_start: 0.5624 (OUTLIER) cc_final: 0.4803 (m170) REVERT: G 160 ASN cc_start: 0.8431 (m-40) cc_final: 0.8070 (m110) REVERT: G 205 GLN cc_start: 0.8890 (tt0) cc_final: 0.8491 (tp40) REVERT: H 149 ASN cc_start: 0.9388 (t0) cc_final: 0.9060 (t0) outliers start: 39 outliers final: 33 residues processed: 169 average time/residue: 0.1296 time to fit residues: 33.9374 Evaluate side-chains 175 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 686 MET Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 803 MET Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 37 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 69 optimal weight: 30.0000 chunk 131 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.124937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.079337 restraints weight = 173603.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.079803 restraints weight = 58051.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.080402 restraints weight = 34015.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.080333 restraints weight = 23973.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.080651 restraints weight = 21957.867| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17837 Z= 0.162 Angle : 0.588 9.737 24127 Z= 0.301 Chirality : 0.040 0.164 2738 Planarity : 0.004 0.053 2952 Dihedral : 8.793 60.097 2746 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.58 % Allowed : 17.54 % Favored : 79.88 % 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: 2.10 (0.18), residues: 2211 helix: 2.51 (0.14), residues: 1359 sheet: -1.39 (0.42), residues: 132 loop : -0.22 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 99 TYR 0.015 0.001 TYR B 519 PHE 0.021 0.001 PHE C 542 TRP 0.047 0.001 TRP D 667 HIS 0.003 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00372 (17829) covalent geometry : angle 0.58765 (24111) SS BOND : bond 0.00508 ( 8) SS BOND : angle 1.30665 ( 16) hydrogen bonds : bond 0.03991 ( 1135) hydrogen bonds : angle 3.95294 ( 3306) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.644 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: 0.3277 (mmp) cc_final: 0.1301 (mmp) REVERT: A 520 GLU cc_start: 0.8374 (mp0) cc_final: 0.7973 (mm-30) REVERT: A 581 MET cc_start: 0.9291 (mmt) cc_final: 0.9009 (mmm) REVERT: B 803 MET cc_start: 0.8567 (mtm) cc_final: 0.8323 (mtm) REVERT: C 670 MET cc_start: -0.1148 (ttt) cc_final: -0.1539 (tpp) REVERT: C 704 MET cc_start: 0.6836 (tpp) cc_final: 0.6501 (ptm) REVERT: C 734 LYS cc_start: 0.4973 (tptt) cc_final: 0.4629 (pttm) REVERT: C 761 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7500 (tptt) REVERT: D 446 TYR cc_start: 0.3398 (OUTLIER) cc_final: 0.2741 (t80) REVERT: D 499 MET cc_start: 0.1515 (tpp) cc_final: 0.0566 (tpt) REVERT: D 686 MET cc_start: 0.3780 (OUTLIER) cc_final: 0.3452 (tpt) REVERT: F 9 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7848 (mm-40) REVERT: F 95 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7754 (tp30) REVERT: F 99 ARG cc_start: 0.8727 (ttm-80) cc_final: 0.8275 (ttm-80) REVERT: F 136 LEU cc_start: 0.9043 (tp) cc_final: 0.8691 (mt) REVERT: F 204 HIS cc_start: 0.5678 (OUTLIER) cc_final: 0.4842 (m170) REVERT: G 160 ASN cc_start: 0.8429 (m-40) cc_final: 0.8059 (m110) REVERT: G 205 GLN cc_start: 0.8888 (tt0) cc_final: 0.8491 (tp40) REVERT: H 24 MET cc_start: 0.9439 (tpt) cc_final: 0.8990 (tpp) REVERT: H 149 ASN cc_start: 0.9400 (t0) cc_final: 0.9117 (t0) outliers start: 37 outliers final: 32 residues processed: 165 average time/residue: 0.1223 time to fit residues: 31.5000 Evaluate side-chains 175 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain D residue 670 MET Chi-restraints excluded: chain D residue 686 MET Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 803 MET Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 160 ASN Chi-restraints excluded: chain H residue 198 HIS Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 3 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 49 optimal weight: 0.0030 chunk 177 optimal weight: 9.9990 chunk 158 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 201 optimal weight: 0.7980 chunk 101 optimal weight: 0.0070 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.5210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.127776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.080415 restraints weight = 137699.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.082799 restraints weight = 48001.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.083675 restraints weight = 25954.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.084121 restraints weight = 17004.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.084226 restraints weight = 15080.586| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 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 = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 17837 Z= 0.108 Angle : 0.578 11.431 24127 Z= 0.291 Chirality : 0.039 0.175 2738 Planarity : 0.004 0.069 2952 Dihedral : 8.274 59.935 2746 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.99 % Allowed : 17.95 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.28 (0.18), residues: 2211 helix: 2.68 (0.14), residues: 1358 sheet: -1.35 (0.42), residues: 132 loop : -0.22 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 74 TYR 0.014 0.001 TYR B 519 PHE 0.018 0.001 PHE C 542 TRP 0.045 0.001 TRP D 667 HIS 0.007 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00233 (17829) covalent geometry : angle 0.57584 (24111) SS BOND : bond 0.00655 ( 8) SS BOND : angle 1.82101 ( 16) hydrogen bonds : bond 0.03537 ( 1135) hydrogen bonds : angle 3.79982 ( 3306) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4422 Ramachandran restraints generated. 2211 Oldfield, 0 Emsley, 2211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.3135 (mmp) cc_final: 0.1105 (mmp) REVERT: A 520 GLU cc_start: 0.8192 (mp0) cc_final: 0.7754 (mm-30) REVERT: A 581 MET cc_start: 0.9315 (mmt) cc_final: 0.9001 (mmm) REVERT: B 803 MET cc_start: 0.8578 (mtm) cc_final: 0.8300 (mtm) REVERT: C 459 MET cc_start: 0.4821 (mtm) cc_final: 0.4582 (mpp) REVERT: C 704 MET cc_start: 0.6811 (tpp) cc_final: 0.6480 (ptm) REVERT: C 734 LYS cc_start: 0.5026 (tptt) cc_final: 0.4704 (pttm) REVERT: C 761 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7526 (tptt) REVERT: D 446 TYR cc_start: 0.3205 (OUTLIER) cc_final: 0.2584 (t80) REVERT: D 494 LEU cc_start: 0.4994 (OUTLIER) cc_final: 0.4679 (pt) REVERT: D 499 MET cc_start: 0.1497 (tpp) cc_final: -0.0057 (tpt) REVERT: D 616 LEU cc_start: 0.9595 (tp) cc_final: 0.9307 (tp) REVERT: D 686 MET cc_start: 0.3506 (OUTLIER) cc_final: 0.3183 (tpt) REVERT: E 206 GLN cc_start: 0.8921 (pt0) cc_final: 0.8691 (pp30) REVERT: F 9 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7916 (mm-40) REVERT: F 136 LEU cc_start: 0.8939 (tp) cc_final: 0.8667 (mt) REVERT: F 204 HIS cc_start: 0.5682 (OUTLIER) cc_final: 0.5006 (m170) REVERT: G 74 ARG cc_start: 0.9048 (ttp80) cc_final: 0.8211 (ttp-110) REVERT: G 160 ASN cc_start: 0.8317 (m-40) cc_final: 0.7938 (m110) REVERT: G 205 GLN cc_start: 0.8857 (tt0) cc_final: 0.8483 (tp40) REVERT: H 149 ASN cc_start: 0.9292 (t0) cc_final: 0.9010 (t0) outliers start: 27 outliers final: 21 residues processed: 178 average time/residue: 0.1124 time to fit residues: 31.2530 Evaluate side-chains 170 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 686 MET Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 198 HIS Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 103 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.126445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.079334 restraints weight = 154786.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082064 restraints weight = 51695.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.081787 restraints weight = 26601.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082004 restraints weight = 22561.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.082108 restraints weight = 19879.385| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 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 = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17837 Z= 0.138 Angle : 0.587 11.281 24127 Z= 0.297 Chirality : 0.039 0.181 2738 Planarity : 0.004 0.063 2952 Dihedral : 8.278 59.463 2746 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.05 % Allowed : 18.24 % Favored : 79.71 % 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: 2.26 (0.18), residues: 2211 helix: 2.65 (0.14), residues: 1359 sheet: -1.27 (0.43), residues: 132 loop : -0.21 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 449 TYR 0.014 0.001 TYR B 420 PHE 0.027 0.001 PHE F 179 TRP 0.042 0.001 TRP D 667 HIS 0.002 0.001 HIS E 204 Details of bonding type rmsd covalent geometry : bond 0.00314 (17829) covalent geometry : angle 0.58576 (24111) SS BOND : bond 0.00737 ( 8) SS BOND : angle 1.68616 ( 16) hydrogen bonds : bond 0.03677 ( 1135) hydrogen bonds : angle 3.84879 ( 3306) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3503.35 seconds wall clock time: 60 minutes 56.19 seconds (3656.19 seconds total)