Starting phenix.real_space_refine on Mon Jun 16 02:34:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3w_17397/06_2025/8p3w_17397_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3w_17397/06_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_17397/06_2025/8p3w_17397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3w_17397/06_2025/8p3w_17397.map" model { file = "/net/cci-nas-00/data/ceres_data/8p3w_17397/06_2025/8p3w_17397_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3w_17397/06_2025/8p3w_17397_neut.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 8} 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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 8} 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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 5} 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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 5} 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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 12, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 12, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} 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: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} 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: 16.86, per 1000 atoms: 0.96 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: 4.99 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 2.03 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: 6.21 Time building geometry restraints manager: 5.73 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 81 \ 5 or resid 1001 through 1002)) 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 815 or resid 1001 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 50.320 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.950 ------------------------------------------------------------------------------- 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 : 8.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (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 TRP 0.049 0.007 TRP D 602 HIS 0.015 0.004 HIS G 204 PHE 0.045 0.005 PHE B 567 TYR 0.030 0.006 TYR F 180 ARG 0.036 0.002 ARG B 595 Details of bonding type rmsd hydrogen bonds : bond 0.13269 ( 1135) hydrogen bonds : angle 5.59580 ( 3306) SS BOND : bond 0.01378 ( 8) SS BOND : angle 2.55807 ( 16) covalent geometry : bond 0.01237 (17829) covalent geometry : angle 1.63055 (24111) *********************** 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 : 2.671 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: 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: -0.4323 (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: 0.7397 (t-90) REVERT: G 10 MET cc_start: 0.9119 (tpp) cc_final: 0.8895 (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: 0.8909 (m-10) outliers start: 40 outliers final: 8 residues processed: 337 average time/residue: 0.4437 time to fit residues: 210.7353 Evaluate side-chains 164 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 1.908 ------------------------------------------------------------------------------- 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 186 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** B 710 GLN C 431 HIS C 582 GLN E 204 HIS G 160 ASN G 204 HIS H 204 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.132265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084541 restraints weight = 141959.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.086602 restraints weight = 48493.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.087308 restraints weight = 25480.843| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17837 Z= 0.128 Angle : 0.567 10.063 24127 Z= 0.298 Chirality : 0.041 0.148 2738 Planarity : 0.004 0.045 2952 Dihedral : 10.639 114.444 2770 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.35 % Allowed : 11.61 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.18), residues: 2211 helix: 2.17 (0.14), residues: 1346 sheet: -1.46 (0.37), residues: 179 loop : -1.02 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 667 HIS 0.006 0.001 HIS E 132 PHE 0.026 0.001 PHE C 542 TYR 0.015 0.001 TYR B 436 ARG 0.006 0.001 ARG H 74 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 1135) hydrogen bonds : angle 3.95127 ( 3306) SS BOND : bond 0.00503 ( 8) SS BOND : angle 0.82542 ( 16) covalent geometry : bond 0.00269 (17829) covalent geometry : angle 0.56689 (24111) *********************** 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 220 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 3.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 GLU cc_start: 0.8351 (mp0) cc_final: 0.8135 (mp0) REVERT: A 717 MET cc_start: 0.9018 (ppp) cc_final: 0.8751 (ppp) REVERT: B 803 MET cc_start: 0.8483 (mtm) cc_final: 0.8172 (mtm) REVERT: C 704 MET cc_start: 0.6954 (tpp) cc_final: 0.6527 (ptm) REVERT: C 717 MET cc_start: 0.7752 (pmm) cc_final: 0.7298 (pmm) REVERT: E 190 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8650 (mm-30) REVERT: G 102 ARG cc_start: 0.8815 (tmt-80) cc_final: 0.8294 (tpt170) REVERT: G 129 ARG cc_start: 0.6114 (OUTLIER) cc_final: 0.5636 (mtm180) REVERT: G 205 GLN cc_start: 0.8758 (tt0) cc_final: 0.8445 (tp40) REVERT: H 56 GLU cc_start: 0.8558 (pm20) cc_final: 0.8234 (mp0) REVERT: H 149 ASN cc_start: 0.9239 (t0) cc_final: 0.8914 (m-40) REVERT: H 204 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7513 (m90) outliers start: 30 outliers final: 13 residues processed: 214 average time/residue: 0.4842 time to fit residues: 158.6716 Evaluate side-chains 161 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 3.604 ------------------------------------------------------------------------------- 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 486 ASP 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 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 G residue 204 HIS 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 66 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 81 optimal weight: 40.0000 chunk 123 optimal weight: 30.0000 chunk 216 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 208 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN F 160 ASN G 132 HIS H 206 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.127670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080554 restraints weight = 152123.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.081167 restraints weight = 55035.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.082066 restraints weight = 31497.166| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 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 = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17837 Z= 0.209 Angle : 0.584 9.610 24127 Z= 0.310 Chirality : 0.041 0.151 2738 Planarity : 0.004 0.041 2952 Dihedral : 10.126 97.702 2755 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.35 % Allowed : 12.73 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.18), residues: 2211 helix: 2.31 (0.14), residues: 1365 sheet: -1.68 (0.37), residues: 157 loop : -0.76 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 667 HIS 0.015 0.002 HIS G 204 PHE 0.025 0.002 PHE F 179 TYR 0.014 0.001 TYR A 643 ARG 0.005 0.001 ARG B 690 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 1135) hydrogen bonds : angle 4.01931 ( 3306) SS BOND : bond 0.00467 ( 8) SS BOND : angle 0.75444 ( 16) covalent geometry : bond 0.00475 (17829) covalent geometry : angle 0.58430 (24111) *********************** 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 182 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 ASP cc_start: 0.8530 (m-30) cc_final: 0.7911 (m-30) REVERT: A 520 GLU cc_start: 0.8441 (mp0) cc_final: 0.8088 (mm-30) REVERT: A 581 MET cc_start: 0.9228 (mmt) cc_final: 0.8911 (mmm) REVERT: B 459 MET cc_start: 0.7251 (mpp) cc_final: 0.6815 (mpp) REVERT: B 686 MET cc_start: 0.8237 (ppp) cc_final: 0.8012 (ppp) REVERT: B 803 MET cc_start: 0.8585 (mtm) cc_final: 0.8321 (mtm) REVERT: C 459 MET cc_start: 0.4859 (mtm) cc_final: 0.4287 (ttm) REVERT: C 704 MET cc_start: 0.6800 (tpp) cc_final: 0.6455 (ptm) REVERT: C 717 MET cc_start: 0.7734 (pmm) cc_final: 0.7341 (pmm) REVERT: C 761 LYS cc_start: 0.7964 (mmtt) cc_final: 0.7560 (tptt) REVERT: E 206 GLN cc_start: 0.8961 (pt0) cc_final: 0.8677 (pp30) REVERT: F 95 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7751 (tp30) REVERT: F 99 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8167 (ttm-80) REVERT: F 204 HIS cc_start: 0.6248 (OUTLIER) cc_final: 0.5218 (m170) REVERT: G 56 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7568 (mm-30) REVERT: G 74 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7717 (ttp-170) REVERT: G 160 ASN cc_start: 0.8425 (m-40) cc_final: 0.8111 (m110) REVERT: G 205 GLN cc_start: 0.8791 (tt0) cc_final: 0.8448 (tp40) REVERT: H 9 GLN cc_start: 0.8852 (mt0) cc_final: 0.8615 (mm-40) REVERT: H 56 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: H 137 SER cc_start: 0.8974 (m) cc_final: 0.8591 (p) REVERT: H 149 ASN cc_start: 0.9331 (t0) cc_final: 0.9091 (t0) outliers start: 31 outliers final: 16 residues processed: 174 average time/residue: 0.3161 time to fit residues: 83.3532 Evaluate side-chains 158 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 LEU 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 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain F residue 11 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 74 ARG Chi-restraints excluded: chain G residue 129 ARG 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 139 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 173 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 211 optimal weight: 9.9990 chunk 77 optimal weight: 30.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS E 160 ASN G 204 HIS H 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.128677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.081765 restraints weight = 147154.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082939 restraints weight = 55405.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.083406 restraints weight = 31962.120| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17837 Z= 0.134 Angle : 0.513 9.756 24127 Z= 0.270 Chirality : 0.039 0.138 2738 Planarity : 0.004 0.042 2952 Dihedral : 9.346 79.289 2751 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.17 % Allowed : 13.55 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.18), residues: 2211 helix: 2.54 (0.14), residues: 1365 sheet: -1.35 (0.39), residues: 150 loop : -0.60 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 667 HIS 0.004 0.001 HIS G 204 PHE 0.019 0.001 PHE F 179 TYR 0.013 0.001 TYR B 519 ARG 0.005 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 1135) hydrogen bonds : angle 3.76336 ( 3306) SS BOND : bond 0.00244 ( 8) SS BOND : angle 0.46943 ( 16) covalent geometry : bond 0.00302 (17829) covalent geometry : angle 0.51333 (24111) *********************** 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 181 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.7231 (mpp) cc_final: 0.6742 (mmm) REVERT: A 520 GLU cc_start: 0.8384 (mp0) cc_final: 0.7928 (mm-30) REVERT: A 523 MET cc_start: 0.8722 (ptm) cc_final: 0.8471 (ptp) REVERT: B 459 MET cc_start: 0.7609 (mpp) cc_final: 0.7398 (mpp) REVERT: B 686 MET cc_start: 0.8245 (ppp) cc_final: 0.8017 (ppp) REVERT: C 670 MET cc_start: -0.2332 (ttt) cc_final: -0.2807 (tpp) REVERT: C 704 MET cc_start: 0.6684 (tpp) cc_final: 0.6349 (ptm) REVERT: C 717 MET cc_start: 0.7279 (pmm) cc_final: 0.6995 (pmm) REVERT: D 499 MET cc_start: 0.2126 (tpp) cc_final: 0.0717 (tpt) REVERT: D 717 MET cc_start: 0.8709 (mmp) cc_final: 0.8327 (mmp) REVERT: E 203 LYS cc_start: 0.8446 (ttpt) cc_final: 0.7934 (tttt) REVERT: E 206 GLN cc_start: 0.9022 (pt0) cc_final: 0.8675 (pp30) REVERT: F 9 GLN cc_start: 0.8397 (mm110) cc_final: 0.8004 (mm-40) REVERT: F 78 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8556 (ptpt) REVERT: F 95 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7983 (tp30) REVERT: F 99 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8274 (ttp80) REVERT: F 204 HIS cc_start: 0.5875 (OUTLIER) cc_final: 0.5055 (m170) REVERT: G 56 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7580 (mm-30) REVERT: G 74 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7724 (ttp-170) REVERT: G 160 ASN cc_start: 0.8474 (m-40) cc_final: 0.8080 (m110) REVERT: G 208 ARG cc_start: 0.7363 (tmm-80) cc_final: 0.7051 (mtt180) REVERT: H 56 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: H 149 ASN cc_start: 0.9275 (t0) cc_final: 0.9019 (t0) outliers start: 28 outliers final: 15 residues processed: 173 average time/residue: 0.2999 time to fit residues: 79.5323 Evaluate side-chains 163 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 1.935 ------------------------------------------------------------------------------- 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 C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 791 VAL 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 78 LYS 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 153 ILE 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 160 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 162 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 199 optimal weight: 0.9980 chunk 26 optimal weight: 0.0670 chunk 78 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 81 optimal weight: 30.0000 overall best weight: 4.0124 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.124454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.076302 restraints weight = 152325.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.078593 restraints weight = 51837.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.079775 restraints weight = 25645.900| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17837 Z= 0.265 Angle : 0.632 10.342 24127 Z= 0.334 Chirality : 0.041 0.165 2738 Planarity : 0.004 0.040 2952 Dihedral : 10.060 79.172 2750 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.82 % Allowed : 14.19 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.18), residues: 2211 helix: 2.26 (0.14), residues: 1364 sheet: -1.64 (0.40), residues: 142 loop : -0.45 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 667 HIS 0.006 0.001 HIS C 431 PHE 0.021 0.002 PHE C 542 TYR 0.021 0.002 TYR A 420 ARG 0.006 0.001 ARG C 711 Details of bonding type rmsd hydrogen bonds : bond 0.04648 ( 1135) hydrogen bonds : angle 4.15787 ( 3306) SS BOND : bond 0.00416 ( 8) SS BOND : angle 0.64081 ( 16) covalent geometry : bond 0.00604 (17829) covalent geometry : angle 0.63181 (24111) *********************** 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 189 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 2.017 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: 0.8361 (mp0) cc_final: 0.8083 (mm-30) REVERT: A 581 MET cc_start: 0.9227 (mmt) cc_final: 0.8981 (mmm) REVERT: C 686 MET cc_start: 0.0442 (tpt) cc_final: 0.0187 (tpt) REVERT: C 704 MET cc_start: 0.6765 (tpp) cc_final: 0.6491 (ptm) REVERT: C 717 MET cc_start: 0.7253 (pmm) cc_final: 0.6948 (pmm) REVERT: C 734 LYS cc_start: 0.5153 (tptt) cc_final: 0.4587 (pttm) REVERT: C 761 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7499 (tptt) REVERT: D 499 MET cc_start: 0.2145 (tpp) cc_final: 0.0617 (tpt) REVERT: E 206 GLN cc_start: 0.8974 (pt0) cc_final: 0.8667 (pp30) REVERT: F 9 GLN cc_start: 0.8471 (mm110) cc_final: 0.8008 (mm-40) REVERT: F 95 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7804 (tp30) REVERT: F 99 ARG cc_start: 0.8711 (ttm-80) cc_final: 0.8274 (ttm-80) REVERT: F 149 ASN cc_start: 0.9471 (t0) cc_final: 0.9199 (t0) REVERT: F 204 HIS cc_start: 0.6282 (OUTLIER) cc_final: 0.5166 (m170) REVERT: G 56 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7704 (mm-30) REVERT: G 160 ASN cc_start: 0.8461 (m-40) cc_final: 0.8102 (m110) REVERT: H 9 GLN cc_start: 0.8934 (mt0) cc_final: 0.8679 (mm110) REVERT: H 58 MET cc_start: 0.8332 (mmm) cc_final: 0.8015 (mmm) REVERT: H 137 SER cc_start: 0.9169 (m) cc_final: 0.8739 (p) REVERT: H 149 ASN cc_start: 0.9358 (t0) cc_final: 0.8990 (t0) outliers start: 41 outliers final: 28 residues processed: 180 average time/residue: 0.3187 time to fit residues: 87.9205 Evaluate side-chains 167 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 397 LEU 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 486 ASP 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 542 PHE Chi-restraints excluded: chain D residue 791 VAL 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 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 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 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 62 optimal weight: 20.0000 chunk 168 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 132 HIS ** 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 = 0.4192 r_free = 0.4192 target = 0.125733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.078890 restraints weight = 171859.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.080736 restraints weight = 52249.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.080650 restraints weight = 29140.193| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 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 = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4506 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= 0.191 Angle : 0.583 11.818 24127 Z= 0.302 Chirality : 0.040 0.212 2738 Planarity : 0.004 0.039 2952 Dihedral : 9.863 79.369 2750 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.70 % Allowed : 15.25 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.18), residues: 2211 helix: 2.35 (0.14), residues: 1364 sheet: -1.54 (0.40), residues: 141 loop : -0.37 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 667 HIS 0.004 0.001 HIS F 204 PHE 0.020 0.001 PHE C 542 TYR 0.019 0.001 TYR A 420 ARG 0.005 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 1135) hydrogen bonds : angle 3.98251 ( 3306) SS BOND : bond 0.00278 ( 8) SS BOND : angle 0.45393 ( 16) covalent geometry : bond 0.00438 (17829) covalent geometry : angle 0.58273 (24111) *********************** 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 186 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 2.023 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: 0.3534 (mmt) cc_final: 0.1470 (mmt) REVERT: A 520 GLU cc_start: 0.8349 (mp0) cc_final: 0.7947 (mm-30) REVERT: A 523 MET cc_start: 0.8867 (ptm) cc_final: 0.8594 (ptp) REVERT: A 666 MET cc_start: 0.8713 (mpp) cc_final: 0.7821 (mpp) REVERT: C 459 MET cc_start: 0.4670 (mpp) cc_final: 0.4421 (mpp) REVERT: C 686 MET cc_start: 0.0690 (tpt) cc_final: 0.0403 (tpt) REVERT: C 704 MET cc_start: 0.6777 (tpp) cc_final: 0.6468 (ptm) REVERT: C 734 LYS cc_start: 0.4953 (tptt) cc_final: 0.4568 (pttm) REVERT: D 492 MET cc_start: 0.6080 (ttm) cc_final: 0.5751 (mtt) REVERT: D 494 LEU cc_start: 0.5038 (OUTLIER) cc_final: 0.4755 (pt) REVERT: D 499 MET cc_start: 0.2231 (tpp) cc_final: 0.0561 (tpt) REVERT: E 206 GLN cc_start: 0.9007 (pt0) cc_final: 0.8669 (pp30) REVERT: F 9 GLN cc_start: 0.8374 (mm110) cc_final: 0.7880 (mm-40) REVERT: F 99 ARG cc_start: 0.8753 (ttm-80) cc_final: 0.8387 (ttp80) REVERT: F 149 ASN cc_start: 0.9415 (t0) cc_final: 0.9211 (t0) REVERT: F 204 HIS cc_start: 0.5928 (OUTLIER) cc_final: 0.5037 (m170) REVERT: G 56 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7686 (mm-30) REVERT: G 69 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8077 (tp) REVERT: G 74 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7752 (ttp-170) REVERT: G 81 ASP cc_start: 0.8669 (t0) cc_final: 0.8457 (t0) REVERT: G 160 ASN cc_start: 0.8466 (m-40) cc_final: 0.8083 (m110) REVERT: H 9 GLN cc_start: 0.8835 (mt0) cc_final: 0.8578 (mm110) REVERT: H 24 MET cc_start: 0.9443 (tpt) cc_final: 0.9084 (tpp) REVERT: H 137 SER cc_start: 0.9056 (m) cc_final: 0.8660 (p) REVERT: H 149 ASN cc_start: 0.9374 (t0) cc_final: 0.9101 (t0) outliers start: 39 outliers final: 28 residues processed: 174 average time/residue: 0.2900 time to fit residues: 78.7173 Evaluate side-chains 172 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 1.754 ------------------------------------------------------------------------------- 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 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 494 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 58 MET 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 69 LEU Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain H residue 104 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 91 optimal weight: 0.9980 chunk 165 optimal weight: 0.5980 chunk 7 optimal weight: 9.9990 chunk 170 optimal weight: 8.9990 chunk 125 optimal weight: 30.0000 chunk 80 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 111 optimal weight: 0.0980 chunk 176 optimal weight: 10.0000 chunk 82 optimal weight: 40.0000 chunk 154 optimal weight: 7.9990 overall best weight: 3.7384 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.123583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.076486 restraints weight = 178288.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.078841 restraints weight = 56820.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.077884 restraints weight = 31660.395| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17837 Z= 0.251 Angle : 0.632 9.377 24127 Z= 0.332 Chirality : 0.042 0.173 2738 Planarity : 0.004 0.040 2952 Dihedral : 10.197 80.621 2750 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.76 % Allowed : 15.43 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.18), residues: 2211 helix: 2.18 (0.14), residues: 1362 sheet: -1.70 (0.39), residues: 135 loop : -0.26 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 667 HIS 0.005 0.001 HIS E 60 PHE 0.020 0.002 PHE C 542 TYR 0.021 0.002 TYR A 420 ARG 0.005 0.001 ARG A 657 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 1135) hydrogen bonds : angle 4.22417 ( 3306) SS BOND : bond 0.00398 ( 8) SS BOND : angle 1.05791 ( 16) covalent geometry : bond 0.00572 (17829) covalent geometry : angle 0.63182 (24111) *********************** 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 178 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 1.872 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: 0.3257 (mmt) cc_final: 0.1687 (mmp) REVERT: A 520 GLU cc_start: 0.8464 (mp0) cc_final: 0.8068 (mm-30) REVERT: A 523 MET cc_start: 0.8948 (ptm) cc_final: 0.8658 (ptp) REVERT: C 686 MET cc_start: 0.1261 (tpt) cc_final: 0.0811 (tpt) REVERT: C 704 MET cc_start: 0.6827 (tpp) cc_final: 0.6528 (ptm) REVERT: C 717 MET cc_start: 0.7278 (pmm) cc_final: 0.6647 (pmm) REVERT: C 734 LYS cc_start: 0.4896 (tptt) cc_final: 0.4647 (pttm) REVERT: C 761 LYS cc_start: 0.7916 (mmtt) cc_final: 0.7401 (tppt) REVERT: D 492 MET cc_start: 0.6700 (ttm) cc_final: 0.6240 (mtt) REVERT: D 499 MET cc_start: 0.2229 (tpp) cc_final: 0.0551 (tpt) REVERT: D 666 MET cc_start: 0.0977 (tpp) cc_final: 0.0128 (tpp) REVERT: D 686 MET cc_start: 0.5864 (tpp) cc_final: 0.5237 (tpp) REVERT: E 206 GLN cc_start: 0.9023 (pt0) cc_final: 0.8668 (pp30) REVERT: F 9 GLN cc_start: 0.8390 (mm110) cc_final: 0.7876 (mm-40) REVERT: F 149 ASN cc_start: 0.9534 (t0) cc_final: 0.9297 (t0) REVERT: F 204 HIS cc_start: 0.6223 (OUTLIER) cc_final: 0.5146 (m170) REVERT: G 56 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7674 (mm-30) REVERT: G 58 MET cc_start: 0.8398 (mmm) cc_final: 0.7958 (tpp) REVERT: G 69 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8207 (tp) REVERT: H 9 GLN cc_start: 0.8841 (mt0) cc_final: 0.8603 (mm110) REVERT: H 137 SER cc_start: 0.9147 (m) cc_final: 0.8707 (p) REVERT: H 149 ASN cc_start: 0.9383 (t0) cc_final: 0.9027 (t0) outliers start: 40 outliers final: 34 residues processed: 168 average time/residue: 0.2764 time to fit residues: 72.6588 Evaluate side-chains 169 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 1.931 ------------------------------------------------------------------------------- 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 421 CYS 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 486 ASP 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 397 LEU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 58 MET 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 69 LEU Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 104 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 199 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 200 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 160 ASN H 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.127301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.079344 restraints weight = 131161.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.082329 restraints weight = 46883.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082182 restraints weight = 23442.267| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17837 Z= 0.114 Angle : 0.548 10.261 24127 Z= 0.279 Chirality : 0.039 0.196 2738 Planarity : 0.003 0.041 2952 Dihedral : 9.168 78.844 2750 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.35 % Allowed : 16.48 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.18), residues: 2211 helix: 2.59 (0.14), residues: 1361 sheet: -1.63 (0.39), residues: 139 loop : -0.14 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP D 667 HIS 0.003 0.001 HIS F 204 PHE 0.017 0.001 PHE C 542 TYR 0.013 0.001 TYR A 420 ARG 0.004 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 1135) hydrogen bonds : angle 3.79079 ( 3306) SS BOND : bond 0.00164 ( 8) SS BOND : angle 0.67474 ( 16) covalent geometry : bond 0.00250 (17829) covalent geometry : angle 0.54782 (24111) *********************** 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 186 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 2.012 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: 0.2835 (mmt) cc_final: 0.0693 (mmt) REVERT: A 499 MET cc_start: 0.9027 (ttt) cc_final: 0.8574 (tpp) REVERT: A 520 GLU cc_start: 0.8328 (mp0) cc_final: 0.7843 (mm-30) REVERT: A 581 MET cc_start: 0.9289 (mmt) cc_final: 0.8824 (mmm) REVERT: C 499 MET cc_start: -0.0588 (OUTLIER) cc_final: -0.0795 (mmm) REVERT: C 686 MET cc_start: 0.1338 (tpt) cc_final: 0.0833 (tpt) REVERT: C 704 MET cc_start: 0.6961 (tpp) cc_final: 0.6619 (ptm) REVERT: C 734 LYS cc_start: 0.4993 (tptt) cc_final: 0.4668 (pttm) REVERT: C 761 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7502 (tptt) REVERT: D 494 LEU cc_start: 0.5039 (OUTLIER) cc_final: 0.4723 (pt) REVERT: D 499 MET cc_start: 0.2245 (tpp) cc_final: 0.0841 (tpt) REVERT: E 206 GLN cc_start: 0.8959 (pt0) cc_final: 0.8623 (pp30) REVERT: F 9 GLN cc_start: 0.8454 (mm110) cc_final: 0.8058 (mm-40) REVERT: F 204 HIS cc_start: 0.5809 (OUTLIER) cc_final: 0.4977 (m170) REVERT: G 56 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7545 (mt-10) REVERT: G 58 MET cc_start: 0.8518 (mmm) cc_final: 0.8137 (tpp) REVERT: G 69 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8350 (tp) REVERT: G 160 ASN cc_start: 0.8410 (m-40) cc_final: 0.8080 (m110) REVERT: H 24 MET cc_start: 0.9411 (tpt) cc_final: 0.9098 (tpp) REVERT: H 149 ASN cc_start: 0.9309 (t0) cc_final: 0.8969 (t0) outliers start: 33 outliers final: 24 residues processed: 177 average time/residue: 0.2868 time to fit residues: 79.7517 Evaluate side-chains 171 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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 781 SER Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 58 MET 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 69 LEU Chi-restraints excluded: chain G residue 74 ARG 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 204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 193 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 94 optimal weight: 0.0270 chunk 211 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 212 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 overall best weight: 1.5842 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.126749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.079533 restraints weight = 170417.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.081989 restraints weight = 55215.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081738 restraints weight = 29124.483| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17837 Z= 0.135 Angle : 0.559 10.176 24127 Z= 0.287 Chirality : 0.039 0.183 2738 Planarity : 0.003 0.040 2952 Dihedral : 8.846 77.838 2750 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.29 % Allowed : 16.95 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.18), residues: 2211 helix: 2.55 (0.14), residues: 1365 sheet: -1.34 (0.40), residues: 133 loop : -0.11 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP D 667 HIS 0.002 0.001 HIS F 204 PHE 0.019 0.001 PHE D 580 TYR 0.014 0.001 TYR A 420 ARG 0.008 0.000 ARG A 657 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 1135) hydrogen bonds : angle 3.81903 ( 3306) SS BOND : bond 0.00236 ( 8) SS BOND : angle 1.22799 ( 16) covalent geometry : bond 0.00308 (17829) covalent geometry : angle 0.55800 (24111) *********************** 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 176 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 1.961 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: 0.2538 (mmt) cc_final: 0.0598 (mmt) REVERT: A 499 MET cc_start: 0.8951 (ttt) cc_final: 0.8584 (tpp) REVERT: A 520 GLU cc_start: 0.8398 (mp0) cc_final: 0.7966 (mm-30) REVERT: A 523 MET cc_start: 0.8676 (ptp) cc_final: 0.8464 (ptp) REVERT: A 581 MET cc_start: 0.9268 (mmt) cc_final: 0.8838 (mmm) REVERT: C 704 MET cc_start: 0.6996 (tpp) cc_final: 0.6739 (ptm) REVERT: C 734 LYS cc_start: 0.4807 (tptt) cc_final: 0.4453 (pttm) REVERT: C 761 LYS cc_start: 0.7928 (mmtt) cc_final: 0.7391 (tptt) REVERT: D 494 LEU cc_start: 0.3096 (OUTLIER) cc_final: 0.2288 (tt) REVERT: D 499 MET cc_start: 0.2056 (tpp) cc_final: 0.0721 (tpt) REVERT: D 686 MET cc_start: 0.5405 (tpp) cc_final: 0.4995 (tpt) REVERT: E 206 GLN cc_start: 0.9014 (pt0) cc_final: 0.8656 (pp30) REVERT: F 9 GLN cc_start: 0.8369 (mm110) cc_final: 0.8089 (mm-40) REVERT: F 136 LEU cc_start: 0.8978 (tp) cc_final: 0.8692 (mt) REVERT: F 204 HIS cc_start: 0.5484 (OUTLIER) cc_final: 0.4769 (m170) REVERT: G 56 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7523 (mt-10) REVERT: G 58 MET cc_start: 0.8502 (mmm) cc_final: 0.8110 (tpp) REVERT: G 160 ASN cc_start: 0.8376 (m-40) cc_final: 0.8037 (m110) REVERT: H 149 ASN cc_start: 0.9287 (t0) cc_final: 0.9035 (t0) outliers start: 32 outliers final: 27 residues processed: 165 average time/residue: 0.2742 time to fit residues: 71.7676 Evaluate side-chains 167 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 510 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 C residue 587 ILE Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 58 MET 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 151 ILE 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 122 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 160 ASN 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 190 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.124386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.075996 restraints weight = 141184.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.078581 restraints weight = 48714.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.078910 restraints weight = 26950.599| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17837 Z= 0.230 Angle : 0.640 12.005 24127 Z= 0.330 Chirality : 0.041 0.209 2738 Planarity : 0.004 0.040 2952 Dihedral : 9.241 78.013 2746 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.17 % Allowed : 17.18 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.18), residues: 2211 helix: 2.33 (0.14), residues: 1365 sheet: -1.46 (0.40), residues: 133 loop : -0.13 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 667 HIS 0.005 0.001 HIS F 60 PHE 0.020 0.002 PHE C 542 TYR 0.019 0.001 TYR A 420 ARG 0.006 0.001 ARG A 657 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 1135) hydrogen bonds : angle 4.10818 ( 3306) SS BOND : bond 0.00486 ( 8) SS BOND : angle 2.31093 ( 16) covalent geometry : bond 0.00528 (17829) covalent geometry : angle 0.63699 (24111) ********************** 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 166 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.940 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 459 MET cc_start: 0.2630 (mmt) cc_final: 0.0590 (mmt) REVERT: A 520 GLU cc_start: 0.8314 (mp0) cc_final: 0.7957 (mm-30) REVERT: A 523 MET cc_start: 0.8768 (ptp) cc_final: 0.8558 (ptp) REVERT: C 686 MET cc_start: 0.1359 (tpt) cc_final: 0.0967 (mmm) REVERT: C 704 MET cc_start: 0.6860 (tpp) cc_final: 0.6565 (ptm) REVERT: C 734 LYS cc_start: 0.5090 (tptt) cc_final: 0.4774 (pttm) REVERT: D 499 MET cc_start: 0.2337 (tpp) cc_final: 0.0947 (tpt) REVERT: D 686 MET cc_start: 0.5798 (tpp) cc_final: 0.5346 (tpt) REVERT: E 206 GLN cc_start: 0.8940 (pt0) cc_final: 0.8642 (pp30) REVERT: F 9 GLN cc_start: 0.8546 (mm110) cc_final: 0.8112 (mm-40) REVERT: F 204 HIS cc_start: 0.6183 (OUTLIER) cc_final: 0.5067 (m170) REVERT: G 56 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7680 (mm-30) REVERT: G 58 MET cc_start: 0.8445 (mmm) cc_final: 0.8033 (tpp) REVERT: G 160 ASN cc_start: 0.8389 (m-40) cc_final: 0.8067 (m110) REVERT: H 137 SER cc_start: 0.9088 (m) cc_final: 0.8743 (p) REVERT: H 149 ASN cc_start: 0.9351 (t0) cc_final: 0.9043 (t0) outliers start: 30 outliers final: 29 residues processed: 157 average time/residue: 0.2791 time to fit residues: 70.3366 Evaluate side-chains 164 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 510 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 C residue 587 ILE Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 58 MET 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 11 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 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 160 ASN 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 153 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 ASN F 9 GLN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.127047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.080045 restraints weight = 147729.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.081388 restraints weight = 54731.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082320 restraints weight = 27672.147| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17837 Z= 0.119 Angle : 0.578 11.520 24127 Z= 0.292 Chirality : 0.039 0.187 2738 Planarity : 0.003 0.041 2952 Dihedral : 8.732 79.378 2746 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.99 % Allowed : 17.54 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.18), residues: 2211 helix: 2.58 (0.14), residues: 1361 sheet: -1.21 (0.40), residues: 146 loop : -0.10 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP D 667 HIS 0.004 0.001 HIS F 60 PHE 0.017 0.001 PHE C 542 TYR 0.014 0.001 TYR B 420 ARG 0.006 0.000 ARG A 657 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 1135) hydrogen bonds : angle 3.85036 ( 3306) SS BOND : bond 0.00498 ( 8) SS BOND : angle 1.68459 ( 16) covalent geometry : bond 0.00264 (17829) covalent geometry : angle 0.57642 (24111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7045.03 seconds wall clock time: 124 minutes 23.99 seconds (7463.99 seconds total)