Starting phenix.real_space_refine on Mon May 19 12:33:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c1p_16379/05_2025/8c1p_16379.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c1p_16379/05_2025/8c1p_16379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c1p_16379/05_2025/8c1p_16379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c1p_16379/05_2025/8c1p_16379.map" model { file = "/net/cci-nas-00/data/ceres_data/8c1p_16379/05_2025/8c1p_16379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c1p_16379/05_2025/8c1p_16379.cif" } resolution = 2.9 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 118 5.16 5 Cl 4 4.86 5 C 11663 2.51 5 N 2850 2.21 5 O 3212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 134 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17849 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2942 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 2915 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 131 Conformer: "B" Number of residues, atoms: 399, 2915 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 131 bond proxies already assigned to first conformer: 2954 Chain: "B" Number of atoms: 3021 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 2984 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 97 Conformer: "B" Number of residues, atoms: 399, 2984 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 97 bond proxies already assigned to first conformer: 3011 Chain: "C" Number of atoms: 2949 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 2931 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 110 Conformer: "B" Number of residues, atoms: 399, 2931 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 110 bond proxies already assigned to first conformer: 2979 Chain: "D" Number of atoms: 3005 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 2968 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 Conformer: "B" Number of residues, atoms: 399, 2968 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 bond proxies already assigned to first conformer: 2994 Chain: "E" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1361 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Chain: "F" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 175, 1361 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 175, 1361 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 bond proxies already assigned to first conformer: 1380 Chain: "G" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1361 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Chain: "H" Number of atoms: 1366 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 175, 1355 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 175, 1355 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1374 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {'CYZ': 1, 'OLC': 1, 'PLM': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {'CYZ': 1, 'OLC': 1, 'PLM': 2} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {'CYZ': 1, 'OLC': 1, 'PLM': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "D" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {'CYZ': 1, 'OLC': 1, 'PLM': 2} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 19 residue: pdb=" N AGLN A 583 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 583 " occ=0.50 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 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 AILE B 587 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE B 587 " 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 7 not shown) Time building chain proxies: 19.86, per 1000 atoms: 1.11 Number of scatterers: 17849 At special positions: 0 Unit cell: (118.944, 118.944, 138.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 118 16.00 P 2 15.00 O 3212 8.00 N 2850 7.00 C 11663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 714 " - pdb=" SG CYS B 769 " distance=2.06 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 714 " - pdb=" SG CYS D 769 " distance=2.02 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.02 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.05 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.02 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.06 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.01 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=2.01 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: 4.43 Conformation dependent library (CDL) restraints added in 4.1 seconds 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4238 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 26 sheets defined 60.3% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.628A pdb=" N GLN A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 removed outlier: 4.287A 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 543 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 620 Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.655A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.596A 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 removed outlier: 3.529A pdb=" N SER A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) 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 815 removed outlier: 3.629A pdb=" N VAL A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLY A 790 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL A 791 " --> pdb=" O ASN A 787 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (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 543 Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 591 through 614 Processing helix chain 'B' and resid 615 through 621 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: 3.652A 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 764 Processing helix chain 'B' and resid 784 through 815 removed outlier: 3.599A pdb=" N VAL B 788 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLY B 790 " --> pdb=" O SER B 786 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 791 " --> pdb=" O ASN B 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.639A pdb=" N GLN C 410 " --> pdb=" O ASN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 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 543 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 621 Processing helix chain 'C' and resid 631 through 638 removed outlier: 3.668A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN C 638 " --> pdb=" O ASP C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 672 removed outlier: 3.576A pdb=" N SER C 672 " --> pdb=" O THR C 668 " (cutoff:3.500A) 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 765 removed outlier: 3.727A pdb=" N ASP C 765 " --> pdb=" O LYS C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 815 removed outlier: 3.616A pdb=" N VAL C 788 " --> pdb=" O SER C 784 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY C 790 " --> pdb=" O SER C 786 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL C 791 " --> pdb=" O ASN C 787 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 415 removed outlier: 4.275A 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 543 Processing helix chain 'D' and resid 568 through 581 Processing helix chain 'D' and resid 591 through 614 Processing helix chain 'D' and resid 615 through 621 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: 3.626A 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 815 removed outlier: 3.595A pdb=" N VAL D 788 " --> pdb=" O SER D 784 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N GLY D 790 " --> pdb=" O SER D 786 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL D 791 " --> pdb=" O ASN D 787 " (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: 3.890A pdb=" N GLU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.936A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 207 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 128 removed outlier: 3.909A pdb=" N GLU F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 161 removed outlier: 3.893A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 207 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: 3.896A pdb=" N GLU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.933A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 207 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 128 removed outlier: 3.912A pdb=" N GLU H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 161 removed outlier: 3.914A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 207 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 440 removed outlier: 3.582A 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: 3.779A 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: 4.091A 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: 6.572A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 4.183A 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: 6.649A pdb=" N TYR B 391 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU B 439 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL B 393 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 3.631A 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: 3.940A 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: 6.541A pdb=" N ALA B 642 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU B 699 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY B 644 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLU B 701 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N TYR B 696 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS B 501 " --> pdb=" O TYR B 696 " (cutoff:3.500A) removed outlier: 4.262A 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 450 removed outlier: 3.859A pdb=" N ALA C 448 " --> pdb=" O ASN C 457 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA C 455 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AB7, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.936A 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: 6.569A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 4.282A 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: 6.303A pdb=" N TYR D 391 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU D 439 " --> pdb=" O TYR D 391 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL D 393 " --> pdb=" O GLU D 439 " (cutoff:3.500A) removed outlier: 3.679A 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: 3.919A 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: 6.598A pdb=" N ALA D 642 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU D 699 " --> pdb=" O ALA D 642 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY D 644 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N GLU D 701 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N TYR D 696 " --> pdb=" O LYS D 501 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS D 501 " --> pdb=" O TYR D 696 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE D 498 " --> pdb=" O VAL D 719 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC6, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AC7, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AC8, first strand: chain 'H' and resid 77 through 79 1134 hydrogen bonds defined for protein. 3323 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: 5.76 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2918 1.32 - 1.45: 6070 1.45 - 1.58: 9004 1.58 - 1.71: 12 1.71 - 1.84: 184 Bond restraints: 18188 Sorted by residual: bond pdb=" C LEU D 646 " pdb=" N GLU D 647 " ideal model delta sigma weight residual 1.330 1.272 0.058 1.47e-02 4.63e+03 1.57e+01 bond pdb=" CA SER H 144 " pdb=" CB SER H 144 " ideal model delta sigma weight residual 1.528 1.474 0.055 1.56e-02 4.11e+03 1.24e+01 bond pdb=" CA SER F 144 " pdb=" CB SER F 144 " ideal model delta sigma weight residual 1.528 1.476 0.052 1.56e-02 4.11e+03 1.12e+01 bond pdb=" CG HIS F 60 " pdb=" CD2 HIS F 60 " ideal model delta sigma weight residual 1.354 1.318 0.036 1.10e-02 8.26e+03 1.04e+01 bond pdb=" CA SER C 533 " pdb=" CB SER C 533 " ideal model delta sigma weight residual 1.528 1.478 0.051 1.59e-02 3.96e+03 1.01e+01 ... (remaining 18183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 21285 2.03 - 4.06: 2911 4.06 - 6.09: 377 6.09 - 8.12: 62 8.12 - 10.16: 10 Bond angle restraints: 24645 Sorted by residual: angle pdb=" O LEU D 646 " pdb=" C LEU D 646 " pdb=" N GLU D 647 " ideal model delta sigma weight residual 123.22 115.79 7.43 1.14e+00 7.69e-01 4.25e+01 angle pdb=" CA GLN C 583 " pdb=" C GLN C 583 " pdb=" N BGLY C 584 " ideal model delta sigma weight residual 119.07 112.02 7.05 1.20e+00 6.94e-01 3.45e+01 angle pdb=" CA HIS H 132 " pdb=" CB HIS H 132 " pdb=" CG HIS H 132 " ideal model delta sigma weight residual 113.80 119.37 -5.57 1.00e+00 1.00e+00 3.11e+01 angle pdb=" C LEU H 69 " pdb=" CA LEU H 69 " pdb=" CB LEU H 69 " ideal model delta sigma weight residual 109.38 118.64 -9.26 1.68e+00 3.54e-01 3.04e+01 angle pdb=" O GLN C 583 " pdb=" C GLN C 583 " pdb=" N BGLY C 584 " ideal model delta sigma weight residual 122.19 127.73 -5.54 1.03e+00 9.43e-01 2.89e+01 ... (remaining 24640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.42: 10195 32.42 - 64.84: 364 64.84 - 97.26: 31 97.26 - 129.68: 18 129.68 - 162.10: 2 Dihedral angle restraints: 10610 sinusoidal: 3970 harmonic: 6640 Sorted by residual: dihedral pdb=" CB CYS C 714 " pdb=" SG CYS C 714 " pdb=" SG CYS C 769 " pdb=" CB CYS C 769 " ideal model delta sinusoidal sigma weight residual -86.00 -172.80 86.80 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS D 714 " pdb=" SG CYS D 714 " pdb=" SG CYS D 769 " pdb=" CB CYS D 769 " ideal model delta sinusoidal sigma weight residual 93.00 165.74 -72.74 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CB CYS B 714 " pdb=" SG CYS B 714 " pdb=" SG CYS B 769 " pdb=" CB CYS B 769 " ideal model delta sinusoidal sigma weight residual 93.00 165.10 -72.10 1 1.00e+01 1.00e-02 6.65e+01 ... (remaining 10607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 2605 0.156 - 0.312: 194 0.312 - 0.468: 9 0.468 - 0.624: 1 0.624 - 0.780: 1 Chirality restraints: 2810 Sorted by residual: chirality pdb=" CA LEU H 69 " pdb=" N LEU H 69 " pdb=" C LEU H 69 " pdb=" CB LEU H 69 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CA HIS H 132 " pdb=" N HIS H 132 " pdb=" C HIS H 132 " pdb=" CB HIS H 132 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" CB THR C 395 " pdb=" CA THR C 395 " pdb=" OG1 THR C 395 " pdb=" CG2 THR C 395 " both_signs ideal model delta sigma weight residual False 2.55 2.09 0.47 2.00e-01 2.50e+01 5.43e+00 ... (remaining 2807 not shown) Planarity restraints: 3013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLC A1403 " -0.091 2.00e-02 2.50e+03 7.77e-02 6.03e+01 pdb=" C11 OLC A1403 " 0.080 2.00e-02 2.50e+03 pdb=" C8 OLC A1403 " 0.074 2.00e-02 2.50e+03 pdb=" C9 OLC A1403 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 602 " 0.067 2.00e-02 2.50e+03 3.35e-02 2.80e+01 pdb=" CG TRP D 602 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP D 602 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 602 " -0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP D 602 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 602 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 602 " -0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 602 " 0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 602 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP D 602 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 583 " -0.025 2.00e-02 2.50e+03 5.12e-02 2.62e+01 pdb=" C GLN B 583 " 0.089 2.00e-02 2.50e+03 pdb=" O GLN B 583 " -0.033 2.00e-02 2.50e+03 pdb=" N BGLY B 584 " -0.030 2.00e-02 2.50e+03 ... (remaining 3010 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4253 2.81 - 3.33: 17698 3.33 - 3.86: 30706 3.86 - 4.38: 34973 4.38 - 4.90: 60088 Nonbonded interactions: 147718 Sorted by model distance: nonbonded pdb=" O GLY C 419 " pdb=" OE1 GLU C 423 " model vdw 2.288 3.040 nonbonded pdb=" O ILE C 396 " pdb=" CG1 VAL C 402 " model vdw 2.334 3.460 nonbonded pdb=" N GLY D 790 " pdb=" O HOH D1501 " model vdw 2.342 3.120 nonbonded pdb=" O GLY D 419 " pdb=" OE1 GLU D 423 " model vdw 2.343 3.040 nonbonded pdb=" N BASP A 586 " pdb=" OD1BASP A 586 " model vdw 2.345 3.120 ... (remaining 147713 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 \ 569 or resid 571 through 582 or resid 588 through 664 or (resid 665 and (name N \ or name CA or name C or name O or name CB )) or resid 666 through 779 or (resid \ 780 and (name N or name CA or name C or name O or name CB )) or resid 781 throu \ gh 815 or resid 1401 through 1404)) 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 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 502 and (name N o \ r name CA or name C or name O or name CB )) or resid 503 or (resid 504 through 5 \ 07 and (name N or name CA or name C or name O or name CB )) or resid 508 through \ 569 or resid 571 through 582 or resid 588 through 622 or (resid 623 through 627 \ and (name N or name CA or name C or name O or name CB )) or resid 628 or (resid \ 629 through 630 and (name N or name CA or name C or name O or name CB )) or res \ id 631 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 (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 683 o \ r (resid 684 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 85 through 690 or (resid 691 through 693 and (name N or name CA or name C or nam \ e O or name CB )) or resid 694 through 705 or (resid 706 and (name N or name CA \ or name C or name O or name CB )) or resid 707 through 815 or resid 1401 or (res \ id 1402 and (name CA or name CB or name C1 or name C2 or name C3 or name C4 or n \ ame C5 or name C6 or name C7 or name C8 or name C9 or name O1 or name O2 )) or r \ esid 1403 or resid 1405)) 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 569 or resid 571 through 582 or resid 588 through 633 or (resid \ 634 and (name N or name CA or name C or name O or name CB )) or resid 635 throu \ gh 691 or (resid 692 through 693 and (name N or name CA or name C or name O or n \ ame CB )) or resid 694 through 705 or (resid 706 and (name N or name CA or name \ C or name O or name CB )) or resid 707 through 708 or (resid 709 and (name N or \ name CA or name C or name O or name CB )) or resid 710 through 779 or (resid 780 \ and (name N or name CA or name C or name O or name CB )) or resid 781 through 8 \ 15 or resid 1401 through 1404)) selection = (chain 'D' and (resid 389 through 466 or (resid 467 through 469 and (name N or n \ ame CA or name C or name O or name CB )) or resid 470 through 500 or (resid 501 \ through 502 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 3 or (resid 504 through 507 and (name N or name CA or name C or name O or name C \ B )) or resid 508 through 569 or resid 571 through 582 or resid 588 through 622 \ or (resid 623 through 627 and (name N or name CA or name C or name O or name CB \ )) or resid 628 or (resid 629 through 630 and (name N or name CA or name C or na \ me O or name CB )) or resid 631 through 646 or (resid 647 through 648 and (name \ N or name CA or name C or name O or name CB )) or resid 649 through 658 or (resi \ d 659 and (name N or name CA or name C or name O or name CB )) or resid 660 thro \ ugh 664 or (resid 665 and (name N or name CA or name C or name O or name CB )) o \ r resid 666 through 691 or (resid 692 through 693 and (name N or name CA or name \ C or name O or name CB )) or resid 694 through 705 or (resid 706 and (name N or \ name CA or name C or name O or name CB )) or resid 707 through 708 or (resid 70 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 710 through \ 779 or (resid 780 and (name N or name CA or name C or name O or name CB )) or re \ sid 781 through 815 or resid 1401 or (resid 1402 and (name CA or name CB or name \ C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 \ or name C9 or name O1 or name O2 )) or resid 1403 or resid 1405)) } ncs_group { reference = (chain 'E' and (resid 5 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 183 or resid 185 through 209)) selection = (chain 'F' and (resid 5 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 183 or resid 185 through 209)) selection = (chain 'G' and (resid 5 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 183 or resid 185 through 209)) selection = (chain 'H' and (resid 5 through 183 or resid 185 through 209)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.040 Extract box with map and model: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 52.100 Find NCS groups from input model: 1.020 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:10.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 0.009 0.077 18199 Z= 0.566 Angle : 1.480 10.666 24667 Z= 0.981 Chirality : 0.091 0.780 2810 Planarity : 0.010 0.154 3013 Dihedral : 17.094 162.101 6339 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 4.44 % Allowed : 6.34 % Favored : 89.23 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 20.00 % 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: -1.55 (0.15), residues: 2275 helix: -0.25 (0.13), residues: 1333 sheet: -2.17 (0.27), residues: 266 loop : -1.84 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.010 TRP D 602 HIS 0.008 0.002 HIS F 132 PHE 0.045 0.008 PHE A 537 TYR 0.042 0.008 TYR B 417 ARG 0.060 0.005 ARG A 711 Details of bonding type rmsd hydrogen bonds : bond 0.15740 ( 1134) hydrogen bonds : angle 6.39410 ( 3323) SS BOND : bond 0.01744 ( 11) SS BOND : angle 5.09813 ( 22) covalent geometry : bond 0.00893 (18188) covalent geometry : angle 1.47291 (24645) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 360 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ILE cc_start: 0.7786 (tt) cc_final: 0.7381 (mt) REVERT: A 398 GLU cc_start: 0.7306 (tp30) cc_final: 0.6969 (tp30) REVERT: A 403 MET cc_start: 0.5753 (mtm) cc_final: 0.5325 (mtp) REVERT: A 459 MET cc_start: 0.7215 (mtm) cc_final: 0.6724 (mtm) REVERT: A 566 GLU cc_start: 0.7382 (pp20) cc_final: 0.7070 (mm-30) REVERT: A 590 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7825 (mpp-170) REVERT: A 637 LYS cc_start: 0.4758 (mmtt) cc_final: 0.4549 (mttm) REVERT: A 690 ARG cc_start: 0.5199 (OUTLIER) cc_final: 0.4819 (mtt90) REVERT: A 724 ASP cc_start: 0.8759 (p0) cc_final: 0.8401 (p0) REVERT: A 726 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7765 (pttp) REVERT: A 803 MET cc_start: 0.8386 (mtm) cc_final: 0.8112 (mtm) REVERT: B 403 MET cc_start: 0.6754 (mtm) cc_final: 0.6074 (mtp) REVERT: B 416 ARG cc_start: 0.5522 (ttp-170) cc_final: 0.5189 (ttp-110) REVERT: B 462 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6291 (tt0) REVERT: B 483 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6416 (mp0) REVERT: B 590 ARG cc_start: 0.8673 (mtm180) cc_final: 0.8261 (mtp180) REVERT: B 615 ASN cc_start: 0.7472 (m-40) cc_final: 0.6879 (t0) REVERT: B 653 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7578 (mp0) REVERT: B 665 LYS cc_start: 0.7017 (ttmm) cc_final: 0.6402 (mmmm) REVERT: B 707 TYR cc_start: 0.7458 (t80) cc_final: 0.7011 (t80) REVERT: B 807 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6514 (tp) REVERT: C 403 MET cc_start: 0.6056 (mtm) cc_final: 0.5541 (mtm) REVERT: C 566 GLU cc_start: 0.7718 (pp20) cc_final: 0.7413 (mm-30) REVERT: C 581 MET cc_start: 0.9027 (mmt) cc_final: 0.8818 (mmt) REVERT: C 709 GLU cc_start: 0.7574 (tt0) cc_final: 0.7320 (tt0) REVERT: D 443 ASP cc_start: 0.5641 (m-30) cc_final: 0.5416 (m-30) REVERT: D 465 TYR cc_start: 0.6101 (m-10) cc_final: 0.5618 (m-10) REVERT: D 467 ARG cc_start: 0.6626 (mpt-90) cc_final: 0.6294 (mpt-90) REVERT: D 482 GLU cc_start: 0.6737 (tp30) cc_final: 0.6446 (tp30) REVERT: D 499 MET cc_start: 0.8882 (ttm) cc_final: 0.8644 (ttp) REVERT: D 507 LYS cc_start: 0.6958 (ptpt) cc_final: 0.6684 (pttp) REVERT: D 566 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7126 (tp30) REVERT: D 638 GLN cc_start: 0.5793 (pp30) cc_final: 0.5304 (pp30) REVERT: D 645 THR cc_start: 0.8072 (m) cc_final: 0.7462 (t) REVERT: D 653 GLU cc_start: 0.7535 (tp30) cc_final: 0.7174 (tp30) REVERT: D 657 ARG cc_start: 0.7298 (ttp-170) cc_final: 0.7027 (mtp85) REVERT: D 754 VAL cc_start: 0.7600 (t) cc_final: 0.7392 (p) REVERT: D 761 LYS cc_start: 0.6943 (tmmt) cc_final: 0.6529 (tptp) REVERT: D 807 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6240 (tt) REVERT: E 24 MET cc_start: 0.7434 (tpt) cc_final: 0.7213 (tpt) REVERT: E 31 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7382 (m-30) REVERT: E 68 CYS cc_start: 0.6873 (m) cc_final: 0.6617 (t) REVERT: F 24 MET cc_start: 0.8526 (tpt) cc_final: 0.7745 (tpt) REVERT: F 37 ARG cc_start: 0.6037 (mtt-85) cc_final: 0.5698 (mmt90) REVERT: F 96 TYR cc_start: 0.6675 (t80) cc_final: 0.6372 (t80) REVERT: F 99 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6727 (mmt180) REVERT: F 207 LEU cc_start: 0.3786 (OUTLIER) cc_final: 0.3433 (pt) REVERT: G 5 ASP cc_start: 0.2420 (OUTLIER) cc_final: 0.2208 (t0) REVERT: G 11 LEU cc_start: 0.7119 (tp) cc_final: 0.6756 (mm) REVERT: G 24 MET cc_start: 0.7910 (tpt) cc_final: 0.7267 (tpp) REVERT: G 30 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7810 (p) REVERT: G 31 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7223 (m-30) REVERT: G 41 ARG cc_start: 0.2626 (OUTLIER) cc_final: 0.2264 (ttt-90) REVERT: G 60 HIS cc_start: 0.7067 (p90) cc_final: 0.6658 (p-80) REVERT: G 65 ARG cc_start: 0.6323 (mtm-85) cc_final: 0.5360 (mpt180) REVERT: G 79 LYS cc_start: 0.5812 (ttmm) cc_final: 0.5388 (tttp) REVERT: G 99 ARG cc_start: 0.6671 (mmp-170) cc_final: 0.6281 (mtt-85) REVERT: G 190 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8355 (mm-30) REVERT: H 12 ILE cc_start: 0.7953 (mt) cc_final: 0.7651 (mm) REVERT: H 14 THR cc_start: 0.8344 (t) cc_final: 0.8083 (m) REVERT: H 58 MET cc_start: 0.5912 (tpt) cc_final: 0.5407 (mmm) REVERT: H 67 CYS cc_start: 0.7540 (m) cc_final: 0.7136 (m) REVERT: H 78 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6574 (ptmt) REVERT: H 99 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6890 (mmm160) REVERT: H 174 SER cc_start: 0.8623 (OUTLIER) cc_final: 0.8360 (m) REVERT: A 1404 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6580 (mm-30) REVERT: C 1404 GLU cc_start: 0.6413 (mt-10) cc_final: 0.5907 (mm-30) outliers start: 74 outliers final: 11 residues processed: 405 average time/residue: 1.3091 time to fit residues: 591.2073 Evaluate side-chains 287 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 260 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 690 ARG Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 207 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS A 743 ASN B 743 ASN C 582 GLN D 752 GLN E 160 ASN F 132 HIS F 204 HIS F 206 GLN G 160 ASN G 204 HIS H 132 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.167700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129418 restraints weight = 62229.622| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.32 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18199 Z= 0.126 Angle : 0.527 9.740 24667 Z= 0.284 Chirality : 0.040 0.185 2810 Planarity : 0.004 0.041 3013 Dihedral : 13.258 167.935 2899 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.11 % Allowed : 13.77 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.09 (0.17), residues: 2275 helix: 2.05 (0.14), residues: 1341 sheet: -1.31 (0.34), residues: 208 loop : -1.21 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 762 HIS 0.004 0.001 HIS F 60 PHE 0.018 0.002 PHE C 570 TYR 0.016 0.001 TYR D 669 ARG 0.007 0.001 ARG C 656 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 1134) hydrogen bonds : angle 4.22094 ( 3323) SS BOND : bond 0.00298 ( 11) SS BOND : angle 1.88873 ( 22) covalent geometry : bond 0.00271 (18188) covalent geometry : angle 0.52376 (24645) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 301 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 665 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7028 (tttp) REVERT: A 803 MET cc_start: 0.8197 (mtm) cc_final: 0.7976 (mtm) REVERT: B 615 ASN cc_start: 0.7599 (m-40) cc_final: 0.7370 (t0) REVERT: B 624 ARG cc_start: 0.6547 (ptp-110) cc_final: 0.6318 (ptp-110) REVERT: B 665 LYS cc_start: 0.7059 (ttmm) cc_final: 0.6751 (tmtp) REVERT: B 707 TYR cc_start: 0.7701 (t80) cc_final: 0.7484 (t80) REVERT: B 807 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7144 (tp) REVERT: C 403 MET cc_start: 0.5962 (mtm) cc_final: 0.5683 (mtm) REVERT: C 812 TYR cc_start: 0.6595 (t80) cc_final: 0.6334 (t80) REVERT: D 482 GLU cc_start: 0.6706 (tp30) cc_final: 0.6424 (tp30) REVERT: D 507 LYS cc_start: 0.7090 (ptpt) cc_final: 0.6825 (pttp) REVERT: D 653 GLU cc_start: 0.6983 (tp30) cc_final: 0.6654 (tp30) REVERT: D 656 ARG cc_start: 0.7625 (ttm110) cc_final: 0.7418 (ttm110) REVERT: D 761 LYS cc_start: 0.7069 (tmmt) cc_final: 0.6765 (ttmm) REVERT: E 8 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.7073 (mt) REVERT: E 31 ASP cc_start: 0.6847 (OUTLIER) cc_final: 0.6542 (m-30) REVERT: E 96 TYR cc_start: 0.6598 (t80) cc_final: 0.6367 (t80) REVERT: E 97 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8375 (mt) REVERT: E 204 HIS cc_start: 0.6609 (OUTLIER) cc_final: 0.6031 (t70) REVERT: F 10 MET cc_start: 0.7343 (mmm) cc_final: 0.7109 (tpt) REVERT: F 24 MET cc_start: 0.8710 (tpt) cc_final: 0.8179 (tpt) REVERT: F 96 TYR cc_start: 0.7562 (t80) cc_final: 0.7277 (t80) REVERT: G 11 LEU cc_start: 0.7882 (tp) cc_final: 0.7281 (mm) REVERT: G 31 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.6722 (m-30) REVERT: G 41 ARG cc_start: 0.3582 (OUTLIER) cc_final: 0.2929 (ttt-90) REVERT: G 65 ARG cc_start: 0.6677 (mtm-85) cc_final: 0.6306 (mtt-85) REVERT: H 12 ILE cc_start: 0.8436 (mt) cc_final: 0.8181 (mm) REVERT: H 207 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.6111 (mt) outliers start: 51 outliers final: 15 residues processed: 331 average time/residue: 1.1862 time to fit residues: 442.2025 Evaluate side-chains 275 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 207 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 160 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 199 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 218 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 196 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: A 582 GLN B 431 HIS C 582 GLN D 615 ASN D 752 GLN H 132 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.163888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127855 restraints weight = 71409.815| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.48 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18199 Z= 0.204 Angle : 0.612 9.134 24667 Z= 0.326 Chirality : 0.043 0.255 2810 Planarity : 0.004 0.042 3013 Dihedral : 12.798 120.819 2854 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.78 % Allowed : 13.94 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.06 (0.17), residues: 2275 helix: 1.96 (0.14), residues: 1331 sheet: -1.09 (0.37), residues: 156 loop : -1.14 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 456 HIS 0.010 0.002 HIS G 60 PHE 0.022 0.002 PHE C 570 TYR 0.020 0.002 TYR F 180 ARG 0.007 0.001 ARG D 481 Details of bonding type rmsd hydrogen bonds : bond 0.05313 ( 1134) hydrogen bonds : angle 4.39938 ( 3323) SS BOND : bond 0.00374 ( 11) SS BOND : angle 1.83094 ( 22) covalent geometry : bond 0.00479 (18188) covalent geometry : angle 0.60965 (24645) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 273 time to evaluate : 1.913 Fit side-chains revert: symmetry clash REVERT: A 665 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7037 (tttp) REVERT: A 708 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7631 (mp) REVERT: A 710 GLN cc_start: 0.6689 (mm-40) cc_final: 0.6325 (mt0) REVERT: A 803 MET cc_start: 0.8199 (mtm) cc_final: 0.7980 (mtm) REVERT: B 427 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6652 (mm-30) REVERT: B 615 ASN cc_start: 0.7757 (m-40) cc_final: 0.7454 (t0) REVERT: B 711 ARG cc_start: 0.5784 (mmp80) cc_final: 0.5554 (mmp80) REVERT: B 807 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7106 (tp) REVERT: C 403 MET cc_start: 0.5947 (mtm) cc_final: 0.5594 (mtm) REVERT: C 812 TYR cc_start: 0.6602 (t80) cc_final: 0.6337 (t80) REVERT: D 507 LYS cc_start: 0.7258 (ptpt) cc_final: 0.6812 (pttp) REVERT: D 653 GLU cc_start: 0.6895 (tp30) cc_final: 0.6627 (tp30) REVERT: D 657 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6511 (mtm180) REVERT: E 8 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.7167 (mp) REVERT: E 79 LYS cc_start: 0.7491 (ttmm) cc_final: 0.6977 (ttpp) REVERT: E 96 TYR cc_start: 0.6534 (t80) cc_final: 0.6315 (t80) REVERT: E 97 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8396 (mt) REVERT: E 202 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.5961 (mp0) REVERT: E 203 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6923 (mttt) REVERT: E 204 HIS cc_start: 0.6739 (OUTLIER) cc_final: 0.6530 (m-70) REVERT: F 24 MET cc_start: 0.8672 (tpt) cc_final: 0.8251 (tpt) REVERT: F 74 ARG cc_start: 0.5940 (tmt90) cc_final: 0.5621 (tmt170) REVERT: F 96 TYR cc_start: 0.7551 (t80) cc_final: 0.7310 (t80) REVERT: G 11 LEU cc_start: 0.7867 (tp) cc_final: 0.7611 (tp) REVERT: G 31 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7191 (m-30) REVERT: G 41 ARG cc_start: 0.3534 (OUTLIER) cc_final: 0.2820 (mtp180) REVERT: G 65 ARG cc_start: 0.6781 (mtm-85) cc_final: 0.6453 (mtt-85) REVERT: G 204 HIS cc_start: 0.7042 (OUTLIER) cc_final: 0.6542 (t-90) REVERT: H 14 THR cc_start: 0.8793 (t) cc_final: 0.8396 (m) REVERT: H 132 HIS cc_start: 0.5818 (OUTLIER) cc_final: 0.5540 (p90) outliers start: 79 outliers final: 31 residues processed: 322 average time/residue: 1.2393 time to fit residues: 446.6866 Evaluate side-chains 297 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 657 ARG Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 147 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 168 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN D 615 ASN D 752 GLN E 205 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126870 restraints weight = 63962.281| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.34 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18199 Z= 0.154 Angle : 0.538 7.848 24667 Z= 0.287 Chirality : 0.040 0.193 2810 Planarity : 0.004 0.043 3013 Dihedral : 11.829 102.758 2850 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.26 % Allowed : 15.44 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.31 (0.18), residues: 2275 helix: 2.15 (0.14), residues: 1341 sheet: -0.97 (0.36), residues: 184 loop : -1.04 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 456 HIS 0.005 0.001 HIS H 132 PHE 0.019 0.002 PHE C 570 TYR 0.017 0.002 TYR D 669 ARG 0.007 0.001 ARG G 37 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 1134) hydrogen bonds : angle 4.18065 ( 3323) SS BOND : bond 0.00290 ( 11) SS BOND : angle 1.44937 ( 22) covalent geometry : bond 0.00355 (18188) covalent geometry : angle 0.53642 (24645) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 265 time to evaluate : 1.685 Fit side-chains revert: symmetry clash REVERT: A 665 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.6987 (tttp) REVERT: A 708 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7663 (mp) REVERT: A 710 GLN cc_start: 0.6676 (mm-40) cc_final: 0.6306 (mt0) REVERT: A 711 ARG cc_start: 0.6144 (mtp85) cc_final: 0.5874 (mtp180) REVERT: A 803 MET cc_start: 0.8206 (mtm) cc_final: 0.7924 (mtm) REVERT: B 465 TYR cc_start: 0.7610 (m-80) cc_final: 0.7358 (m-80) REVERT: B 615 ASN cc_start: 0.7770 (m-40) cc_final: 0.7557 (t0) REVERT: B 807 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7073 (tp) REVERT: C 403 MET cc_start: 0.5972 (mtm) cc_final: 0.5639 (mtm) REVERT: C 812 TYR cc_start: 0.6603 (t80) cc_final: 0.6329 (t80) REVERT: D 653 GLU cc_start: 0.6942 (tp30) cc_final: 0.6669 (tp30) REVERT: D 657 ARG cc_start: 0.6767 (mtm110) cc_final: 0.6488 (mtm180) REVERT: D 748 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7109 (ttmt) REVERT: E 79 LYS cc_start: 0.7498 (ttmm) cc_final: 0.6999 (ttpp) REVERT: E 96 TYR cc_start: 0.6530 (t80) cc_final: 0.6282 (t80) REVERT: E 97 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8360 (mt) REVERT: E 202 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.5923 (mp0) REVERT: E 204 HIS cc_start: 0.6701 (OUTLIER) cc_final: 0.5872 (t70) REVERT: F 96 TYR cc_start: 0.7522 (t80) cc_final: 0.7266 (t80) REVERT: G 31 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7387 (m-30) REVERT: G 37 ARG cc_start: 0.6311 (ptp-110) cc_final: 0.5966 (ptp-110) REVERT: G 41 ARG cc_start: 0.3518 (OUTLIER) cc_final: 0.2793 (mtp180) REVERT: G 65 ARG cc_start: 0.6860 (mtm-85) cc_final: 0.6543 (mtt-85) REVERT: G 79 LYS cc_start: 0.6665 (OUTLIER) cc_final: 0.6445 (mttt) REVERT: G 204 HIS cc_start: 0.6952 (OUTLIER) cc_final: 0.6582 (t-90) outliers start: 69 outliers final: 35 residues processed: 306 average time/residue: 1.2085 time to fit residues: 415.2499 Evaluate side-chains 295 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 717 MET Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 28 optimal weight: 7.9990 chunk 196 optimal weight: 8.9990 chunk 171 optimal weight: 0.7980 chunk 170 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 211 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN D 615 ASN D 752 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.164726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128155 restraints weight = 72838.460| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.55 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18199 Z= 0.166 Angle : 0.553 8.469 24667 Z= 0.294 Chirality : 0.041 0.207 2810 Planarity : 0.004 0.045 3013 Dihedral : 11.775 104.528 2850 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.55 % Allowed : 15.84 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.26 (0.17), residues: 2275 helix: 2.13 (0.14), residues: 1335 sheet: -0.96 (0.38), residues: 152 loop : -1.11 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 456 HIS 0.004 0.001 HIS F 204 PHE 0.018 0.002 PHE C 570 TYR 0.018 0.002 TYR G 32 ARG 0.008 0.001 ARG B 624 Details of bonding type rmsd hydrogen bonds : bond 0.04737 ( 1134) hydrogen bonds : angle 4.22326 ( 3323) SS BOND : bond 0.00347 ( 11) SS BOND : angle 1.41980 ( 22) covalent geometry : bond 0.00386 (18188) covalent geometry : angle 0.55199 (24645) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 257 time to evaluate : 1.993 Fit side-chains revert: symmetry clash REVERT: A 665 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.6989 (tttp) REVERT: A 679 VAL cc_start: 0.7849 (OUTLIER) cc_final: 0.7617 (p) REVERT: A 708 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7619 (mp) REVERT: A 710 GLN cc_start: 0.6640 (mm-40) cc_final: 0.6291 (mt0) REVERT: A 711 ARG cc_start: 0.6276 (mtp85) cc_final: 0.5977 (mtp180) REVERT: A 803 MET cc_start: 0.8208 (mtm) cc_final: 0.7937 (mtm) REVERT: B 615 ASN cc_start: 0.7780 (m-40) cc_final: 0.7498 (t0) REVERT: B 807 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7092 (tp) REVERT: C 403 MET cc_start: 0.6043 (mtm) cc_final: 0.5724 (mtm) REVERT: C 449 ARG cc_start: 0.6598 (ttp80) cc_final: 0.6351 (ptm160) REVERT: C 590 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7624 (mtp85) REVERT: C 812 TYR cc_start: 0.6609 (t80) cc_final: 0.6326 (t80) REVERT: D 653 GLU cc_start: 0.6973 (tp30) cc_final: 0.6710 (tp30) REVERT: D 657 ARG cc_start: 0.6912 (mtm110) cc_final: 0.6650 (mtm180) REVERT: D 748 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7153 (ttmt) REVERT: E 79 LYS cc_start: 0.7450 (ttmm) cc_final: 0.6975 (ttpp) REVERT: E 96 TYR cc_start: 0.6553 (t80) cc_final: 0.6267 (t80) REVERT: E 97 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8353 (mt) REVERT: E 190 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8549 (mm-30) REVERT: E 202 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.5936 (mp0) REVERT: E 204 HIS cc_start: 0.6740 (OUTLIER) cc_final: 0.5883 (t70) REVERT: F 79 LYS cc_start: 0.7707 (tmmm) cc_final: 0.7467 (mttt) REVERT: F 95 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.7013 (tt0) REVERT: F 96 TYR cc_start: 0.7494 (t80) cc_final: 0.7257 (t80) REVERT: G 41 ARG cc_start: 0.3373 (OUTLIER) cc_final: 0.2697 (mtp180) REVERT: G 65 ARG cc_start: 0.6760 (mtm-85) cc_final: 0.6478 (mtt-85) REVERT: G 76 VAL cc_start: 0.7142 (p) cc_final: 0.6733 (t) REVERT: G 79 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.6327 (mttt) REVERT: G 204 HIS cc_start: 0.6863 (OUTLIER) cc_final: 0.6544 (t-90) outliers start: 74 outliers final: 38 residues processed: 301 average time/residue: 1.2541 time to fit residues: 423.2769 Evaluate side-chains 299 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 248 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 590 ARG Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 124 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 152 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN D 615 ASN D 752 GLN E 132 HIS E 205 GLN F 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.165003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.129517 restraints weight = 81202.870| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.68 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18199 Z= 0.178 Angle : 0.564 8.386 24667 Z= 0.299 Chirality : 0.041 0.213 2810 Planarity : 0.004 0.046 3013 Dihedral : 11.755 105.222 2847 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.49 % Allowed : 16.07 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.18 (0.17), residues: 2275 helix: 2.07 (0.14), residues: 1335 sheet: -0.99 (0.38), residues: 152 loop : -1.14 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 456 HIS 0.004 0.001 HIS E 60 PHE 0.018 0.002 PHE C 570 TYR 0.020 0.002 TYR G 32 ARG 0.010 0.001 ARG B 624 Details of bonding type rmsd hydrogen bonds : bond 0.04804 ( 1134) hydrogen bonds : angle 4.23538 ( 3323) SS BOND : bond 0.00338 ( 11) SS BOND : angle 1.42331 ( 22) covalent geometry : bond 0.00416 (18188) covalent geometry : angle 0.56236 (24645) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 257 time to evaluate : 1.811 Fit side-chains revert: symmetry clash REVERT: A 665 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7033 (tttp) REVERT: A 679 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7669 (p) REVERT: A 710 GLN cc_start: 0.6587 (mm-40) cc_final: 0.6259 (mt0) REVERT: A 711 ARG cc_start: 0.6294 (mtp85) cc_final: 0.6076 (mtp85) REVERT: A 803 MET cc_start: 0.8231 (mtm) cc_final: 0.7941 (mtm) REVERT: B 615 ASN cc_start: 0.7795 (m-40) cc_final: 0.7495 (t0) REVERT: B 711 ARG cc_start: 0.5698 (mmp-170) cc_final: 0.5462 (mmp80) REVERT: B 807 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7120 (tp) REVERT: C 403 MET cc_start: 0.6080 (mtm) cc_final: 0.5757 (mtm) REVERT: C 590 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7628 (mtp85) REVERT: D 459 MET cc_start: 0.7504 (mtm) cc_final: 0.7098 (mmm) REVERT: D 653 GLU cc_start: 0.6980 (tp30) cc_final: 0.6769 (tp30) REVERT: D 657 ARG cc_start: 0.6973 (mtm110) cc_final: 0.6724 (mtm180) REVERT: D 748 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7163 (ttmt) REVERT: E 41 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.5542 (tmm-80) REVERT: E 79 LYS cc_start: 0.7508 (ttmm) cc_final: 0.7076 (ttpp) REVERT: E 96 TYR cc_start: 0.6565 (t80) cc_final: 0.6309 (t80) REVERT: E 97 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8375 (mt) REVERT: E 202 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.5945 (mp0) REVERT: F 95 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.7014 (tt0) REVERT: F 96 TYR cc_start: 0.7524 (t80) cc_final: 0.7176 (t80) REVERT: G 41 ARG cc_start: 0.3505 (OUTLIER) cc_final: 0.2866 (mtp180) REVERT: G 76 VAL cc_start: 0.7178 (p) cc_final: 0.6780 (t) REVERT: G 79 LYS cc_start: 0.6670 (OUTLIER) cc_final: 0.6412 (mttt) REVERT: G 204 HIS cc_start: 0.6897 (OUTLIER) cc_final: 0.6553 (t-90) REVERT: H 203 LYS cc_start: 0.7573 (tppt) cc_final: 0.7367 (ttmm) outliers start: 73 outliers final: 40 residues processed: 305 average time/residue: 1.3080 time to fit residues: 444.5900 Evaluate side-chains 301 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 249 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 590 ARG Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 79 LYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 199 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 117 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 114 optimal weight: 0.0470 chunk 63 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN D 615 ASN D 752 GLN E 205 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.166493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130680 restraints weight = 78951.254| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.54 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18199 Z= 0.123 Angle : 0.503 8.356 24667 Z= 0.268 Chirality : 0.039 0.161 2810 Planarity : 0.004 0.044 3013 Dihedral : 11.023 99.615 2847 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.63 % Allowed : 17.86 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.51 (0.18), residues: 2275 helix: 2.38 (0.14), residues: 1341 sheet: -1.16 (0.33), residues: 210 loop : -1.00 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 177 HIS 0.004 0.001 HIS F 204 PHE 0.013 0.001 PHE C 570 TYR 0.020 0.001 TYR C 434 ARG 0.010 0.000 ARG G 37 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 1134) hydrogen bonds : angle 4.04334 ( 3323) SS BOND : bond 0.00305 ( 11) SS BOND : angle 1.24454 ( 22) covalent geometry : bond 0.00272 (18188) covalent geometry : angle 0.50218 (24645) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 262 time to evaluate : 1.874 Fit side-chains revert: symmetry clash REVERT: A 679 VAL cc_start: 0.7858 (OUTLIER) cc_final: 0.7634 (p) REVERT: A 710 GLN cc_start: 0.6578 (mm-40) cc_final: 0.6276 (mt0) REVERT: A 803 MET cc_start: 0.8207 (mtm) cc_final: 0.7955 (mtm) REVERT: B 459 MET cc_start: 0.7960 (mtm) cc_final: 0.7735 (mtm) REVERT: B 615 ASN cc_start: 0.7745 (m-40) cc_final: 0.7458 (t0) REVERT: B 711 ARG cc_start: 0.5641 (mmp-170) cc_final: 0.5388 (mmp80) REVERT: B 807 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7065 (tp) REVERT: C 403 MET cc_start: 0.6045 (mtm) cc_final: 0.5676 (mtm) REVERT: C 812 TYR cc_start: 0.6613 (t80) cc_final: 0.6359 (t80) REVERT: D 615 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7597 (m110) REVERT: D 653 GLU cc_start: 0.6963 (tp30) cc_final: 0.6744 (tp30) REVERT: D 657 ARG cc_start: 0.6925 (mtm110) cc_final: 0.6685 (mtm180) REVERT: D 748 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7672 (mtmm) REVERT: E 79 LYS cc_start: 0.7480 (ttmm) cc_final: 0.7014 (ttpp) REVERT: E 97 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8364 (mt) REVERT: E 204 HIS cc_start: 0.6400 (m-70) cc_final: 0.6114 (t70) REVERT: F 24 MET cc_start: 0.8509 (tpt) cc_final: 0.8270 (tpt) REVERT: F 95 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.7031 (tt0) REVERT: F 96 TYR cc_start: 0.7541 (t80) cc_final: 0.7241 (t80) REVERT: G 37 ARG cc_start: 0.6258 (ptp-110) cc_final: 0.5923 (ptp-110) REVERT: G 41 ARG cc_start: 0.3467 (OUTLIER) cc_final: 0.2919 (mtp180) REVERT: G 76 VAL cc_start: 0.7127 (p) cc_final: 0.6712 (t) REVERT: G 184 PHE cc_start: 0.7339 (m-80) cc_final: 0.6742 (t80) REVERT: H 203 LYS cc_start: 0.7584 (tppt) cc_final: 0.7351 (ttmm) outliers start: 58 outliers final: 35 residues processed: 294 average time/residue: 1.2338 time to fit residues: 406.2509 Evaluate side-chains 297 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 255 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 128 optimal weight: 0.2980 chunk 151 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 12 optimal weight: 0.3980 chunk 212 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN D 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.165223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.129038 restraints weight = 78778.550| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.67 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18199 Z= 0.167 Angle : 0.551 9.301 24667 Z= 0.292 Chirality : 0.041 0.206 2810 Planarity : 0.004 0.046 3013 Dihedral : 11.409 103.735 2847 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.86 % Allowed : 17.63 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.33 (0.18), residues: 2275 helix: 2.19 (0.14), residues: 1339 sheet: -0.99 (0.39), residues: 152 loop : -1.07 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 64 HIS 0.004 0.001 HIS G 60 PHE 0.016 0.002 PHE C 570 TYR 0.022 0.002 TYR G 32 ARG 0.012 0.001 ARG B 624 Details of bonding type rmsd hydrogen bonds : bond 0.04669 ( 1134) hydrogen bonds : angle 4.17028 ( 3323) SS BOND : bond 0.00440 ( 11) SS BOND : angle 1.69416 ( 22) covalent geometry : bond 0.00388 (18188) covalent geometry : angle 0.54870 (24645) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 259 time to evaluate : 2.001 Fit side-chains revert: symmetry clash REVERT: A 679 VAL cc_start: 0.7868 (OUTLIER) cc_final: 0.7658 (p) REVERT: A 710 GLN cc_start: 0.6616 (mm-40) cc_final: 0.6300 (mt0) REVERT: A 803 MET cc_start: 0.8213 (mtm) cc_final: 0.7920 (mtm) REVERT: B 615 ASN cc_start: 0.7810 (m-40) cc_final: 0.7472 (t0) REVERT: B 807 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7110 (tp) REVERT: C 403 MET cc_start: 0.6123 (mtm) cc_final: 0.5772 (mtm) REVERT: C 590 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7654 (mtp85) REVERT: C 812 TYR cc_start: 0.6605 (t80) cc_final: 0.6355 (t80) REVERT: D 615 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7686 (m110) REVERT: D 657 ARG cc_start: 0.6970 (mtm110) cc_final: 0.6744 (mtm180) REVERT: D 748 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7651 (mtmm) REVERT: E 79 LYS cc_start: 0.7512 (ttmm) cc_final: 0.7035 (ttpp) REVERT: E 97 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8363 (mt) REVERT: E 202 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.5933 (mp0) REVERT: F 95 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: F 96 TYR cc_start: 0.7492 (t80) cc_final: 0.7251 (t80) REVERT: G 41 ARG cc_start: 0.3377 (OUTLIER) cc_final: 0.2846 (mtp180) REVERT: G 76 VAL cc_start: 0.7181 (p) cc_final: 0.6762 (t) REVERT: H 203 LYS cc_start: 0.7621 (tppt) cc_final: 0.7382 (ttmm) outliers start: 62 outliers final: 38 residues processed: 298 average time/residue: 1.3048 time to fit residues: 434.8053 Evaluate side-chains 299 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 252 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 590 ARG Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 135 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 178 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN D 615 ASN D 752 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.166440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.131117 restraints weight = 85346.491| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.72 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18199 Z= 0.142 Angle : 0.525 8.526 24667 Z= 0.278 Chirality : 0.039 0.180 2810 Planarity : 0.004 0.045 3013 Dihedral : 11.042 101.428 2847 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.46 % Allowed : 18.32 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.45 (0.18), residues: 2275 helix: 2.30 (0.14), residues: 1341 sheet: -1.18 (0.33), residues: 210 loop : -0.98 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 667 HIS 0.005 0.001 HIS G 60 PHE 0.015 0.001 PHE C 570 TYR 0.021 0.002 TYR G 32 ARG 0.011 0.001 ARG G 37 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 1134) hydrogen bonds : angle 4.09247 ( 3323) SS BOND : bond 0.00350 ( 11) SS BOND : angle 1.46347 ( 22) covalent geometry : bond 0.00324 (18188) covalent geometry : angle 0.52294 (24645) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 259 time to evaluate : 1.744 Fit side-chains revert: symmetry clash REVERT: A 541 ARG cc_start: 0.6793 (mmm160) cc_final: 0.6511 (mmm160) REVERT: A 665 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7065 (tttp) REVERT: A 679 VAL cc_start: 0.7894 (OUTLIER) cc_final: 0.7680 (p) REVERT: A 710 GLN cc_start: 0.6567 (mm-40) cc_final: 0.6265 (mt0) REVERT: A 803 MET cc_start: 0.8221 (mtm) cc_final: 0.7955 (mtm) REVERT: B 459 MET cc_start: 0.7914 (mtm) cc_final: 0.7532 (mmm) REVERT: B 463 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6448 (mm) REVERT: B 615 ASN cc_start: 0.7794 (m-40) cc_final: 0.7478 (t0) REVERT: B 678 PHE cc_start: 0.8059 (m-80) cc_final: 0.7813 (m-80) REVERT: B 807 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7082 (tp) REVERT: C 403 MET cc_start: 0.6143 (mtm) cc_final: 0.5781 (mtm) REVERT: C 590 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7628 (mtp85) REVERT: C 812 TYR cc_start: 0.6635 (t80) cc_final: 0.6387 (t80) REVERT: D 615 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7641 (m110) REVERT: D 657 ARG cc_start: 0.6859 (mtm110) cc_final: 0.6657 (mtm110) REVERT: D 748 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7089 (ttmt) REVERT: E 79 LYS cc_start: 0.7495 (ttmm) cc_final: 0.6968 (ttpp) REVERT: E 97 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8376 (mt) REVERT: E 202 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.5937 (mp0) REVERT: F 95 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.7024 (tt0) REVERT: F 96 TYR cc_start: 0.7483 (t80) cc_final: 0.7231 (t80) REVERT: G 37 ARG cc_start: 0.6219 (ptp-110) cc_final: 0.5862 (ptp-110) REVERT: G 41 ARG cc_start: 0.3126 (OUTLIER) cc_final: 0.2811 (mtp180) REVERT: G 76 VAL cc_start: 0.7162 (p) cc_final: 0.6738 (t) REVERT: G 184 PHE cc_start: 0.7263 (m-80) cc_final: 0.6761 (t80) REVERT: H 203 LYS cc_start: 0.7558 (tppt) cc_final: 0.7307 (ttmm) outliers start: 55 outliers final: 39 residues processed: 294 average time/residue: 1.2863 time to fit residues: 422.5856 Evaluate side-chains 298 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 248 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 590 ARG Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 55 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN D 615 ASN D 752 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.167398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131647 restraints weight = 74658.021| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.45 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18199 Z= 0.124 Angle : 0.508 8.543 24667 Z= 0.270 Chirality : 0.039 0.164 2810 Planarity : 0.004 0.047 3013 Dihedral : 10.836 100.212 2847 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.05 % Allowed : 18.84 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.57 (0.18), residues: 2275 helix: 2.42 (0.14), residues: 1341 sheet: -1.15 (0.33), residues: 210 loop : -0.95 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 667 HIS 0.005 0.001 HIS G 60 PHE 0.013 0.001 PHE C 570 TYR 0.021 0.001 TYR G 32 ARG 0.011 0.000 ARG G 37 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 1134) hydrogen bonds : angle 4.04729 ( 3323) SS BOND : bond 0.00330 ( 11) SS BOND : angle 1.36479 ( 22) covalent geometry : bond 0.00274 (18188) covalent geometry : angle 0.50653 (24645) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 254 time to evaluate : 2.012 Fit side-chains revert: symmetry clash REVERT: A 541 ARG cc_start: 0.6753 (mmm160) cc_final: 0.6455 (mmm160) REVERT: A 665 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.6976 (tttp) REVERT: A 679 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7703 (p) REVERT: A 710 GLN cc_start: 0.6540 (mm-40) cc_final: 0.6238 (mt0) REVERT: A 803 MET cc_start: 0.8220 (mtm) cc_final: 0.7968 (mtm) REVERT: B 463 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6416 (mm) REVERT: B 615 ASN cc_start: 0.7827 (m-40) cc_final: 0.7585 (t0) REVERT: B 678 PHE cc_start: 0.8031 (m-80) cc_final: 0.7789 (m-80) REVERT: B 807 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7084 (tp) REVERT: C 403 MET cc_start: 0.6122 (mtm) cc_final: 0.5756 (mtm) REVERT: C 590 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7631 (mtp85) REVERT: C 812 TYR cc_start: 0.6569 (t80) cc_final: 0.6330 (t80) REVERT: D 542 PHE cc_start: 0.5228 (OUTLIER) cc_final: 0.4984 (t80) REVERT: D 653 GLU cc_start: 0.7233 (tp30) cc_final: 0.6794 (tp30) REVERT: D 748 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7151 (ttmt) REVERT: E 79 LYS cc_start: 0.7487 (ttmm) cc_final: 0.7081 (ttpp) REVERT: E 97 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8356 (mt) REVERT: F 79 LYS cc_start: 0.7720 (tmmm) cc_final: 0.7473 (mttt) REVERT: F 95 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.7037 (tt0) REVERT: F 96 TYR cc_start: 0.7467 (t80) cc_final: 0.7238 (t80) REVERT: G 37 ARG cc_start: 0.6185 (ptp-110) cc_final: 0.5840 (ptp-110) REVERT: G 76 VAL cc_start: 0.7114 (p) cc_final: 0.6656 (t) REVERT: G 184 PHE cc_start: 0.7214 (m-80) cc_final: 0.6675 (t80) REVERT: H 203 LYS cc_start: 0.7551 (tppt) cc_final: 0.7343 (ttmm) outliers start: 48 outliers final: 31 residues processed: 283 average time/residue: 1.2578 time to fit residues: 398.9842 Evaluate side-chains 292 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 590 ARG Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 44 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 149 optimal weight: 0.0370 chunk 171 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 overall best weight: 2.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN D 615 ASN D 752 GLN E 205 GLN F 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.129430 restraints weight = 75395.546| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.57 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18199 Z= 0.191 Angle : 0.579 8.628 24667 Z= 0.305 Chirality : 0.042 0.220 2810 Planarity : 0.004 0.047 3013 Dihedral : 11.367 104.705 2843 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.28 % Allowed : 18.38 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 1.27 (0.18), residues: 2275 helix: 2.11 (0.14), residues: 1339 sheet: -0.96 (0.39), residues: 152 loop : -1.06 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 667 HIS 0.005 0.002 HIS G 60 PHE 0.017 0.002 PHE C 570 TYR 0.027 0.002 TYR G 32 ARG 0.008 0.001 ARG G 37 Details of bonding type rmsd hydrogen bonds : bond 0.04855 ( 1134) hydrogen bonds : angle 4.21707 ( 3323) SS BOND : bond 0.00373 ( 11) SS BOND : angle 1.60934 ( 22) covalent geometry : bond 0.00451 (18188) covalent geometry : angle 0.57712 (24645) =============================================================================== Job complete usr+sys time: 10361.53 seconds wall clock time: 179 minutes 22.50 seconds (10762.50 seconds total)