Starting phenix.real_space_refine on Sat Jul 4 04:54:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c1p_16379/07_2026/8c1p_16379.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c1p_16379/07_2026/8c1p_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_16379/07_2026/8c1p_16379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c1p_16379/07_2026/8c1p_16379.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8c1p_16379/07_2026/8c1p_16379.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c1p_16379/07_2026/8c1p_16379.cif" model { file = "/net/cci-nas-00/data/ceres_data/8c1p_16379/07_2026/8c1p_16379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c1p_16379/07_2026/8c1p_16379.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'ARG:plan': 7, 'ASP:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 2, 'GLU:plan': 15, 'TYR:plan': 1} 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: {'ARG:plan': 7, 'ASP:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 2, 'GLU:plan': 15, 'TYR:plan': 1} 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: {'ARG:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1} 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: {'ARG:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1} 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: {'ARG:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 2, 'GLU:plan': 13, 'ASP:plan': 4, 'TYR:plan': 1} 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: {'ARG:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 2, 'GLU:plan': 13, 'ASP:plan': 4, 'TYR:plan': 1} 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: {'ARG:plan': 5, 'TYR:plan': 2, 'ASP:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 11} 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: {'ARG:plan': 5, 'TYR:plan': 2, 'ASP:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 11} 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: 5.61, per 1000 atoms: 0.31 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: 1.27 Conformation dependent library (CDL) restraints added in 1.2 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: 0.38 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: 2.59 Time building geometry restraints manager: 1.69 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 - 20.87: 9583 20.87 - 41.74: 685 41.74 - 62.62: 186 62.62 - 83.49: 15 83.49 - 104.36: 9 Dihedral angle restraints: 10478 sinusoidal: 3838 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 10475 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 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 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 nam \ e C6 or name C7 or name C8 or name C9 or name O1 or name O2 )) or resid 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 1 \ 404)) 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 1401 or (resid 1402 and (name CA or name CB or name C1 or name C \ 2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 o \ r 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.460 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:8.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 : 15.680 104.362 6207 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.75 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.060 0.005 ARG A 711 TYR 0.042 0.008 TYR B 417 PHE 0.045 0.008 PHE A 537 TRP 0.067 0.010 TRP D 602 HIS 0.008 0.002 HIS F 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00893 / 0.57 (18188) covalent geometry : angle 1.47291 / 0.98 (24645) SS BOND : bond 0.01744 / 1.22 ( 11) SS BOND : angle 5.09813 / 3.62 ( 22) hydrogen bonds : bond 0.15740 / 10.46 ( 1134) hydrogen bonds : angle 6.39410 / 4.56 ( 3323) *********************** 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 : 0.555 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: 0.5417 (m-30) REVERT: D 465 TYR cc_start: 0.6100 (m-10) cc_final: 0.5617 (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: 0.6616 (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: 0.5500 time to fit residues: 248.2293 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 : 0.641 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 H 132 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.167050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128814 restraints weight = 59836.700| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.28 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1954 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= 0.132 Angle : 0.527 9.281 24667 Z= 0.287 Chirality : 0.040 0.186 2810 Planarity : 0.004 0.036 3013 Dihedral : 11.211 88.655 2767 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.28 % Allowed : 13.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.17), residues: 2275 helix: 2.00 (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 ARG 0.006 0.001 ARG C 656 TYR 0.016 0.001 TYR D 669 PHE 0.019 0.002 PHE C 570 TRP 0.011 0.001 TRP B 762 HIS 0.003 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (18188) covalent geometry : angle 0.52322 / 0.29 (24645) SS BOND : bond 0.00548 / 0.39 ( 11) SS BOND : angle 2.06093 / 1.38 ( 22) hydrogen bonds : bond 0.04553 / 3.06 ( 1134) hydrogen bonds : angle 4.24697 / 3.04 ( 3323) *********************** 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 356 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 302 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 MET cc_start: 0.5822 (mtm) cc_final: 0.5595 (mtp) REVERT: A 459 MET cc_start: 0.7822 (mtm) cc_final: 0.7613 (mtm) REVERT: A 665 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7020 (tttp) REVERT: A 803 MET cc_start: 0.8215 (mtm) cc_final: 0.7984 (mtm) REVERT: B 615 ASN cc_start: 0.7601 (m-40) cc_final: 0.7382 (t0) REVERT: B 624 ARG cc_start: 0.6565 (ptp-110) cc_final: 0.6325 (ptp-110) REVERT: B 665 LYS cc_start: 0.7094 (ttmm) cc_final: 0.6780 (tmtp) REVERT: B 707 TYR cc_start: 0.7727 (t80) cc_final: 0.7507 (t80) REVERT: B 807 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7150 (tp) REVERT: C 403 MET cc_start: 0.5984 (mtm) cc_final: 0.5719 (mtm) REVERT: C 653 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7268 (pt0) REVERT: C 812 TYR cc_start: 0.6583 (t80) cc_final: 0.6316 (t80) REVERT: D 482 GLU cc_start: 0.6742 (tp30) cc_final: 0.6466 (tp30) REVERT: D 507 LYS cc_start: 0.7086 (ptpt) cc_final: 0.6818 (pttp) REVERT: D 653 GLU cc_start: 0.6976 (tp30) cc_final: 0.6566 (tp30) REVERT: D 656 ARG cc_start: 0.7608 (ttm110) cc_final: 0.7340 (ttm-80) REVERT: D 687 ILE cc_start: 0.8045 (mm) cc_final: 0.7833 (mm) REVERT: D 761 LYS cc_start: 0.7069 (tmmt) cc_final: 0.6761 (ttmm) REVERT: E 31 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6564 (m-30) REVERT: E 96 TYR cc_start: 0.6598 (t80) cc_final: 0.6362 (t80) REVERT: E 97 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8379 (mt) REVERT: E 204 HIS cc_start: 0.6639 (OUTLIER) cc_final: 0.6013 (t70) REVERT: F 10 MET cc_start: 0.7351 (mmm) cc_final: 0.7119 (tpt) REVERT: F 24 MET cc_start: 0.8720 (tpt) cc_final: 0.8235 (tpt) REVERT: F 96 TYR cc_start: 0.7567 (t80) cc_final: 0.7272 (t80) REVERT: G 11 LEU cc_start: 0.7891 (tp) cc_final: 0.7298 (mm) REVERT: G 31 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.6739 (m-30) REVERT: G 41 ARG cc_start: 0.3526 (OUTLIER) cc_final: 0.2877 (ttt-90) REVERT: G 65 ARG cc_start: 0.6667 (mtm-85) cc_final: 0.6328 (mtt-85) REVERT: G 190 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8588 (mm-30) REVERT: G 204 HIS cc_start: 0.6924 (OUTLIER) cc_final: 0.6294 (t-90) REVERT: H 12 ILE cc_start: 0.8435 (mt) cc_final: 0.8186 (mm) REVERT: H 99 ARG cc_start: 0.7267 (mmt-90) cc_final: 0.6955 (mmm160) REVERT: H 207 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.6074 (mt) outliers start: 54 outliers final: 15 residues processed: 332 average time/residue: 0.5075 time to fit residues: 189.5192 Evaluate side-chains 276 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 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 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 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 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 139 optimal weight: 0.0170 chunk 55 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 44 optimal weight: 9.9990 chunk 216 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 GLN B 431 HIS D 615 ASN D 752 GLN G 204 HIS H 132 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.166442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130121 restraints weight = 72656.784| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.54 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18199 Z= 0.121 Angle : 0.501 8.821 24667 Z= 0.270 Chirality : 0.038 0.158 2810 Planarity : 0.003 0.038 3013 Dihedral : 9.811 88.665 2722 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.46 % Allowed : 15.15 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.18), residues: 2275 helix: 2.52 (0.14), residues: 1341 sheet: -1.04 (0.35), residues: 170 loop : -1.09 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 656 TYR 0.019 0.001 TYR C 434 PHE 0.017 0.001 PHE C 570 TRP 0.011 0.001 TRP D 762 HIS 0.012 0.001 HIS G 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (18188) covalent geometry : angle 0.49940 / 0.27 (24645) SS BOND : bond 0.00332 / 0.24 ( 11) SS BOND : angle 1.44218 / 1.00 ( 22) hydrogen bonds : bond 0.04194 / 2.82 ( 1134) hydrogen bonds : angle 4.05343 / 2.90 ( 3323) *********************** 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 331 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 274 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 665 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.6978 (tttp) REVERT: A 710 GLN cc_start: 0.6672 (mm-40) cc_final: 0.6315 (mt0) REVERT: A 803 MET cc_start: 0.8204 (mtm) cc_final: 0.7960 (mtm) REVERT: B 615 ASN cc_start: 0.7656 (m-40) cc_final: 0.7435 (t0) REVERT: B 807 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7047 (tp) REVERT: C 403 MET cc_start: 0.5948 (mtm) cc_final: 0.5651 (mtm) REVERT: C 486 ASP cc_start: 0.7071 (m-30) cc_final: 0.6836 (t0) REVERT: C 812 TYR cc_start: 0.6549 (t80) cc_final: 0.6312 (t80) REVERT: D 507 LYS cc_start: 0.7120 (ptpt) cc_final: 0.6765 (pttp) REVERT: D 657 ARG cc_start: 0.6792 (mtm110) cc_final: 0.6304 (ttp80) REVERT: D 687 ILE cc_start: 0.7967 (mm) cc_final: 0.7758 (mm) REVERT: D 761 LYS cc_start: 0.7052 (tmmt) cc_final: 0.6799 (ttmm) REVERT: E 8 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6936 (mt) REVERT: E 31 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6398 (m-30) REVERT: E 97 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8373 (mt) REVERT: E 204 HIS cc_start: 0.6592 (OUTLIER) cc_final: 0.6008 (t70) REVERT: F 24 MET cc_start: 0.8688 (tpt) cc_final: 0.8221 (tpt) REVERT: G 31 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.6790 (m-30) REVERT: G 37 ARG cc_start: 0.6385 (ptp-110) cc_final: 0.5994 (ptp-110) REVERT: G 41 ARG cc_start: 0.3509 (OUTLIER) cc_final: 0.2884 (mtp180) REVERT: G 65 ARG cc_start: 0.6684 (mtm-85) cc_final: 0.6348 (mtt-85) outliers start: 57 outliers final: 23 residues processed: 309 average time/residue: 0.5095 time to fit residues: 176.9270 Evaluate side-chains 279 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 B residue 393 VAL Chi-restraints excluded: chain B residue 499 MET 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 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 E residue 8 ILE Chi-restraints excluded: chain E residue 31 ASP 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 204 HIS 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 31 ASP Chi-restraints excluded: chain G residue 41 ARG 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 152 optimal weight: 0.7980 chunk 210 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 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 = 0.3847 r_free = 0.3847 target = 0.164227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127669 restraints weight = 75192.463| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.61 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2719 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= 0.189 Angle : 0.575 8.187 24667 Z= 0.307 Chirality : 0.042 0.219 2810 Planarity : 0.004 0.044 3013 Dihedral : 10.171 93.462 2720 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.55 % Allowed : 14.63 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.17), residues: 2275 helix: 2.11 (0.14), residues: 1339 sheet: -0.88 (0.39), residues: 156 loop : -1.03 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 656 TYR 0.013 0.002 TYR A 669 PHE 0.020 0.002 PHE C 570 TRP 0.011 0.002 TRP D 456 HIS 0.005 0.002 HIS H 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (18188) covalent geometry : angle 0.57366 / 0.31 (24645) SS BOND : bond 0.00343 / 0.24 ( 11) SS BOND : angle 1.52681 / 1.05 ( 22) hydrogen bonds : bond 0.05018 / 3.38 ( 1134) hydrogen bonds : angle 4.27917 / 3.06 ( 3323) *********************** 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 341 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 266 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 665 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7026 (tttp) REVERT: A 708 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7705 (mp) REVERT: A 710 GLN cc_start: 0.6650 (mm-40) cc_final: 0.6285 (mt0) REVERT: A 803 MET cc_start: 0.8198 (mtm) cc_final: 0.7953 (mtm) REVERT: B 615 ASN cc_start: 0.7767 (m-40) cc_final: 0.7498 (t0) REVERT: B 678 PHE cc_start: 0.8269 (m-80) cc_final: 0.7993 (m-80) REVERT: B 711 ARG cc_start: 0.5806 (mmp80) cc_final: 0.5567 (mmp80) REVERT: B 807 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7085 (tp) REVERT: C 403 MET cc_start: 0.5899 (mtm) cc_final: 0.5568 (mtm) REVERT: C 812 TYR cc_start: 0.6562 (t80) cc_final: 0.6322 (t80) REVERT: D 507 LYS cc_start: 0.7303 (ptpt) cc_final: 0.6858 (pttp) REVERT: D 687 ILE cc_start: 0.8082 (mm) cc_final: 0.7877 (mm) REVERT: E 8 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6846 (mm) REVERT: E 31 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.6631 (m-30) REVERT: E 78 LYS cc_start: 0.6994 (tttt) cc_final: 0.6746 (tttp) REVERT: E 79 LYS cc_start: 0.7492 (ttmm) cc_final: 0.6960 (ttpp) REVERT: E 97 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8351 (mt) REVERT: E 202 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.5966 (mp0) REVERT: F 24 MET cc_start: 0.8633 (tpt) cc_final: 0.8225 (tpt) REVERT: G 31 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: G 37 ARG cc_start: 0.6341 (ptp-110) cc_final: 0.6026 (ptp-110) REVERT: G 41 ARG cc_start: 0.3575 (OUTLIER) cc_final: 0.2818 (mtp180) REVERT: G 65 ARG cc_start: 0.6787 (mtm-85) cc_final: 0.6467 (mtt-85) REVERT: G 79 LYS cc_start: 0.6691 (OUTLIER) cc_final: 0.6464 (mttt) REVERT: G 204 HIS cc_start: 0.6883 (OUTLIER) cc_final: 0.6407 (t-90) outliers start: 75 outliers final: 32 residues processed: 311 average time/residue: 0.5026 time to fit residues: 176.0410 Evaluate side-chains 287 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 244 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 708 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 499 MET 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 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 E residue 8 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 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 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 31 ASP Chi-restraints excluded: chain G residue 41 ARG 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 61 SER Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 97 LEU 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 177 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 192 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 615 ASN D 752 GLN E 205 GLN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.164965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126848 restraints weight = 59781.803| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.34 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2924 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 : 0.559 8.375 24667 Z= 0.298 Chirality : 0.041 0.210 2810 Planarity : 0.004 0.045 3013 Dihedral : 9.861 92.841 2720 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.55 % Allowed : 15.90 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.17), residues: 2275 helix: 2.08 (0.14), residues: 1335 sheet: -0.93 (0.39), residues: 152 loop : -1.09 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 624 TYR 0.018 0.002 TYR C 434 PHE 0.018 0.002 PHE C 570 TRP 0.010 0.002 TRP D 456 HIS 0.004 0.001 HIS F 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (18188) covalent geometry : angle 0.55703 / 0.30 (24645) SS BOND : bond 0.00376 / 0.27 ( 11) SS BOND : angle 1.47811 / 1.02 ( 22) hydrogen bonds : bond 0.04801 / 3.24 ( 1134) hydrogen bonds : angle 4.25123 / 3.04 ( 3323) *********************** 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 329 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 255 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 665 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.6988 (tttp) REVERT: A 679 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7591 (p) REVERT: A 708 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7608 (mp) REVERT: A 710 GLN cc_start: 0.6539 (mm-40) cc_final: 0.6220 (mt0) REVERT: A 803 MET cc_start: 0.8251 (mtm) cc_final: 0.7982 (mtm) REVERT: B 465 TYR cc_start: 0.7511 (m-80) cc_final: 0.7134 (m-80) REVERT: B 615 ASN cc_start: 0.7676 (m-40) cc_final: 0.7368 (t0) REVERT: B 678 PHE cc_start: 0.8267 (m-80) cc_final: 0.7979 (m-80) REVERT: B 711 ARG cc_start: 0.5831 (mmp80) cc_final: 0.5327 (mmp-170) REVERT: B 807 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7098 (tp) REVERT: C 403 MET cc_start: 0.6000 (mtm) cc_final: 0.5633 (mtm) REVERT: C 812 TYR cc_start: 0.6580 (t80) cc_final: 0.6319 (t80) REVERT: D 687 ILE cc_start: 0.8073 (mm) cc_final: 0.7857 (mm) REVERT: D 748 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7151 (ttmt) REVERT: E 8 ILE cc_start: 0.7084 (OUTLIER) cc_final: 0.6723 (mm) REVERT: E 79 LYS cc_start: 0.7487 (ttmm) cc_final: 0.6980 (ttpp) REVERT: E 97 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8360 (mt) REVERT: E 190 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8478 (mm-30) REVERT: E 202 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.5961 (mp0) REVERT: F 24 MET cc_start: 0.8645 (tpt) cc_final: 0.8261 (tpt) REVERT: G 37 ARG cc_start: 0.6266 (ptp-110) cc_final: 0.5971 (ptp-110) REVERT: G 41 ARG cc_start: 0.3501 (OUTLIER) cc_final: 0.2782 (mtp180) REVERT: G 65 ARG cc_start: 0.6745 (mtm-85) cc_final: 0.6482 (mtt-85) REVERT: G 76 VAL cc_start: 0.7142 (p) cc_final: 0.6729 (t) REVERT: G 204 HIS cc_start: 0.6867 (OUTLIER) cc_final: 0.6485 (t-90) outliers start: 74 outliers final: 35 residues processed: 296 average time/residue: 0.5246 time to fit residues: 174.0769 Evaluate side-chains 293 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 248 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 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 748 LYS Chi-restraints excluded: chain E residue 8 ILE 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 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 11 LEU Chi-restraints excluded: chain G residue 24 MET 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 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 153 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 12 optimal weight: 0.0770 chunk 186 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 615 ASN D 752 GLN E 205 GLN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.165609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.128243 restraints weight = 64155.791| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.43 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18199 Z= 0.150 Angle : 0.526 8.243 24667 Z= 0.281 Chirality : 0.040 0.186 2810 Planarity : 0.004 0.045 3013 Dihedral : 9.466 91.572 2717 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.15 % Allowed : 16.19 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.18), residues: 2275 helix: 2.22 (0.14), residues: 1339 sheet: -1.24 (0.35), residues: 180 loop : -1.05 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 656 TYR 0.016 0.002 TYR D 669 PHE 0.016 0.002 PHE C 570 TRP 0.009 0.001 TRP D 456 HIS 0.004 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (18188) covalent geometry : angle 0.52431 / 0.28 (24645) SS BOND : bond 0.00319 / 0.23 ( 11) SS BOND : angle 1.35332 / 0.94 ( 22) hydrogen bonds : bond 0.04482 / 3.02 ( 1134) hydrogen bonds : angle 4.15378 / 2.96 ( 3323) *********************** 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 326 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 259 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 665 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.6996 (tttp) REVERT: A 679 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7592 (p) REVERT: A 710 GLN cc_start: 0.6557 (mm-40) cc_final: 0.6229 (mt0) REVERT: A 803 MET cc_start: 0.8218 (mtm) cc_final: 0.7948 (mtm) REVERT: B 615 ASN cc_start: 0.7763 (m-40) cc_final: 0.7442 (t0) REVERT: B 624 ARG cc_start: 0.6546 (ptp-110) cc_final: 0.6210 (ptp-110) REVERT: B 678 PHE cc_start: 0.8234 (m-80) cc_final: 0.7969 (m-80) REVERT: B 807 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7058 (tp) REVERT: C 403 MET cc_start: 0.6138 (mtm) cc_final: 0.5769 (mtm) REVERT: C 590 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7856 (mtt90) REVERT: C 812 TYR cc_start: 0.6588 (t80) cc_final: 0.6320 (t80) REVERT: D 638 GLN cc_start: 0.7051 (pp30) cc_final: 0.6551 (pp30) REVERT: D 748 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7709 (mtmm) REVERT: E 8 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6665 (mm) REVERT: E 41 ARG cc_start: 0.5747 (OUTLIER) cc_final: 0.5452 (tmm-80) REVERT: E 79 LYS cc_start: 0.7485 (ttmm) cc_final: 0.7025 (ttpp) REVERT: E 97 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8355 (mt) REVERT: E 190 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8552 (mm-30) REVERT: E 202 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.5942 (mp0) REVERT: F 79 LYS cc_start: 0.7665 (tmmm) cc_final: 0.7450 (mttt) REVERT: G 41 ARG cc_start: 0.3402 (OUTLIER) cc_final: 0.2703 (mtp180) REVERT: G 65 ARG cc_start: 0.6741 (mtm-85) cc_final: 0.6464 (mtt-85) REVERT: G 76 VAL cc_start: 0.7165 (p) cc_final: 0.6753 (t) REVERT: G 204 HIS cc_start: 0.6838 (OUTLIER) cc_final: 0.6518 (t-90) outliers start: 67 outliers final: 35 residues processed: 302 average time/residue: 0.5085 time to fit residues: 172.4019 Evaluate side-chains 298 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 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 732 THR 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 719 VAL Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain E residue 8 ILE 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 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 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 31 ASP 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 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 27 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 615 ASN D 752 GLN E 132 HIS E 205 GLN F 204 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.165005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128828 restraints weight = 75399.943| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.54 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 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 = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18199 Z= 0.169 Angle : 0.547 8.378 24667 Z= 0.292 Chirality : 0.040 0.208 2810 Planarity : 0.004 0.046 3013 Dihedral : 9.614 93.157 2717 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.32 % Allowed : 16.47 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.18), residues: 2275 helix: 2.11 (0.14), residues: 1335 sheet: -1.24 (0.35), residues: 180 loop : -1.12 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 624 TYR 0.015 0.002 TYR C 434 PHE 0.017 0.002 PHE C 570 TRP 0.009 0.002 TRP G 64 HIS 0.004 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (18188) covalent geometry : angle 0.54554 / 0.29 (24645) SS BOND : bond 0.00339 / 0.24 ( 11) SS BOND : angle 1.45641 / 1.00 ( 22) hydrogen bonds : bond 0.04735 / 3.19 ( 1134) hydrogen bonds : angle 4.22499 / 3.01 ( 3323) *********************** 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 323 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 253 time to evaluate : 0.912 Fit side-chains REVERT: A 665 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7069 (tttp) REVERT: A 679 VAL cc_start: 0.7829 (OUTLIER) cc_final: 0.7590 (p) REVERT: A 708 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7656 (mp) REVERT: A 710 GLN cc_start: 0.6550 (mm-40) cc_final: 0.6220 (mt0) REVERT: A 803 MET cc_start: 0.8209 (mtm) cc_final: 0.7923 (mtm) REVERT: B 615 ASN cc_start: 0.7825 (m-40) cc_final: 0.7501 (t0) REVERT: B 678 PHE cc_start: 0.8230 (m-80) cc_final: 0.7966 (m-80) REVERT: B 807 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7119 (tp) REVERT: C 403 MET cc_start: 0.6138 (mtm) cc_final: 0.5799 (mtm) REVERT: C 590 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7893 (mtt90) REVERT: D 638 GLN cc_start: 0.7082 (pp30) cc_final: 0.6523 (pp30) REVERT: D 748 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7710 (mtmm) REVERT: E 8 ILE cc_start: 0.7051 (OUTLIER) cc_final: 0.6681 (mm) REVERT: E 79 LYS cc_start: 0.7477 (ttmm) cc_final: 0.7009 (ttpp) REVERT: E 97 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8348 (mt) REVERT: E 202 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.5946 (mp0) REVERT: G 41 ARG cc_start: 0.3462 (OUTLIER) cc_final: 0.2829 (mtp180) REVERT: G 76 VAL cc_start: 0.7198 (p) cc_final: 0.6778 (t) REVERT: G 184 PHE cc_start: 0.7412 (m-80) cc_final: 0.6893 (t80) REVERT: G 204 HIS cc_start: 0.6861 (OUTLIER) cc_final: 0.6549 (t-90) outliers start: 70 outliers final: 41 residues processed: 296 average time/residue: 0.5172 time to fit residues: 171.6794 Evaluate side-chains 300 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 248 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 719 VAL Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain E residue 8 ILE 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 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 31 ASP Chi-restraints excluded: chain G residue 37 ARG 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 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 204 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 135 optimal weight: 0.6980 chunk 213 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 615 ASN D 752 GLN E 205 GLN F 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.164547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129235 restraints weight = 81510.475| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.59 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18199 Z= 0.209 Angle : 0.595 8.525 24667 Z= 0.316 Chirality : 0.042 0.237 2810 Planarity : 0.004 0.047 3013 Dihedral : 9.806 93.970 2717 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.09 % Allowed : 17.28 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.17), residues: 2275 helix: 1.95 (0.14), residues: 1329 sheet: -0.94 (0.39), residues: 154 loop : -1.17 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 624 TYR 0.017 0.002 TYR D 669 PHE 0.018 0.002 PHE A 604 TRP 0.011 0.002 TRP G 64 HIS 0.010 0.002 HIS F 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (18188) covalent geometry : angle 0.59345 / 0.32 (24645) SS BOND : bond 0.00354 / 0.25 ( 11) SS BOND : angle 1.61949 / 1.10 ( 22) hydrogen bonds : bond 0.05107 / 3.44 ( 1134) hydrogen bonds : angle 4.34502 / 3.10 ( 3323) *********************** 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 320 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 254 time to evaluate : 0.625 Fit side-chains REVERT: A 665 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7153 (tttp) REVERT: A 679 VAL cc_start: 0.7818 (OUTLIER) cc_final: 0.7604 (p) REVERT: A 708 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7636 (mp) REVERT: A 710 GLN cc_start: 0.6549 (mm-40) cc_final: 0.6224 (mt0) REVERT: A 803 MET cc_start: 0.8235 (mtm) cc_final: 0.7939 (mtm) REVERT: B 615 ASN cc_start: 0.7852 (m-40) cc_final: 0.7548 (t0) REVERT: B 807 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7132 (tp) REVERT: C 403 MET cc_start: 0.6051 (mtm) cc_final: 0.5725 (mtm) REVERT: C 590 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7599 (mtp85) REVERT: D 748 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7163 (ttmt) REVERT: E 8 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6685 (mm) REVERT: E 79 LYS cc_start: 0.7507 (ttmm) cc_final: 0.6963 (ttpp) REVERT: E 97 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8377 (mt) REVERT: E 202 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.5941 (mp0) REVERT: G 41 ARG cc_start: 0.3246 (OUTLIER) cc_final: 0.2730 (mtp180) REVERT: G 76 VAL cc_start: 0.7193 (p) cc_final: 0.6780 (t) REVERT: G 204 HIS cc_start: 0.6891 (OUTLIER) cc_final: 0.6498 (t-90) outliers start: 66 outliers final: 41 residues processed: 295 average time/residue: 0.5450 time to fit residues: 179.7934 Evaluate side-chains 299 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 247 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 686 MET 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 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 719 VAL Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain D residue 754 VAL Chi-restraints excluded: chain E residue 8 ILE 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 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 31 ASP Chi-restraints excluded: chain G residue 37 ARG 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 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 204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 153 optimal weight: 0.4980 chunk 155 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 215 optimal weight: 0.0980 chunk 221 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 84 optimal weight: 0.0870 chunk 89 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 752 GLN E 205 GLN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.169519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.134393 restraints weight = 78048.121| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.55 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18199 Z= 0.103 Angle : 0.475 8.543 24667 Z= 0.253 Chirality : 0.038 0.161 2810 Planarity : 0.003 0.049 3013 Dihedral : 8.585 86.030 2717 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.53 % Allowed : 18.89 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.18), residues: 2275 helix: 2.55 (0.14), residues: 1341 sheet: -1.04 (0.34), residues: 210 loop : -0.93 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 656 TYR 0.022 0.001 TYR C 434 PHE 0.010 0.001 PHE C 570 TRP 0.016 0.001 TRP G 177 HIS 0.005 0.001 HIS F 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (18188) covalent geometry : angle 0.47343 / 0.25 (24645) SS BOND : bond 0.00302 / 0.21 ( 11) SS BOND : angle 1.30836 / 0.84 ( 22) hydrogen bonds : bond 0.03615 / 2.43 ( 1134) hydrogen bonds : angle 3.94877 / 2.80 ( 3323) *********************** 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 310 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 271 time to evaluate : 0.439 Fit side-chains REVERT: A 541 ARG cc_start: 0.6698 (mmm160) cc_final: 0.6432 (mmm160) REVERT: A 679 VAL cc_start: 0.7848 (OUTLIER) cc_final: 0.7612 (p) REVERT: B 459 MET cc_start: 0.7790 (mtm) cc_final: 0.7576 (tpp) REVERT: B 463 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6350 (mm) REVERT: B 615 ASN cc_start: 0.7838 (m-40) cc_final: 0.7596 (t0) REVERT: B 807 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7013 (tp) REVERT: C 403 MET cc_start: 0.6062 (mtm) cc_final: 0.5686 (mtm) REVERT: C 812 TYR cc_start: 0.6598 (t80) cc_final: 0.6342 (t80) REVERT: D 542 PHE cc_start: 0.5230 (OUTLIER) cc_final: 0.5004 (t80) REVERT: D 615 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7560 (m110) REVERT: E 8 ILE cc_start: 0.6939 (mm) cc_final: 0.6705 (mt) REVERT: E 79 LYS cc_start: 0.7465 (ttmm) cc_final: 0.7053 (ttpp) REVERT: F 24 MET cc_start: 0.8526 (tpt) cc_final: 0.8220 (tpt) REVERT: F 79 LYS cc_start: 0.7647 (tmmm) cc_final: 0.7417 (mttm) REVERT: G 41 ARG cc_start: 0.3182 (OUTLIER) cc_final: 0.2833 (mtp180) REVERT: G 76 VAL cc_start: 0.6958 (p) cc_final: 0.6516 (t) REVERT: G 184 PHE cc_start: 0.7139 (m-80) cc_final: 0.6574 (t80) outliers start: 39 outliers final: 21 residues processed: 291 average time/residue: 0.5049 time to fit residues: 165.3436 Evaluate side-chains 281 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 463 LEU 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 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 754 VAL Chi-restraints excluded: chain E residue 12 ILE 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 120 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 11 LEU 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 H residue 68 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 32 optimal weight: 0.0870 chunk 75 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 186 optimal weight: 0.9980 chunk 190 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 752 GLN E 205 GLN E 206 GLN H 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.168950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.133201 restraints weight = 70940.173| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.37 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18199 Z= 0.106 Angle : 0.482 8.562 24667 Z= 0.256 Chirality : 0.038 0.156 2810 Planarity : 0.003 0.047 3013 Dihedral : 8.390 87.832 2717 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.02 % Allowed : 20.05 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.18), residues: 2275 helix: 2.65 (0.14), residues: 1341 sheet: -0.92 (0.34), residues: 208 loop : -0.89 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 656 TYR 0.030 0.001 TYR C 707 PHE 0.012 0.001 PHE C 570 TRP 0.012 0.001 TRP G 177 HIS 0.002 0.000 HIS F 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (18188) covalent geometry : angle 0.48066 / 0.26 (24645) SS BOND : bond 0.00312 / 0.21 ( 11) SS BOND : angle 1.34558 / 0.86 ( 22) hydrogen bonds : bond 0.03737 / 2.51 ( 1134) hydrogen bonds : angle 3.93463 / 2.80 ( 3323) ********************** 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 289 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 259 time to evaluate : 0.698 Fit side-chains REVERT: A 541 ARG cc_start: 0.6680 (mmm160) cc_final: 0.6420 (mmm160) REVERT: A 679 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7672 (p) REVERT: B 463 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6326 (mm) REVERT: B 615 ASN cc_start: 0.7822 (m-40) cc_final: 0.7570 (t0) REVERT: B 717 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8241 (ptm) REVERT: B 807 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6996 (tp) REVERT: C 391 TYR cc_start: 0.7010 (m-80) cc_final: 0.6801 (m-80) REVERT: C 403 MET cc_start: 0.6100 (mtm) cc_final: 0.5751 (mtm) REVERT: C 812 TYR cc_start: 0.6569 (t80) cc_final: 0.6319 (t80) REVERT: D 615 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7519 (m110) REVERT: E 8 ILE cc_start: 0.6905 (mm) cc_final: 0.6563 (mm) REVERT: E 79 LYS cc_start: 0.7416 (ttmm) cc_final: 0.7022 (ttpp) REVERT: F 24 MET cc_start: 0.8515 (tpt) cc_final: 0.8174 (tpt) REVERT: F 79 LYS cc_start: 0.7640 (tmmm) cc_final: 0.7422 (mttm) REVERT: G 41 ARG cc_start: 0.2976 (OUTLIER) cc_final: 0.2751 (mtp180) REVERT: G 65 ARG cc_start: 0.6609 (mtt-85) cc_final: 0.6050 (mtt180) REVERT: G 76 VAL cc_start: 0.6920 (p) cc_final: 0.6460 (t) REVERT: G 184 PHE cc_start: 0.7150 (m-80) cc_final: 0.6581 (t80) outliers start: 30 outliers final: 17 residues processed: 277 average time/residue: 0.5138 time to fit residues: 159.7478 Evaluate side-chains 276 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 253 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 717 MET 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 D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain E residue 12 ILE 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 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU 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 H residue 68 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 22 optimal weight: 9.9990 chunk 162 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 615 ASN D 752 GLN E 205 GLN E 206 GLN H 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.167162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.130982 restraints weight = 67855.816| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.31 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3355 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= 0.132 Angle : 0.515 8.713 24667 Z= 0.272 Chirality : 0.039 0.168 2810 Planarity : 0.004 0.045 3013 Dihedral : 8.605 90.412 2715 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.02 % Allowed : 20.10 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.18), residues: 2275 helix: 2.55 (0.14), residues: 1337 sheet: -0.95 (0.34), residues: 210 loop : -0.92 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 656 TYR 0.040 0.001 TYR C 707 PHE 0.014 0.001 PHE C 570 TRP 0.014 0.001 TRP C 667 HIS 0.003 0.001 HIS H 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (18188) covalent geometry : angle 0.51354 / 0.27 (24645) SS BOND : bond 0.00328 / 0.22 ( 11) SS BOND : angle 1.45760 / 0.94 ( 22) hydrogen bonds : bond 0.04183 / 2.82 ( 1134) hydrogen bonds : angle 4.03681 / 2.88 ( 3323) =============================================================================== Job complete usr+sys time: 4359.70 seconds wall clock time: 75 minutes 16.09 seconds (4516.09 seconds total)