Starting phenix.real_space_refine on Wed Jan 22 20:55:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c1q_16380/01_2025/8c1q_16380.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c1q_16380/01_2025/8c1q_16380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c1q_16380/01_2025/8c1q_16380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c1q_16380/01_2025/8c1q_16380.map" model { file = "/net/cci-nas-00/data/ceres_data/8c1q_16380/01_2025/8c1q_16380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c1q_16380/01_2025/8c1q_16380.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 10 5.49 5 S 109 5.16 5 C 12060 2.51 5 N 2937 2.21 5 O 3334 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 18462 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 3179 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 405, 3150 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 390} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 405, 3150 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 390} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 3187 Chain: "B" Number of atoms: 3012 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 2977 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 385} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 107 Conformer: "B" Number of residues, atoms: 400, 2977 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 385} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 107 bond proxies already assigned to first conformer: 3005 Chain: "C" Number of atoms: 3116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 406, 3087 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 65 Conformer: "B" Number of residues, atoms: 406, 3087 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 65 bond proxies already assigned to first conformer: 3124 Chain: "D" Number of atoms: 3152 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3117 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 400, 3117 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 3147 Chain: "E" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "F" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "G" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'OLC': 1, 'PLM': 1, 'ZK1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'OLC': 1, 'PLM': 1, 'ZK1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'OLC': 1, 'PLM': 1, 'ZK1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'OLC': 1, 'PLM': 1, 'ZK1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "F" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 16 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 A 619 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 619 " 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 APHE B 619 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 619 " 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 residue: pdb=" N APHE C 619 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 619 " occ=0.50 ... (remaining 4 not shown) Time building chain proxies: 15.98, per 1000 atoms: 0.87 Number of scatterers: 18462 At special positions: 0 Unit cell: (117.66, 121.9, 135.68, 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) S 109 16.00 P 10 15.00 F 12 9.00 O 3334 8.00 N 2937 7.00 C 12060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.02 Simple disulfide: pdb=" SG CYS B 714 " - pdb=" SG CYS B 769 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.02 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=2.00 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.06 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.06 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.00 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.06 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.06 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.61 Conformation dependent library (CDL) restraints added in 3.8 seconds 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4258 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 26 sheets defined 59.8% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.915A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 623 Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.697A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 660 through 672 Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 702 through 710 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 784 through 787 Processing helix chain 'A' and resid 788 through 814 removed outlier: 3.548A 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 458 through 465 Processing helix chain 'B' and resid 478 through 485 removed outlier: 3.887A pdb=" N VAL B 484 " --> pdb=" O VAL B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 518 through 542 Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 591 through 622 Processing helix chain 'B' and resid 631 through 638 removed outlier: 3.760A pdb=" N LEU B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 658 Processing helix chain 'B' and resid 660 through 672 Processing helix chain 'B' and resid 681 through 692 removed outlier: 3.640A pdb=" N SER B 692 " --> pdb=" O ARG B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 710 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 787 Processing helix chain 'B' and resid 788 through 815 removed outlier: 3.569A pdb=" N PHE B 792 " --> pdb=" O VAL B 788 " (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 removed outlier: 3.670A pdb=" N GLU C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 518 through 542 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 623 Processing helix chain 'C' and resid 631 through 638 removed outlier: 3.626A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) removed outlier: 3.735A 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 Processing helix chain 'C' and resid 681 through 693 removed outlier: 4.145A pdb=" N LYS C 693 " --> pdb=" O VAL C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 710 Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 788 through 814 removed outlier: 3.528A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 415 No H-bonds generated for 'chain 'D' and resid 413 through 415' Processing helix chain 'D' and resid 419 through 433 removed outlier: 3.677A pdb=" N GLU D 423 " --> pdb=" O GLY D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 465 Processing helix chain 'D' and resid 478 through 485 removed outlier: 3.850A pdb=" N VAL D 484 " --> pdb=" O VAL D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 518 through 542 Processing helix chain 'D' and resid 568 through 581 Processing helix chain 'D' and resid 591 through 622 Processing helix chain 'D' and resid 631 through 638 removed outlier: 3.681A pdb=" N LEU D 635 " --> pdb=" O SER D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 657 removed outlier: 3.995A pdb=" N GLU D 653 " --> pdb=" O GLY D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 672 Processing helix chain 'D' and resid 681 through 692 Processing helix chain 'D' and resid 702 through 710 Processing helix chain 'D' and resid 738 through 752 Processing helix chain 'D' and resid 753 through 764 Processing helix chain 'D' and resid 784 through 787 Processing helix chain 'D' and resid 788 through 815 removed outlier: 3.561A pdb=" N PHE D 792 " --> pdb=" O VAL D 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 93 through 105 Processing helix chain 'E' and resid 105 through 128 removed outlier: 4.243A pdb=" N GLU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 162 removed outlier: 3.895A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 209 removed outlier: 3.548A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 105 through 126 removed outlier: 3.829A pdb=" N GLU F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.824A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 209 removed outlier: 3.541A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG F 208 " --> pdb=" O HIS F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 93 through 105 Processing helix chain 'G' and resid 105 through 128 removed outlier: 4.240A pdb=" N GLU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 162 removed outlier: 3.894A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 209 removed outlier: 3.541A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 105 through 126 removed outlier: 3.834A pdb=" N GLU H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.819A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 209 removed outlier: 3.546A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG H 208 " --> pdb=" O HIS H 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 437 removed outlier: 3.783A pdb=" N VAL A 470 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ALA A 473 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLY A 729 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU A 475 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY A 727 " --> pdb=" O LEU A 475 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 437 removed outlier: 3.783A pdb=" N VAL A 470 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ALA A 473 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLY A 729 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU A 475 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY A 727 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA4, first strand: chain 'A' and resid 449 through 450 removed outlier: 3.617A pdb=" N ALA A 455 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 642 through 644 removed outlier: 6.611A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 437 through 438 removed outlier: 3.691A pdb=" N VAL B 470 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ALA B 473 " --> pdb=" O GLY B 729 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY B 729 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU B 475 " --> pdb=" O GLY B 727 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY B 727 " --> pdb=" O LEU B 475 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 437 through 438 removed outlier: 3.691A pdb=" N VAL B 470 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ALA B 473 " --> pdb=" O GLY B 729 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY B 729 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU B 475 " --> pdb=" O GLY B 727 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY B 727 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 492 " --> pdb=" O TYR B 728 " (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 448 through 450 removed outlier: 3.620A pdb=" N ALA B 455 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 642 through 644 removed outlier: 6.562A pdb=" N ALA B 642 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU B 699 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY B 644 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N GLU B 701 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N TYR B 696 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LYS B 501 " --> pdb=" O TYR B 696 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE B 498 " --> pdb=" O VAL B 719 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 435 through 440 removed outlier: 3.754A pdb=" N VAL C 470 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA C 473 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLY C 729 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU C 475 " --> pdb=" O GLY C 727 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY C 727 " --> pdb=" O LEU C 475 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 435 through 440 removed outlier: 3.754A pdb=" N VAL C 470 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA C 473 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLY C 729 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU C 475 " --> pdb=" O GLY C 727 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY C 727 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) 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 448 through 450 removed outlier: 4.293A pdb=" N ALA C 448 " --> pdb=" O ASN C 457 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA C 455 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.511A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 436 through 438 removed outlier: 3.680A pdb=" N VAL D 470 " --> pdb=" O ILE D 392 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ALA D 473 " --> pdb=" O GLY D 729 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLY D 729 " --> pdb=" O ALA D 473 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU D 475 " --> pdb=" O GLY D 727 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY D 727 " --> pdb=" O LEU D 475 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 436 through 438 removed outlier: 3.680A pdb=" N VAL D 470 " --> pdb=" O ILE D 392 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ALA D 473 " --> pdb=" O GLY D 729 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLY D 729 " --> pdb=" O ALA D 473 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU D 475 " --> pdb=" O GLY D 727 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY D 727 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET D 492 " --> pdb=" O TYR D 728 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 403 through 404 Processing sheet with id=AC1, first strand: chain 'D' and resid 449 through 450 removed outlier: 3.650A pdb=" N ALA D 455 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 642 through 644 removed outlier: 6.504A pdb=" N ALA D 642 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU D 699 " --> pdb=" O ALA D 642 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY D 644 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N GLU D 701 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N TYR D 696 " --> pdb=" O LYS D 501 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LYS D 501 " --> pdb=" O TYR D 696 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE D 498 " --> pdb=" O VAL D 719 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AC4, first strand: chain 'E' and resid 37 through 38 Processing sheet with id=AC5, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AC6, first strand: chain 'G' and resid 34 through 35 Processing sheet with id=AC7, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AC8, first strand: chain 'H' and resid 77 through 79 1175 hydrogen bonds defined for protein. 3436 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.85 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2837 1.29 - 1.43: 5269 1.43 - 1.57: 10555 1.57 - 1.71: 12 1.71 - 1.85: 174 Bond restraints: 18847 Sorted by residual: bond pdb=" C LEU B 616 " pdb=" O LEU B 616 " ideal model delta sigma weight residual 1.237 1.154 0.082 1.19e-02 7.06e+03 4.80e+01 bond pdb=" CAO ZK1 A 901 " pdb=" PBA ZK1 A 901 " ideal model delta sigma weight residual 1.896 1.779 0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" CAO ZK1 D 901 " pdb=" PBA ZK1 D 901 " ideal model delta sigma weight residual 1.896 1.795 0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" CA SER D 611 " pdb=" CB SER D 611 " ideal model delta sigma weight residual 1.528 1.458 0.070 1.56e-02 4.11e+03 2.04e+01 bond pdb=" CA SER C 576 " pdb=" CB SER C 576 " ideal model delta sigma weight residual 1.528 1.464 0.065 1.56e-02 4.11e+03 1.71e+01 ... (remaining 18842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 23103 2.28 - 4.56: 2144 4.56 - 6.83: 173 6.83 - 9.11: 29 9.11 - 11.39: 7 Bond angle restraints: 25456 Sorted by residual: angle pdb=" N GLN B 583 " pdb=" CA GLN B 583 " pdb=" C GLN B 583 " ideal model delta sigma weight residual 109.63 99.18 10.45 1.49e+00 4.50e-01 4.92e+01 angle pdb=" C GLU B 684 " pdb=" CA GLU B 684 " pdb=" CB GLU B 684 " ideal model delta sigma weight residual 110.85 121.97 -11.12 1.70e+00 3.46e-01 4.28e+01 angle pdb=" CA ASP B 724 " pdb=" CB ASP B 724 " pdb=" CG ASP B 724 " ideal model delta sigma weight residual 112.60 118.63 -6.03 1.00e+00 1.00e+00 3.63e+01 angle pdb=" CA PHE D 570 " pdb=" CB PHE D 570 " pdb=" CG PHE D 570 " ideal model delta sigma weight residual 113.80 119.80 -6.00 1.00e+00 1.00e+00 3.60e+01 angle pdb=" CA ASP A 724 " pdb=" CB ASP A 724 " pdb=" CG ASP A 724 " ideal model delta sigma weight residual 112.60 118.10 -5.50 1.00e+00 1.00e+00 3.02e+01 ... (remaining 25451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.16: 10172 21.16 - 42.31: 702 42.31 - 63.47: 178 63.47 - 84.63: 30 84.63 - 105.78: 12 Dihedral angle restraints: 11094 sinusoidal: 4410 harmonic: 6684 Sorted by residual: dihedral pdb=" CA BCYS D 585 " pdb=" C BCYS D 585 " pdb=" N BASP D 586 " pdb=" CA BASP D 586 " ideal model delta harmonic sigma weight residual -180.00 -150.22 -29.78 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" C GLU B 684 " pdb=" N GLU B 684 " pdb=" CA GLU B 684 " pdb=" CB GLU B 684 " ideal model delta harmonic sigma weight residual -122.60 -137.15 14.55 0 2.50e+00 1.60e-01 3.39e+01 dihedral pdb=" CA BCYS A 585 " pdb=" C BCYS A 585 " pdb=" N BASP A 586 " pdb=" CA BASP A 586 " ideal model delta harmonic sigma weight residual -180.00 -155.86 -24.14 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 11091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2092 0.092 - 0.185: 631 0.185 - 0.277: 80 0.277 - 0.369: 7 0.369 - 0.462: 1 Chirality restraints: 2811 Sorted by residual: chirality pdb=" CA GLU B 684 " pdb=" N GLU B 684 " pdb=" C GLU B 684 " pdb=" CB GLU B 684 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" CB VAL B 791 " pdb=" CA VAL B 791 " pdb=" CG1 VAL B 791 " pdb=" CG2 VAL B 791 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB VAL D 791 " pdb=" CA VAL D 791 " pdb=" CG1 VAL D 791 " pdb=" CG2 VAL D 791 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 2808 not shown) Planarity restraints: 3111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV H1302 " -0.106 2.00e-02 2.50e+03 1.11e-01 1.22e+02 pdb=" C29 POV H1302 " 0.092 2.00e-02 2.50e+03 pdb="C210 POV H1302 " 0.127 2.00e-02 2.50e+03 pdb="C211 POV H1302 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV F1302 " -0.097 2.00e-02 2.50e+03 9.70e-02 9.41e+01 pdb=" C29 POV F1302 " 0.099 2.00e-02 2.50e+03 pdb="C210 POV F1302 " 0.095 2.00e-02 2.50e+03 pdb="C211 POV F1302 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 583 " -0.043 2.00e-02 2.50e+03 8.60e-02 7.40e+01 pdb=" C GLN D 583 " 0.149 2.00e-02 2.50e+03 pdb=" O GLN D 583 " -0.055 2.00e-02 2.50e+03 pdb=" N BGLY D 584 " -0.051 2.00e-02 2.50e+03 ... (remaining 3108 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 758 2.72 - 3.26: 19007 3.26 - 3.81: 30052 3.81 - 4.35: 37773 4.35 - 4.90: 63737 Nonbonded interactions: 151327 Sorted by model distance: nonbonded pdb=" O PHE C 654 " pdb=" OG SER C 658 " model vdw 2.171 3.040 nonbonded pdb=" NH1 ARG B 690 " pdb=" OD1 ASP B 715 " model vdw 2.184 3.120 nonbonded pdb=" NH2 ARG A 711 " pdb=" O LYS A 766 " model vdw 2.204 3.120 nonbonded pdb=" N AASP D 586 " pdb=" OD1AASP D 586 " model vdw 2.223 3.120 nonbonded pdb=" N BASP D 586 " pdb=" OD1BASP D 586 " model vdw 2.239 3.120 ... (remaining 151322 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 390 through 391 or (resid 392 and (name N or name CA or na \ me C or name O or name CB or name CG1)) or resid 393 through 398 or (resid 399 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 400 \ through 403 or (resid 404 and (name N or name CA or name C or name O or name CB \ or name CG )) or resid 405 or (resid 406 and (name N or name CA or name C or nam \ e O or name CB )) or resid 407 through 408 or (resid 409 through 410 and (name N \ or name CA or name C or name O or name CB )) or resid 411 or (resid 412 and (na \ me N or name CA or name C or name O or name CB )) or resid 413 through 414 or (r \ esid 415 and (name N or name CA or name C or name O or name CB )) or resid 416 t \ hrough 422 or (resid 423 and (name N or name CA or name C or name O or name CB o \ r name CG )) or resid 424 through 429 or (resid 430 and (name N or name CA or na \ me C or name O or name CB )) or resid 431 through 433 or (resid 434 and (name N \ or name CA or name C or name O or name CB or name CG )) or (resid 435 and (name \ N or name CA or name C or name O or name CB )) or resid 436 or (resid 437 and (n \ ame N or name CA or name C or name O or name CB )) or resid 438 or (resid 439 an \ d (name N or name CA or name C or name O or name CB or name CG )) or resid 440 t \ hrough 441 or (resid 442 and (name N or name CA or name C or name O or name CB ) \ ) or resid 443 through 448 or (resid 449 through 452 and (name N or name CA or n \ ame C or name O or name CB )) or resid 453 or (resid 454 through 455 and (name N \ or name CA or name C or name O or name CB )) or resid 456 or (resid 457 and (na \ me N or name CA or name C or name O or name CB )) or resid 458 through 466 or (r \ esid 467 through 468 and (name N or name CA or name C or name O or name CB )) or \ resid 469 through 504 or (resid 505 and (name N or name CA or name C or name O \ or name CB )) or resid 506 or (resid 507 and (name N or name CA or name C or nam \ e O or name CB )) or resid 508 through 546 or resid 567 through 581 or resid 583 \ or resid 587 through 618 or resid 620 through 637 or (resid 638 through 640 and \ (name N or name CA or name C or name O or name CB )) or resid 641 through 646 o \ r (resid 647 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 648 through 656 or (resid 657 and (name N or name CA or name C or name \ O or name CB )) or resid 658 or (resid 659 and (name N or name CA or name C or \ name O or name CB )) or resid 660 through 663 or (resid 664 and (name N or name \ CA or name C or name O or name CB )) or resid 665 or (resid 666 and (name N or n \ ame CA or name C or name O or name CB )) or resid 667 through 670 or (resid 671 \ and (name N or name CA or name C or name O or name CB )) or resid 672 through 67 \ 3 or (resid 674 and (name N or name CA or name C or name O or name CB )) or resi \ d 675 through 679 or (resid 680 and (name N or name CA or name C or name O or na \ me CB )) or resid 681 through 682 or (resid 683 and (name N or name CA or name C \ or name O or name CB )) or resid 684 through 685 or (resid 686 and (name N or n \ ame CA or name C or name O or name CB )) or resid 687 through 694 or (resid 695 \ and (name N or name CA or name C or name O or name CB )) or resid 696 through 70 \ 0 or (resid 701 and (name N or name CA or name C or name O or name CB )) or resi \ d 702 through 733 or (resid 734 and (name N or name CA or name C or name O or na \ me CB )) or resid 735 through 747 or (resid 748 and (name N or name CA or name C \ or name O or name CB )) or resid 749 through 750 or (resid 751 through 752 and \ (name N or name CA or name C or name O or name CB )) or resid 753 or (resid 754 \ and (name N or name CA or name C or name O or name CB or name CG1)) or resid 755 \ through 756 or (resid 757 and (name N or name CA or name C or name O or name CB \ )) or resid 758 through 770 or (resid 772 through 773 and (name N or name CA or \ name C or name O or name CB )) or resid 779 through 815 or resid 901 through 90 \ 3)) selection = (chain 'B' and (resid 390 through 456 or (resid 457 and (name N or name CA or na \ me C or name O or name CB )) or resid 458 through 504 or (resid 505 and (name N \ or name CA or name C or name O or name CB )) or resid 506 or (resid 507 and (nam \ e N or name CA or name C or name O or name CB )) or resid 508 through 545 or (re \ sid 566 and (name N or name CA or name C or name O or name CB )) or resid 567 th \ rough 581 or resid 583 or resid 587 through 618 or resid 620 through 658 or (res \ id 659 and (name N or name CA or name C or name O or name CB )) or resid 660 thr \ ough 663 or (resid 664 and (name N or name CA or name C or name O or name CB )) \ or resid 665 or (resid 666 and (name N or name CA or name C or name O or name CB \ )) or resid 667 through 685 or (resid 686 and (name N or name CA or name C or n \ ame O or name CB )) or resid 687 through 753 or (resid 754 and (name N or name C \ A or name C or name O or name CB or name CG1)) or resid 755 through 777 or (resi \ d 778 and (name N or name CA or name C or name O or name CB )) or resid 779 thro \ ugh 813 or (resid 814 through 815 and (name N or name CA or name C or name O or \ name CB )) or resid 901 through 903)) selection = (chain 'C' and (resid 390 through 391 or (resid 392 and (name N or name CA or na \ me C or name O or name CB or name CG1)) or resid 393 through 398 or (resid 399 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 400 \ through 403 or (resid 404 and (name N or name CA or name C or name O or name CB \ or name CG )) or resid 405 through 409 or (resid 410 and (name N or name CA or n \ ame C or name O or name CB )) or resid 411 or (resid 412 and (name N or name CA \ or name C or name O or name CB )) or resid 413 through 414 or (resid 415 and (na \ me N or name CA or name C or name O or name CB )) or resid 416 through 422 or (r \ esid 423 and (name N or name CA or name C or name O or name CB or name CG )) or \ resid 424 through 429 or (resid 430 and (name N or name CA or name C or name O o \ r name CB )) or resid 431 through 433 or (resid 434 and (name N or name CA or na \ me C or name O or name CB or name CG )) or (resid 435 and (name N or name CA or \ name C or name O or name CB )) or resid 436 through 438 or (resid 439 and (name \ N or name CA or name C or name O or name CB or name CG )) or resid 440 through 4 \ 41 or (resid 442 and (name N or name CA or name C or name O or name CB )) or res \ id 443 through 448 or (resid 449 through 452 and (name N or name CA or name C or \ name O or name CB )) or resid 453 through 466 or (resid 467 through 468 and (na \ me N or name CA or name C or name O or name CB )) or resid 469 through 546 or re \ sid 567 through 581 or resid 583 or resid 587 through 618 or resid 620 through 6 \ 37 or (resid 638 through 640 and (name N or name CA or name C or name O or name \ CB )) or resid 641 through 646 or (resid 647 and (name N or name CA or name C or \ name O or name CB or name CG )) or resid 648 through 673 or (resid 674 and (nam \ e N or name CA or name C or name O or name CB )) or resid 675 through 679 or (re \ sid 680 and (name N or name CA or name C or name O or name CB )) or resid 681 th \ rough 700 or (resid 701 and (name N or name CA or name C or name O or name CB )) \ or resid 702 through 747 or (resid 748 and (name N or name CA or name C or name \ O or name CB )) or resid 749 through 750 or (resid 751 through 752 and (name N \ or name CA or name C or name O or name CB )) or resid 753 or (resid 754 and (nam \ e N or name CA or name C or name O or name CB or name CG1)) or resid 755 through \ 756 or (resid 757 and (name N or name CA or name C or name O or name CB )) or r \ esid 758 through 770 or (resid 772 through 773 and (name N or name CA or name C \ or name O or name CB )) or resid 779 through 815 or resid 901 through 903)) selection = (chain 'D' and (resid 390 through 391 or (resid 392 and (name N or name CA or na \ me C or name O or name CB or name CG1)) or resid 393 through 403 or (resid 404 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 405 \ or (resid 406 and (name N or name CA or name C or name O or name CB )) or resid \ 407 through 408 or (resid 409 through 410 and (name N or name CA or name C or na \ me O or name CB )) or resid 411 or (resid 412 and (name N or name CA or name C o \ r name O or name CB )) or resid 413 through 414 or (resid 415 and (name N or nam \ e CA or name C or name O or name CB )) or resid 416 through 422 or (resid 423 an \ d (name N or name CA or name C or name O or name CB or name CG )) or resid 424 t \ hrough 429 or (resid 430 and (name N or name CA or name C or name O or name CB ) \ ) or resid 431 through 433 or (resid 434 and (name N or name CA or name C or nam \ e O or name CB or name CG )) or (resid 435 and (name N or name CA or name C or n \ ame O or name CB )) or resid 436 or (resid 437 and (name N or name CA or name C \ or name O or name CB )) or resid 438 or (resid 439 and (name N or name CA or nam \ e C or name O or name CB or name CG )) or resid 440 through 441 or (resid 442 an \ d (name N or name CA or name C or name O or name CB )) or resid 443 through 448 \ or (resid 449 through 452 and (name N or name CA or name C or name O or name CB \ )) or resid 453 or (resid 454 through 455 and (name N or name CA or name C or na \ me O or name CB )) or resid 456 or (resid 457 and (name N or name CA or name C o \ r name O or name CB )) or resid 458 through 466 or (resid 467 through 468 and (n \ ame N or name CA or name C or name O or name CB )) or resid 469 through 504 or ( \ resid 505 and (name N or name CA or name C or name O or name CB )) or resid 506 \ or (resid 507 and (name N or name CA or name C or name O or name CB )) or resid \ 508 through 545 or (resid 566 and (name N or name CA or name C or name O or name \ CB )) or resid 567 through 581 or resid 583 or resid 587 through 618 or resid 6 \ 20 through 637 or (resid 638 through 640 and (name N or name CA or name C or nam \ e O or name CB )) or resid 641 through 646 or (resid 647 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 648 through 656 or (resid \ 657 and (name N or name CA or name C or name O or name CB )) or resid 658 or (re \ sid 659 and (name N or name CA or name C or name O or name CB )) or resid 660 th \ rough 663 or (resid 664 and (name N or name CA or name C or name O or name CB )) \ or resid 665 or (resid 666 and (name N or name CA or name C or name O or name C \ B )) or resid 667 through 670 or (resid 671 and (name N or name CA or name C or \ name O or name CB )) or resid 672 through 673 or (resid 674 and (name N or name \ CA or name C or name O or name CB )) or resid 675 through 679 or (resid 680 and \ (name N or name CA or name C or name O or name CB )) or resid 681 through 682 or \ (resid 683 and (name N or name CA or name C or name O or name CB )) or resid 68 \ 4 through 685 or (resid 686 and (name N or name CA or name C or name O or name C \ B )) or resid 687 through 694 or (resid 695 and (name N or name CA or name C or \ name O or name CB )) or resid 696 through 700 or (resid 701 and (name N or name \ CA or name C or name O or name CB )) or resid 702 through 711 or (resid 712 and \ (name N or name CA or name C or name O or name CB )) or resid 713 through 733 or \ (resid 734 and (name N or name CA or name C or name O or name CB )) or resid 73 \ 5 through 747 or (resid 748 and (name N or name CA or name C or name O or name C \ B )) or resid 749 through 750 or (resid 751 through 752 and (name N or name CA o \ r name C or name O or name CB )) or resid 753 through 756 or (resid 757 and (nam \ e N or name CA or name C or name O or name CB )) or resid 758 through 777 or (re \ sid 778 and (name N or name CA or name C or name O or name CB )) or resid 779 th \ rough 813 or (resid 814 through 815 and (name N or name CA or name C or name O o \ r name CB )) or resid 901 through 903)) } ncs_group { reference = (chain 'E' and (resid 5 through 209 or (resid 1201 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P or name C210 or name C211)))) selection = (chain 'F' and (resid 5 through 209 or (resid 1301 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P or name C210 or name C211)))) selection = (chain 'G' and (resid 5 through 209 or (resid 1201 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P or name C210 or name C211)))) selection = (chain 'H' and (resid 5 through 209 or (resid 1301 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P or name C210 or name C211)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 48.190 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:13.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 0.010 0.117 18847 Z= 0.670 Angle : 1.401 11.389 25456 Z= 0.911 Chirality : 0.084 0.462 2811 Planarity : 0.014 0.189 3111 Dihedral : 16.038 105.783 6800 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.66 % Favored : 97.30 % Rotamer: Outliers : 2.54 % Allowed : 4.11 % Favored : 93.35 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.16), residues: 2293 helix: 0.48 (0.13), residues: 1359 sheet: -1.04 (0.38), residues: 170 loop : -2.03 (0.18), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.012 TRP C 602 HIS 0.022 0.007 HIS G 60 PHE 0.050 0.010 PHE D 810 TYR 0.062 0.010 TYR A 612 ARG 0.073 0.005 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 338 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8129 (mm-30) REVERT: A 431 HIS cc_start: 0.8029 (m90) cc_final: 0.7200 (m90) REVERT: A 438 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 588 SER cc_start: 0.9261 (OUTLIER) cc_final: 0.8931 (p) REVERT: A 657 ARG cc_start: 0.8233 (mtm110) cc_final: 0.7861 (ptt-90) REVERT: A 664 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8051 (mt-10) REVERT: A 752 GLN cc_start: 0.8393 (mt0) cc_final: 0.8155 (mt0) REVERT: B 475 LEU cc_start: 0.8084 (tp) cc_final: 0.7785 (tp) REVERT: B 623 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8486 (mp0) REVERT: B 809 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6724 (tt0) REVERT: C 423 GLU cc_start: 0.8572 (mp0) cc_final: 0.8361 (mp0) REVERT: C 445 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6761 (pttm) REVERT: C 504 GLN cc_start: 0.7410 (pt0) cc_final: 0.7204 (pt0) REVERT: C 630 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7839 (pp20) REVERT: C 724 ASP cc_start: 0.7131 (t70) cc_final: 0.6798 (p0) REVERT: C 803 MET cc_start: 0.8911 (mtm) cc_final: 0.8635 (mtp) REVERT: D 397 LEU cc_start: 0.7723 (mm) cc_final: 0.7430 (mm) REVERT: D 657 ARG cc_start: 0.8377 (ptm-80) cc_final: 0.7922 (ppt170) REVERT: D 678 PHE cc_start: 0.7788 (m-10) cc_final: 0.7549 (m-10) REVERT: E 126 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6983 (tt0) REVERT: E 127 PHE cc_start: 0.6478 (m-10) cc_final: 0.6270 (m-10) REVERT: E 129 ARG cc_start: 0.6285 (mtt-85) cc_final: 0.6080 (mmm160) REVERT: F 24 MET cc_start: 0.8390 (tpt) cc_final: 0.8092 (tpt) REVERT: F 59 THR cc_start: 0.7945 (p) cc_final: 0.7594 (t) REVERT: F 202 GLU cc_start: 0.8224 (tt0) cc_final: 0.7940 (pt0) REVERT: G 10 MET cc_start: 0.7000 (tpp) cc_final: 0.6737 (tpt) REVERT: G 41 ARG cc_start: 0.6390 (ttp80) cc_final: 0.5797 (ppp80) REVERT: G 127 PHE cc_start: 0.5442 (m-10) cc_final: 0.5001 (t80) REVERT: G 190 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8282 (tp30) REVERT: H 24 MET cc_start: 0.8657 (tpt) cc_final: 0.8449 (tpt) REVERT: H 81 ASP cc_start: 0.8182 (p0) cc_final: 0.7736 (t70) outliers start: 38 outliers final: 10 residues processed: 369 average time/residue: 1.4586 time to fit residues: 597.2864 Evaluate side-chains 258 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 244 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 630 GLU Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain E residue 174 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 ASN B 710 GLN C 504 GLN E 204 HIS F 204 HIS G 204 HIS H 160 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.159951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115650 restraints weight = 69149.378| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 4.17 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18847 Z= 0.186 Angle : 0.562 10.706 25456 Z= 0.297 Chirality : 0.040 0.238 2811 Planarity : 0.004 0.090 3111 Dihedral : 12.084 84.980 2959 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.97 % Allowed : 11.35 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 2293 helix: 2.33 (0.14), residues: 1350 sheet: -1.09 (0.41), residues: 154 loop : -1.20 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 762 HIS 0.003 0.001 HIS C 431 PHE 0.016 0.001 PHE A 542 TYR 0.016 0.001 TYR A 669 ARG 0.011 0.001 ARG C 688 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 294 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8023 (mm-30) REVERT: A 431 HIS cc_start: 0.7994 (m90) cc_final: 0.7294 (m90) REVERT: A 438 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8127 (mp) REVERT: B 431 HIS cc_start: 0.6364 (t-90) cc_final: 0.6011 (t-90) REVERT: C 389 ARG cc_start: 0.7528 (ptm160) cc_final: 0.7150 (ptm160) REVERT: C 667 TRP cc_start: 0.7283 (t-100) cc_final: 0.7019 (t-100) REVERT: C 693 LYS cc_start: 0.5918 (tppt) cc_final: 0.5556 (mmmm) REVERT: C 710 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7521 (mt0) REVERT: C 743 ASN cc_start: 0.7650 (t0) cc_final: 0.7377 (t0) REVERT: C 803 MET cc_start: 0.8915 (mtm) cc_final: 0.8644 (mtp) REVERT: D 397 LEU cc_start: 0.7944 (mm) cc_final: 0.7676 (mm) REVERT: D 482 GLU cc_start: 0.8202 (tp30) cc_final: 0.7875 (tp30) REVERT: E 31 ASP cc_start: 0.7672 (m-30) cc_final: 0.7469 (m-30) REVERT: E 99 ARG cc_start: 0.7142 (mtm-85) cc_final: 0.6717 (tpp80) REVERT: E 127 PHE cc_start: 0.6879 (m-10) cc_final: 0.6649 (m-10) REVERT: F 79 LYS cc_start: 0.8119 (mptt) cc_final: 0.7444 (mppt) REVERT: G 73 PHE cc_start: 0.6201 (OUTLIER) cc_final: 0.5992 (m-80) REVERT: H 58 MET cc_start: 0.6538 (OUTLIER) cc_final: 0.6296 (tpt) outliers start: 47 outliers final: 19 residues processed: 321 average time/residue: 1.3854 time to fit residues: 495.7534 Evaluate side-chains 263 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 241 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 207 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 125 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN H 132 HIS H 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.155494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111135 restraints weight = 78150.985| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 4.31 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 18847 Z= 0.441 Angle : 0.660 12.296 25456 Z= 0.350 Chirality : 0.046 0.354 2811 Planarity : 0.005 0.085 3111 Dihedral : 12.300 89.488 2939 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.32 % Allowed : 13.40 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2293 helix: 1.90 (0.14), residues: 1341 sheet: -1.02 (0.36), residues: 200 loop : -1.11 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 762 HIS 0.007 0.002 HIS E 60 PHE 0.021 0.003 PHE C 604 TYR 0.017 0.002 TYR F 180 ARG 0.007 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 254 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 HIS cc_start: 0.8023 (m90) cc_final: 0.7244 (m90) REVERT: A 438 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8169 (mp) REVERT: C 667 TRP cc_start: 0.7307 (t-100) cc_final: 0.7034 (t-100) REVERT: C 743 ASN cc_start: 0.7853 (t0) cc_final: 0.7540 (t0) REVERT: C 803 MET cc_start: 0.8899 (mtm) cc_final: 0.8580 (mtp) REVERT: F 10 MET cc_start: 0.8548 (mmm) cc_final: 0.8019 (tpt) REVERT: G 73 PHE cc_start: 0.6316 (OUTLIER) cc_final: 0.6072 (m-80) REVERT: H 65 ARG cc_start: 0.7050 (mtm-85) cc_final: 0.6823 (mtt180) REVERT: H 95 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: H 202 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7126 (tp30) outliers start: 73 outliers final: 37 residues processed: 294 average time/residue: 1.4006 time to fit residues: 460.9109 Evaluate side-chains 273 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 809 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 207 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 45 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN A 431 HIS B 407 ASN B 504 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.155951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106271 restraints weight = 59837.982| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.95 r_work: 0.2844 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 18847 Z= 0.400 Angle : 0.614 12.653 25456 Z= 0.326 Chirality : 0.045 0.377 2811 Planarity : 0.005 0.088 3111 Dihedral : 11.864 88.670 2939 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.32 % Allowed : 14.59 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.18), residues: 2293 helix: 1.86 (0.14), residues: 1341 sheet: -0.88 (0.36), residues: 202 loop : -1.08 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 762 HIS 0.005 0.001 HIS H 60 PHE 0.021 0.002 PHE C 810 TYR 0.020 0.002 TYR A 812 ARG 0.006 0.001 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 244 time to evaluate : 2.370 Fit side-chains revert: symmetry clash REVERT: A 431 HIS cc_start: 0.8120 (m-70) cc_final: 0.7407 (m90) REVERT: A 438 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8212 (mp) REVERT: B 656 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7196 (ptm160) REVERT: B 688 ARG cc_start: 0.8050 (ttt180) cc_final: 0.7754 (ttt180) REVERT: B 711 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6609 (mmm160) REVERT: B 724 ASP cc_start: 0.7434 (t70) cc_final: 0.7230 (t0) REVERT: C 423 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: C 504 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6784 (pm20) REVERT: C 630 GLU cc_start: 0.7794 (pp20) cc_final: 0.7013 (tm-30) REVERT: C 667 TRP cc_start: 0.7767 (t-100) cc_final: 0.7241 (t-100) REVERT: C 743 ASN cc_start: 0.7657 (t0) cc_final: 0.7228 (t0) REVERT: C 803 MET cc_start: 0.9252 (mtm) cc_final: 0.8913 (mtp) REVERT: E 8 ILE cc_start: 0.8412 (mm) cc_final: 0.8092 (pt) REVERT: E 95 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7778 (tp30) REVERT: F 10 MET cc_start: 0.8765 (mmm) cc_final: 0.8285 (tpt) REVERT: F 79 LYS cc_start: 0.8125 (mptt) cc_final: 0.7389 (mppt) REVERT: H 95 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: H 202 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7760 (tp30) outliers start: 73 outliers final: 35 residues processed: 286 average time/residue: 1.4925 time to fit residues: 474.0627 Evaluate side-chains 271 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 ARG Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 711 ARG Chi-restraints excluded: chain B residue 722 ASN Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 809 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 70 optimal weight: 0.7980 chunk 220 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 71 optimal weight: 9.9990 chunk 136 optimal weight: 0.6980 chunk 199 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN B 705 ASN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN G 204 HIS H 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.158558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.112431 restraints weight = 66129.353| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 4.03 r_work: 0.2863 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18847 Z= 0.210 Angle : 0.524 13.483 25456 Z= 0.278 Chirality : 0.040 0.389 2811 Planarity : 0.005 0.087 3111 Dihedral : 11.022 87.905 2939 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.24 % Allowed : 16.69 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 2293 helix: 2.30 (0.14), residues: 1340 sheet: -0.88 (0.37), residues: 194 loop : -0.96 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 456 HIS 0.003 0.001 HIS E 60 PHE 0.017 0.001 PHE D 542 TYR 0.018 0.001 TYR A 812 ARG 0.006 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 2.278 Fit side-chains revert: symmetry clash REVERT: A 431 HIS cc_start: 0.8074 (m-70) cc_final: 0.7357 (m90) REVERT: A 438 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8385 (mm) REVERT: B 459 MET cc_start: 0.6441 (tpp) cc_final: 0.6147 (tpt) REVERT: C 423 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: C 504 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6717 (pm20) REVERT: C 630 GLU cc_start: 0.7609 (pp20) cc_final: 0.6885 (tm-30) REVERT: C 667 TRP cc_start: 0.7881 (t-100) cc_final: 0.7429 (t-100) REVERT: C 710 GLN cc_start: 0.7575 (mt0) cc_final: 0.7118 (mt0) REVERT: C 743 ASN cc_start: 0.7677 (t0) cc_final: 0.7229 (t0) REVERT: C 803 MET cc_start: 0.9243 (mtm) cc_final: 0.8993 (mtp) REVERT: D 397 LEU cc_start: 0.7766 (mm) cc_final: 0.7458 (mm) REVERT: E 8 ILE cc_start: 0.8365 (mm) cc_final: 0.8089 (pt) REVERT: E 95 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7777 (tp30) REVERT: F 10 MET cc_start: 0.8835 (mmm) cc_final: 0.8447 (tpt) REVERT: F 79 LYS cc_start: 0.8044 (mptt) cc_final: 0.7340 (mppt) REVERT: H 41 ARG cc_start: 0.6046 (ppp80) cc_final: 0.5291 (ttp-170) REVERT: H 95 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: H 202 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7830 (tp30) outliers start: 53 outliers final: 28 residues processed: 274 average time/residue: 1.4739 time to fit residues: 450.8243 Evaluate side-chains 256 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 809 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 167 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 196 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 12 optimal weight: 0.0770 chunk 62 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN G 204 HIS H 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.159232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.114450 restraints weight = 69428.524| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 4.21 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 18847 Z= 0.197 Angle : 0.512 13.217 25456 Z= 0.271 Chirality : 0.040 0.388 2811 Planarity : 0.005 0.087 3111 Dihedral : 10.569 89.380 2938 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.24 % Allowed : 17.34 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.18), residues: 2293 helix: 2.42 (0.14), residues: 1346 sheet: -0.95 (0.39), residues: 174 loop : -0.90 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 456 HIS 0.003 0.001 HIS G 204 PHE 0.013 0.001 PHE E 107 TYR 0.017 0.001 TYR A 669 ARG 0.006 0.001 ARG H 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 242 time to evaluate : 1.968 Fit side-chains revert: symmetry clash REVERT: A 431 HIS cc_start: 0.7927 (m-70) cc_final: 0.7330 (m90) REVERT: B 459 MET cc_start: 0.6895 (tpp) cc_final: 0.6658 (tpt) REVERT: C 423 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: C 504 GLN cc_start: 0.6181 (OUTLIER) cc_final: 0.5981 (pm20) REVERT: C 630 GLU cc_start: 0.6988 (pp20) cc_final: 0.6670 (tm-30) REVERT: C 743 ASN cc_start: 0.7789 (t0) cc_final: 0.7451 (t0) REVERT: C 803 MET cc_start: 0.8893 (mtm) cc_final: 0.8537 (mtp) REVERT: D 397 LEU cc_start: 0.7702 (mm) cc_final: 0.7362 (mm) REVERT: E 99 ARG cc_start: 0.7338 (mtm-85) cc_final: 0.7017 (tpp80) REVERT: E 128 HIS cc_start: 0.6817 (OUTLIER) cc_final: 0.6443 (m-70) REVERT: F 10 MET cc_start: 0.8594 (mmm) cc_final: 0.8261 (tpt) REVERT: F 79 LYS cc_start: 0.7970 (mptt) cc_final: 0.7358 (mppt) REVERT: H 41 ARG cc_start: 0.5760 (ppp80) cc_final: 0.5158 (ttp-110) REVERT: H 95 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: H 202 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7165 (tp30) outliers start: 54 outliers final: 30 residues processed: 275 average time/residue: 1.4581 time to fit residues: 446.1441 Evaluate side-chains 263 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 128 HIS Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 137 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN G 204 HIS H 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.158153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.111475 restraints weight = 72016.297| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 4.43 r_work: 0.2855 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18847 Z= 0.238 Angle : 0.533 13.789 25456 Z= 0.281 Chirality : 0.040 0.403 2811 Planarity : 0.005 0.086 3111 Dihedral : 10.483 88.645 2936 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.03 % Allowed : 18.10 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.18), residues: 2293 helix: 2.36 (0.14), residues: 1341 sheet: -1.02 (0.39), residues: 174 loop : -0.89 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 456 HIS 0.003 0.001 HIS E 204 PHE 0.019 0.001 PHE D 542 TYR 0.018 0.001 TYR D 812 ARG 0.007 0.001 ARG E 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 HIS cc_start: 0.8107 (m-70) cc_final: 0.7384 (m90) REVERT: B 704 MET cc_start: 0.7470 (tpp) cc_final: 0.7194 (tpp) REVERT: C 504 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6796 (pm20) REVERT: C 630 GLU cc_start: 0.7513 (pp20) cc_final: 0.6829 (tm-30) REVERT: C 667 TRP cc_start: 0.7680 (t-100) cc_final: 0.7293 (t-100) REVERT: C 743 ASN cc_start: 0.7699 (t0) cc_final: 0.7243 (t0) REVERT: C 803 MET cc_start: 0.9247 (mtm) cc_final: 0.8888 (mtp) REVERT: E 65 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7373 (mtm110) REVERT: E 99 ARG cc_start: 0.7518 (mtm-85) cc_final: 0.7097 (tpp80) REVERT: F 10 MET cc_start: 0.8876 (mmm) cc_final: 0.8481 (tpt) REVERT: F 79 LYS cc_start: 0.8000 (mptt) cc_final: 0.7326 (mppt) REVERT: H 41 ARG cc_start: 0.5981 (ppp80) cc_final: 0.5372 (ttp-110) REVERT: H 95 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: H 202 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7758 (tp30) outliers start: 50 outliers final: 32 residues processed: 267 average time/residue: 1.5006 time to fit residues: 447.5091 Evaluate side-chains 261 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 504 GLN Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 50 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN F 160 ASN G 204 HIS H 206 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.157119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.111373 restraints weight = 72384.795| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 4.35 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18847 Z= 0.299 Angle : 0.567 14.437 25456 Z= 0.297 Chirality : 0.042 0.417 2811 Planarity : 0.005 0.086 3111 Dihedral : 10.702 87.536 2936 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.35 % Allowed : 17.88 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.18), residues: 2293 helix: 2.23 (0.14), residues: 1341 sheet: -0.99 (0.38), residues: 178 loop : -0.95 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 762 HIS 0.004 0.001 HIS H 132 PHE 0.021 0.002 PHE C 810 TYR 0.017 0.002 TYR A 812 ARG 0.007 0.001 ARG F 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 240 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 630 GLU cc_start: 0.7072 (pp20) cc_final: 0.6691 (tm-30) REVERT: C 667 TRP cc_start: 0.7204 (t-100) cc_final: 0.6871 (t-100) REVERT: C 743 ASN cc_start: 0.7862 (t0) cc_final: 0.7489 (t0) REVERT: C 803 MET cc_start: 0.8887 (mtm) cc_final: 0.8546 (mtp) REVERT: D 397 LEU cc_start: 0.7692 (mm) cc_final: 0.7352 (mm) REVERT: E 65 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.7283 (mtm110) REVERT: E 99 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.7007 (tpp80) REVERT: F 10 MET cc_start: 0.8627 (mmm) cc_final: 0.8077 (tpt) REVERT: F 37 ARG cc_start: 0.7354 (mmm-85) cc_final: 0.6928 (mmm-85) REVERT: F 79 LYS cc_start: 0.7958 (mptt) cc_final: 0.7320 (mppt) REVERT: H 41 ARG cc_start: 0.5785 (ppp80) cc_final: 0.5102 (ttp-170) REVERT: H 95 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7266 (tt0) REVERT: H 202 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7178 (tp30) outliers start: 56 outliers final: 38 residues processed: 277 average time/residue: 1.4419 time to fit residues: 444.6101 Evaluate side-chains 266 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 809 GLU Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 99 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 131 optimal weight: 0.0270 chunk 41 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 138 optimal weight: 0.2980 chunk 206 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS B 504 GLN E 132 HIS E 204 HIS F 160 ASN G 204 HIS H 160 ASN H 206 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.160378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.116619 restraints weight = 76795.947| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 4.31 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18847 Z= 0.170 Angle : 0.508 13.142 25456 Z= 0.266 Chirality : 0.039 0.376 2811 Planarity : 0.004 0.086 3111 Dihedral : 10.021 88.795 2936 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.65 % Allowed : 18.69 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.18), residues: 2293 helix: 2.54 (0.14), residues: 1346 sheet: -0.93 (0.41), residues: 164 loop : -0.90 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 762 HIS 0.003 0.001 HIS F 82 PHE 0.017 0.001 PHE D 542 TYR 0.014 0.001 TYR A 812 ARG 0.007 0.001 ARG F 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8024 (mm-30) REVERT: A 431 HIS cc_start: 0.7983 (m-70) cc_final: 0.7422 (m90) REVERT: A 659 LYS cc_start: 0.8453 (mmpt) cc_final: 0.8212 (mmmt) REVERT: C 630 GLU cc_start: 0.7033 (pp20) cc_final: 0.6714 (tm-30) REVERT: C 667 TRP cc_start: 0.7123 (t-100) cc_final: 0.6840 (t-100) REVERT: C 743 ASN cc_start: 0.7795 (t0) cc_final: 0.7438 (t0) REVERT: C 803 MET cc_start: 0.8880 (mtm) cc_final: 0.8580 (mtp) REVERT: E 14 THR cc_start: 0.8188 (m) cc_final: 0.7969 (p) REVERT: E 31 ASP cc_start: 0.6977 (m-30) cc_final: 0.6694 (m-30) REVERT: E 65 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.7112 (mtm110) REVERT: E 99 ARG cc_start: 0.7287 (mtm-85) cc_final: 0.7006 (tpp80) REVERT: F 10 MET cc_start: 0.8554 (mmm) cc_final: 0.8208 (tpt) REVERT: F 37 ARG cc_start: 0.7285 (mmm-85) cc_final: 0.6885 (mmm-85) REVERT: F 79 LYS cc_start: 0.7966 (mptt) cc_final: 0.7326 (mppt) REVERT: H 41 ARG cc_start: 0.5845 (ppp80) cc_final: 0.5178 (ttp-170) REVERT: H 56 GLU cc_start: 0.6648 (pp20) cc_final: 0.6380 (pp20) REVERT: H 95 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: H 202 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7164 (tp30) outliers start: 43 outliers final: 29 residues processed: 262 average time/residue: 1.4598 time to fit residues: 426.6170 Evaluate side-chains 256 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 202 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 0.4980 chunk 163 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN F 160 ASN G 204 HIS H 160 ASN H 206 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.155979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111223 restraints weight = 74958.849| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 4.28 r_work: 0.2812 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 18847 Z= 0.408 Angle : 0.632 15.246 25456 Z= 0.329 Chirality : 0.045 0.447 2811 Planarity : 0.005 0.086 3111 Dihedral : 10.736 85.786 2935 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.76 % Allowed : 18.64 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.18), residues: 2293 helix: 2.07 (0.14), residues: 1339 sheet: -1.10 (0.39), residues: 174 loop : -0.99 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 574 HIS 0.015 0.002 HIS E 204 PHE 0.024 0.002 PHE C 810 TYR 0.018 0.002 TYR D 812 ARG 0.012 0.001 ARG D 449 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 HIS cc_start: 0.8145 (m-70) cc_final: 0.7448 (m90) REVERT: A 659 LYS cc_start: 0.8619 (mmpt) cc_final: 0.8350 (mmmt) REVERT: C 459 MET cc_start: 0.6100 (mmm) cc_final: 0.5639 (tpt) REVERT: C 630 GLU cc_start: 0.7603 (pp20) cc_final: 0.6902 (tm-30) REVERT: C 667 TRP cc_start: 0.7629 (t-100) cc_final: 0.7166 (t-100) REVERT: C 743 ASN cc_start: 0.7774 (t0) cc_final: 0.7324 (t0) REVERT: C 803 MET cc_start: 0.9262 (mtm) cc_final: 0.8978 (mtp) REVERT: D 640 GLU cc_start: 0.7303 (pm20) cc_final: 0.7034 (pm20) REVERT: E 31 ASP cc_start: 0.7588 (m-30) cc_final: 0.7272 (m-30) REVERT: E 65 ARG cc_start: 0.7671 (mtm-85) cc_final: 0.7277 (mtm110) REVERT: E 99 ARG cc_start: 0.7522 (mtm-85) cc_final: 0.7111 (tpp80) REVERT: F 10 MET cc_start: 0.8855 (mmm) cc_final: 0.8567 (tpp) REVERT: F 79 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7360 (mppt) REVERT: H 41 ARG cc_start: 0.5908 (ppp80) cc_final: 0.5140 (ttp-170) REVERT: H 95 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: H 202 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7803 (tp30) outliers start: 45 outliers final: 33 residues processed: 261 average time/residue: 1.4931 time to fit residues: 434.8972 Evaluate side-chains 261 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 202 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.7457 > 50: distance: 21 - 25: 9.749 distance: 25 - 26: 13.135 distance: 26 - 27: 36.743 distance: 26 - 29: 35.269 distance: 27 - 28: 24.847 distance: 27 - 33: 49.159 distance: 29 - 30: 31.763 distance: 30 - 31: 25.425 distance: 31 - 32: 27.674 distance: 33 - 34: 39.527 distance: 34 - 35: 21.221 distance: 34 - 37: 37.715 distance: 35 - 36: 17.051 distance: 35 - 40: 23.150 distance: 37 - 38: 44.014 distance: 37 - 39: 48.352 distance: 40 - 41: 19.042 distance: 41 - 42: 23.473 distance: 41 - 44: 47.949 distance: 42 - 43: 36.862 distance: 42 - 46: 20.390 distance: 44 - 45: 25.499 distance: 46 - 47: 10.953 distance: 46 - 52: 44.599 distance: 47 - 48: 22.940 distance: 47 - 50: 16.919 distance: 48 - 49: 24.769 distance: 48 - 53: 18.133 distance: 50 - 51: 34.582 distance: 51 - 52: 6.239 distance: 53 - 54: 12.811 distance: 54 - 55: 8.948 distance: 54 - 57: 10.938 distance: 55 - 56: 39.830 distance: 55 - 61: 38.113 distance: 57 - 58: 25.769 distance: 57 - 59: 39.531 distance: 58 - 60: 15.205 distance: 61 - 62: 12.334 distance: 62 - 63: 43.323 distance: 62 - 65: 43.980 distance: 63 - 70: 27.019 distance: 65 - 66: 13.312 distance: 66 - 67: 30.267 distance: 67 - 68: 31.863 distance: 67 - 69: 31.132 distance: 70 - 71: 34.087 distance: 71 - 72: 18.536 distance: 71 - 74: 26.512 distance: 72 - 73: 11.983 distance: 72 - 76: 44.210 distance: 74 - 75: 40.775 distance: 76 - 77: 23.917 distance: 77 - 78: 19.734 distance: 77 - 80: 18.818 distance: 78 - 79: 7.704 distance: 78 - 81: 25.891 distance: 79 - 106: 31.605 distance: 81 - 82: 19.180 distance: 82 - 83: 14.469 distance: 82 - 85: 28.795 distance: 83 - 84: 33.957 distance: 83 - 90: 27.324 distance: 84 - 111: 35.577 distance: 85 - 86: 12.498 distance: 86 - 87: 37.715 distance: 87 - 88: 21.955 distance: 87 - 89: 18.006 distance: 90 - 91: 24.862 distance: 91 - 92: 36.582 distance: 91 - 94: 14.560 distance: 92 - 93: 34.045 distance: 92 - 98: 25.464 distance: 94 - 95: 21.096 distance: 95 - 96: 26.568 distance: 95 - 97: 11.789