Starting phenix.real_space_refine on Thu Mar 5 02:16:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xnv_33327/03_2026/7xnv_33327.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnv_33327/03_2026/7xnv_33327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xnv_33327/03_2026/7xnv_33327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnv_33327/03_2026/7xnv_33327.map" model { file = "/net/cci-nas-00/data/ceres_data/7xnv_33327/03_2026/7xnv_33327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnv_33327/03_2026/7xnv_33327.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 12618 2.51 5 N 2712 2.21 5 O 2892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18378 Number of models: 1 Model: "" Number of chains: 24 Chain: "G" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "H" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "I" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "J" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "K" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "L" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "A" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "B" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "C" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "D" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "E" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "F" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "G" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-1': 11, 'MC3:plan-2': 11} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-1': 11, 'MC3:plan-2': 11} Unresolved non-hydrogen planarities: 68 Chain: "I" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-1': 11, 'MC3:plan-2': 11} Unresolved non-hydrogen planarities: 68 Chain: "J" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-1': 11, 'MC3:plan-2': 11} Unresolved non-hydrogen planarities: 68 Chain: "K" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-1': 11, 'MC3:plan-2': 11} Unresolved non-hydrogen planarities: 68 Chain: "L" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-1': 11, 'MC3:plan-2': 11} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-1': 8, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-1': 8, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-1': 8, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-1': 8, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 48 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-1': 8, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-1': 8, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 48 Time building chain proxies: 4.49, per 1000 atoms: 0.24 Number of scatterers: 18378 At special positions: 0 Unit cell: (104.622, 115.15, 144.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 2892 8.00 N 2712 7.00 C 12618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.03 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.03 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.03 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.03 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 757.6 milliseconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 12 sheets defined 74.7% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'G' and resid 3 through 15 removed outlier: 4.227A pdb=" N LEU G 7 " --> pdb=" O GLU G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 34 Processing helix chain 'G' and resid 34 through 39 Processing helix chain 'G' and resid 41 through 46 removed outlier: 4.011A pdb=" N VAL G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 41 through 46' Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 74 through 87 Processing helix chain 'G' and resid 87 through 100 removed outlier: 4.211A pdb=" N PHE G 93 " --> pdb=" O PRO G 89 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ILE G 94 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL G 98 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN G 100 " --> pdb=" O TYR G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 221 Processing helix chain 'G' and resid 246 through 276 removed outlier: 3.596A pdb=" N LYS G 250 " --> pdb=" O ARG G 246 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE G 253 " --> pdb=" O GLU G 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 15 removed outlier: 4.256A pdb=" N LEU H 7 " --> pdb=" O GLU H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 34 Processing helix chain 'H' and resid 34 through 39 Processing helix chain 'H' and resid 41 through 46 removed outlier: 4.019A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 41 through 46' Processing helix chain 'H' and resid 61 through 71 Processing helix chain 'H' and resid 74 through 87 Processing helix chain 'H' and resid 87 through 100 removed outlier: 4.242A pdb=" N PHE H 93 " --> pdb=" O PRO H 89 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ILE H 94 " --> pdb=" O SER H 90 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL H 98 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 221 Processing helix chain 'H' and resid 246 through 276 removed outlier: 3.599A pdb=" N LYS H 250 " --> pdb=" O ARG H 246 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR H 251 " --> pdb=" O PRO H 247 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 15 removed outlier: 4.218A pdb=" N LEU I 7 " --> pdb=" O GLU I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 34 Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 41 through 46 removed outlier: 4.020A pdb=" N VAL I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 41 through 46' Processing helix chain 'I' and resid 61 through 71 Processing helix chain 'I' and resid 74 through 87 Processing helix chain 'I' and resid 87 through 100 removed outlier: 4.237A pdb=" N PHE I 93 " --> pdb=" O PRO I 89 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE I 94 " --> pdb=" O SER I 90 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL I 98 " --> pdb=" O ILE I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 221 Processing helix chain 'I' and resid 246 through 276 removed outlier: 3.601A pdb=" N LYS I 250 " --> pdb=" O ARG I 246 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR I 251 " --> pdb=" O PRO I 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE I 253 " --> pdb=" O GLU I 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 15 removed outlier: 4.228A pdb=" N LEU J 7 " --> pdb=" O GLU J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 34 Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 41 through 46 removed outlier: 4.014A pdb=" N VAL J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 41 through 46' Processing helix chain 'J' and resid 61 through 71 Processing helix chain 'J' and resid 74 through 87 Processing helix chain 'J' and resid 87 through 100 removed outlier: 4.208A pdb=" N PHE J 93 " --> pdb=" O PRO J 89 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE J 94 " --> pdb=" O SER J 90 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR J 95 " --> pdb=" O LEU J 91 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL J 98 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN J 100 " --> pdb=" O TYR J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 221 Processing helix chain 'J' and resid 246 through 276 removed outlier: 3.605A pdb=" N LYS J 250 " --> pdb=" O ARG J 246 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR J 251 " --> pdb=" O PRO J 247 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE J 253 " --> pdb=" O GLU J 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 15 removed outlier: 4.255A pdb=" N LEU K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 34 Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 41 through 46 removed outlier: 4.020A pdb=" N VAL K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 41 through 46' Processing helix chain 'K' and resid 61 through 71 Processing helix chain 'K' and resid 74 through 87 Processing helix chain 'K' and resid 87 through 100 removed outlier: 4.207A pdb=" N PHE K 93 " --> pdb=" O PRO K 89 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE K 94 " --> pdb=" O SER K 90 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR K 95 " --> pdb=" O LEU K 91 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL K 98 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 221 Processing helix chain 'K' and resid 246 through 276 removed outlier: 3.602A pdb=" N LYS K 250 " --> pdb=" O ARG K 246 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR K 251 " --> pdb=" O PRO K 247 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE K 253 " --> pdb=" O GLU K 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 15 removed outlier: 4.215A pdb=" N LEU L 7 " --> pdb=" O GLU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 34 Processing helix chain 'L' and resid 34 through 39 Processing helix chain 'L' and resid 41 through 46 removed outlier: 4.019A pdb=" N VAL L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR L 46 " --> pdb=" O GLY L 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 41 through 46' Processing helix chain 'L' and resid 61 through 71 Processing helix chain 'L' and resid 74 through 87 Processing helix chain 'L' and resid 87 through 100 removed outlier: 4.192A pdb=" N PHE L 93 " --> pdb=" O PRO L 89 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE L 94 " --> pdb=" O SER L 90 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR L 95 " --> pdb=" O LEU L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 221 Processing helix chain 'L' and resid 246 through 276 removed outlier: 3.603A pdb=" N LYS L 250 " --> pdb=" O ARG L 246 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR L 251 " --> pdb=" O PRO L 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE L 253 " --> pdb=" O GLU L 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 41 removed outlier: 4.105A pdb=" N ARG A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 removed outlier: 3.728A pdb=" N VAL A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 46' Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 87 through 100 removed outlier: 3.635A pdb=" N LEU A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 246 through 276 Processing helix chain 'B' and resid 20 through 41 removed outlier: 4.059A pdb=" N ARG B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.770A pdb=" N VAL B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 46' Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 87 through 100 removed outlier: 3.577A pdb=" N LEU B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 222 Processing helix chain 'B' and resid 246 through 276 Processing helix chain 'C' and resid 20 through 41 removed outlier: 4.214A pdb=" N ARG C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.769A pdb=" N VAL C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 46' Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 74 through 86 Processing helix chain 'C' and resid 87 through 100 removed outlier: 3.616A pdb=" N LEU C 91 " --> pdb=" O CYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 222 Processing helix chain 'C' and resid 246 through 276 Processing helix chain 'D' and resid 20 through 41 removed outlier: 4.114A pdb=" N ARG D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.765A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 46' Processing helix chain 'D' and resid 61 through 71 Processing helix chain 'D' and resid 74 through 86 Processing helix chain 'D' and resid 87 through 100 removed outlier: 3.633A pdb=" N LEU D 91 " --> pdb=" O CYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 222 Processing helix chain 'D' and resid 246 through 276 Processing helix chain 'E' and resid 20 through 41 removed outlier: 4.108A pdb=" N ARG E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.773A pdb=" N VAL E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 41 through 46' Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'E' and resid 87 through 100 removed outlier: 3.574A pdb=" N LEU E 91 " --> pdb=" O CYS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 222 Processing helix chain 'E' and resid 246 through 276 Processing helix chain 'F' and resid 20 through 41 removed outlier: 4.300A pdb=" N ARG F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE F 25 " --> pdb=" O MET F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.740A pdb=" N VAL F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 61 through 71 Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 87 through 100 removed outlier: 3.621A pdb=" N LEU F 91 " --> pdb=" O CYS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 222 Processing helix chain 'F' and resid 246 through 276 Processing sheet with id=AA1, first strand: chain 'G' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'H' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'I' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'J' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'K' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA9, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AB2, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AB3, first strand: chain 'F' and resid 54 through 55 1153 hydrogen bonds defined for protein. 3387 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5181 1.34 - 1.46: 4404 1.46 - 1.58: 8889 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 18678 Sorted by residual: bond pdb=" CB LEU F 26 " pdb=" CG LEU F 26 " ideal model delta sigma weight residual 1.530 1.560 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C11 MC3 D 407 " pdb=" C12 MC3 D 407 " ideal model delta sigma weight residual 1.502 1.529 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" C11 MC3 E 407 " pdb=" C12 MC3 E 407 " ideal model delta sigma weight residual 1.502 1.529 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C11 MC3 F 407 " pdb=" C12 MC3 F 407 " ideal model delta sigma weight residual 1.502 1.528 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C11 MC3 B 404 " pdb=" C12 MC3 B 404 " ideal model delta sigma weight residual 1.502 1.528 -0.026 2.00e-02 2.50e+03 1.74e+00 ... (remaining 18673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 22837 1.57 - 3.14: 841 3.14 - 4.71: 900 4.71 - 6.28: 187 6.28 - 7.84: 15 Bond angle restraints: 24780 Sorted by residual: angle pdb=" C CYS C 236 " pdb=" N ILE C 237 " pdb=" CA ILE C 237 " ideal model delta sigma weight residual 121.80 125.72 -3.92 1.40e+00 5.10e-01 7.86e+00 angle pdb=" C CYS A 236 " pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta sigma weight residual 121.80 125.59 -3.79 1.40e+00 5.10e-01 7.33e+00 angle pdb=" N ILE L 237 " pdb=" CA ILE L 237 " pdb=" C ILE L 237 " ideal model delta sigma weight residual 109.80 106.31 3.49 1.33e+00 5.65e-01 6.87e+00 angle pdb=" C LEU F 58 " pdb=" N GLN F 59 " pdb=" CA GLN F 59 " ideal model delta sigma weight residual 121.61 125.14 -3.53 1.39e+00 5.18e-01 6.43e+00 angle pdb=" C LEU E 58 " pdb=" N GLN E 59 " pdb=" CA GLN E 59 " ideal model delta sigma weight residual 121.61 125.13 -3.52 1.39e+00 5.18e-01 6.40e+00 ... (remaining 24775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 9657 16.81 - 33.63: 1147 33.63 - 50.44: 363 50.44 - 67.25: 119 67.25 - 84.07: 24 Dihedral angle restraints: 11310 sinusoidal: 5190 harmonic: 6120 Sorted by residual: dihedral pdb=" CB GLU B 241 " pdb=" CG GLU B 241 " pdb=" CD GLU B 241 " pdb=" OE1 GLU B 241 " ideal model delta sinusoidal sigma weight residual 0.00 84.07 -84.07 1 3.00e+01 1.11e-03 9.56e+00 dihedral pdb=" CB GLU C 241 " pdb=" CG GLU C 241 " pdb=" CD GLU C 241 " pdb=" OE1 GLU C 241 " ideal model delta sinusoidal sigma weight residual 0.00 83.98 -83.98 1 3.00e+01 1.11e-03 9.55e+00 dihedral pdb=" CB GLU F 241 " pdb=" CG GLU F 241 " pdb=" CD GLU F 241 " pdb=" OE1 GLU F 241 " ideal model delta sinusoidal sigma weight residual 0.00 83.91 -83.91 1 3.00e+01 1.11e-03 9.54e+00 ... (remaining 11307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1614 0.035 - 0.069: 752 0.069 - 0.104: 283 0.104 - 0.139: 71 0.139 - 0.174: 10 Chirality restraints: 2730 Sorted by residual: chirality pdb=" CA VAL A 240 " pdb=" N VAL A 240 " pdb=" C VAL A 240 " pdb=" CB VAL A 240 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA VAL E 240 " pdb=" N VAL E 240 " pdb=" C VAL E 240 " pdb=" CB VAL E 240 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CA VAL C 240 " pdb=" N VAL C 240 " pdb=" C VAL C 240 " pdb=" CB VAL C 240 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.34e-01 ... (remaining 2727 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 77 " 0.093 9.50e-02 1.11e+02 4.32e-02 2.77e+00 pdb=" NE ARG F 77 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG F 77 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG F 77 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG F 77 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 77 " -0.091 9.50e-02 1.11e+02 4.23e-02 2.75e+00 pdb=" NE ARG C 77 " -0.002 2.00e-02 2.50e+03 pdb=" CZ ARG C 77 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG C 77 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 77 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 77 " 0.090 9.50e-02 1.11e+02 4.18e-02 2.62e+00 pdb=" NE ARG B 77 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG B 77 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG B 77 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 77 " 0.011 2.00e-02 2.50e+03 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2299 2.75 - 3.29: 16225 3.29 - 3.83: 29467 3.83 - 4.36: 33943 4.36 - 4.90: 61975 Nonbonded interactions: 143909 Sorted by model distance: nonbonded pdb=" OE1 GLU H 230 " pdb=" NZ LYS E 238 " model vdw 2.213 3.120 nonbonded pdb=" OE1 GLU G 230 " pdb=" NZ LYS D 238 " model vdw 2.213 3.120 nonbonded pdb=" OE1 GLU K 230 " pdb=" NZ LYS B 238 " model vdw 2.218 3.120 nonbonded pdb=" OE1 GLU I 230 " pdb=" NZ LYS F 238 " model vdw 2.227 3.120 nonbonded pdb=" OE1 GLU L 230 " pdb=" NZ LYS C 238 " model vdw 2.237 3.120 ... (remaining 143904 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 through 403 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (resid 404 a \ nd (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)) or resid 405 \ through 407 or (resid 408 and (name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'B' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 and (name C31 or name C32 or name C33 or name C34 or name C35 or name C \ 36 or name C37 or name C38 or name C39 or name C40)) or (resid 403 and (name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20)) or (resid 404 and (name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or na \ me C22 or name C23 or name C24)) or resid 405 through 407 or (resid 408 and (nam \ e C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C40)))) selection = (chain 'C' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 through 403 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (resid 404 a \ nd (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)) or resid 405 \ through 407 or (resid 408 and (name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'D' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 through 403 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (resid 404 a \ nd (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)) or resid 405 \ through 407 or (resid 408 and (name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'E' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 through 403 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (resid 404 a \ nd (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)) or resid 405 \ through 407 or (resid 408 and (name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'F' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 through 403 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (resid 404 a \ nd (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)) or resid 405 \ through 407 or (resid 408 and (name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'G' and (resid 19 through 100 or resid 196 through 276 or resid 403 throu \ gh 405 or (resid 406 and (name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or na \ me C44)) or resid 407 through 409 or (resid 410 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40)))) selection = (chain 'H' and (resid 19 through 100 or resid 196 through 276 or resid 403 throu \ gh 405 or (resid 406 and (name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or na \ me C44)) or resid 407 through 409 or (resid 410 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40)))) selection = (chain 'I' and (resid 19 through 100 or resid 196 through 276 or resid 403 throu \ gh 405 or (resid 406 and (name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or na \ me C44)) or resid 407 through 409 or (resid 410 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40)))) selection = (chain 'J' and (resid 19 through 100 or resid 196 through 276 or resid 403 throu \ gh 405 or (resid 406 and (name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or na \ me C44)) or resid 407 through 409 or (resid 410 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40)))) selection = (chain 'K' and (resid 19 through 100 or resid 196 through 276 or resid 403 throu \ gh 405 or (resid 406 and (name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or na \ me C44)) or resid 407 through 409 or (resid 410 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40)))) selection = (chain 'L' and (resid 19 through 100 or resid 196 through 276 or resid 403 or (r \ esid 404 through 405 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or resid 406 th \ rough 410)) } 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=1.00 max=1.00 mean=1.00 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.360 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.500 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 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 : 0.005 0.043 18726 Z= 0.216 Angle : 1.073 7.844 24852 Z= 0.462 Chirality : 0.046 0.174 2730 Planarity : 0.005 0.043 2904 Dihedral : 16.869 84.065 7266 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.59 % Allowed : 1.03 % Favored : 98.38 % Rotamer: Outliers : 0.90 % Allowed : 11.25 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.17), residues: 2040 helix: 0.92 (0.13), residues: 1380 sheet: -0.28 (0.36), residues: 204 loop : -1.81 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG C 77 TYR 0.018 0.002 TYR H 96 PHE 0.019 0.001 PHE C 198 TRP 0.005 0.001 TRP I 79 HIS 0.004 0.001 HIS I 75 Details of bonding type rmsd covalent geometry : bond 0.00499 (18678) covalent geometry : angle 1.07200 (24780) SS BOND : bond 0.00169 ( 36) SS BOND : angle 1.31813 ( 72) hydrogen bonds : bond 0.13170 ( 1153) hydrogen bonds : angle 4.76323 ( 3387) Misc. bond : bond 0.00070 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 390 time to evaluate : 0.680 Fit side-chains REVERT: I 69 ARG cc_start: 0.7919 (tpt170) cc_final: 0.7702 (tpt90) REVERT: I 204 VAL cc_start: 0.9039 (t) cc_final: 0.8819 (m) REVERT: I 207 ASN cc_start: 0.8431 (m-40) cc_final: 0.8109 (m110) REVERT: L 204 VAL cc_start: 0.9029 (t) cc_final: 0.8816 (m) REVERT: A 69 ARG cc_start: 0.7874 (tpt170) cc_final: 0.7651 (ttm-80) REVERT: B 69 ARG cc_start: 0.7889 (tpt170) cc_final: 0.7650 (ttm-80) REVERT: B 77 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8141 (mpt180) REVERT: B 232 ASN cc_start: 0.9042 (p0) cc_final: 0.8831 (p0) REVERT: B 275 LEU cc_start: 0.6905 (mp) cc_final: 0.6692 (mp) REVERT: C 69 ARG cc_start: 0.7838 (tpt170) cc_final: 0.7635 (ttm-80) REVERT: C 275 LEU cc_start: 0.6725 (mp) cc_final: 0.6502 (mp) REVERT: D 77 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8209 (mpt180) REVERT: E 69 ARG cc_start: 0.7861 (tpt170) cc_final: 0.7631 (ttm-80) REVERT: E 232 ASN cc_start: 0.9046 (p0) cc_final: 0.8839 (p0) REVERT: E 239 GLU cc_start: 0.8360 (tt0) cc_final: 0.8120 (tt0) REVERT: E 275 LEU cc_start: 0.6905 (mp) cc_final: 0.6689 (mp) REVERT: F 275 LEU cc_start: 0.6756 (mp) cc_final: 0.6503 (mp) outliers start: 17 outliers final: 13 residues processed: 399 average time/residue: 0.1484 time to fit residues: 89.1582 Evaluate side-chains 344 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 329 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 253 PHE Chi-restraints excluded: chain H residue 253 PHE Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain J residue 253 PHE Chi-restraints excluded: chain K residue 253 PHE Chi-restraints excluded: chain L residue 253 PHE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 77 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 50 GLN H 50 GLN I 50 GLN J 50 GLN K 50 GLN L 50 GLN ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN A 82 GLN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN B 82 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 82 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 82 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN E 82 GLN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 82 GLN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.144650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.112759 restraints weight = 20159.003| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.36 r_work: 0.2732 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18726 Z= 0.125 Angle : 0.512 5.613 24852 Z= 0.275 Chirality : 0.041 0.136 2730 Planarity : 0.003 0.024 2904 Dihedral : 13.834 59.934 3525 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 0.69 % Favored : 99.02 % Rotamer: Outliers : 3.03 % Allowed : 13.75 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.18), residues: 2040 helix: 2.13 (0.13), residues: 1380 sheet: 0.40 (0.37), residues: 174 loop : -1.06 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 69 TYR 0.010 0.001 TYR H 96 PHE 0.011 0.001 PHE A 53 TRP 0.012 0.001 TRP E 277 HIS 0.003 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00277 (18678) covalent geometry : angle 0.51075 (24780) SS BOND : bond 0.00169 ( 36) SS BOND : angle 0.76871 ( 72) hydrogen bonds : bond 0.05124 ( 1153) hydrogen bonds : angle 3.68017 ( 3387) Misc. bond : bond 0.00029 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 348 time to evaluate : 0.652 Fit side-chains REVERT: H 29 VAL cc_start: 0.8871 (t) cc_final: 0.8669 (t) REVERT: I 34 ARG cc_start: 0.8513 (mtt180) cc_final: 0.8266 (mtt180) REVERT: I 69 ARG cc_start: 0.8919 (tpt170) cc_final: 0.8569 (tpt90) REVERT: I 230 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8232 (mm-30) REVERT: K 29 VAL cc_start: 0.8868 (t) cc_final: 0.8667 (t) REVERT: L 34 ARG cc_start: 0.8504 (mtt180) cc_final: 0.8249 (mtt180) REVERT: L 230 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8236 (mm-30) REVERT: L 237 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8305 (mm) REVERT: A 69 ARG cc_start: 0.9061 (tpt170) cc_final: 0.8720 (ttm-80) REVERT: B 69 ARG cc_start: 0.9037 (tpt170) cc_final: 0.8691 (ttm-80) REVERT: B 275 LEU cc_start: 0.7343 (mp) cc_final: 0.7061 (mp) REVERT: C 69 ARG cc_start: 0.9014 (tpt170) cc_final: 0.8655 (ttm-80) REVERT: C 238 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8202 (mtmt) REVERT: C 275 LEU cc_start: 0.7272 (mp) cc_final: 0.6969 (mp) REVERT: D 22 ILE cc_start: 0.6082 (OUTLIER) cc_final: 0.5867 (mp) REVERT: D 238 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8296 (mtmt) REVERT: E 69 ARG cc_start: 0.9033 (tpt170) cc_final: 0.8685 (ttm-80) REVERT: E 275 LEU cc_start: 0.7461 (mp) cc_final: 0.7189 (mp) REVERT: F 238 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8257 (mtmm) REVERT: F 275 LEU cc_start: 0.7235 (mp) cc_final: 0.6947 (mp) outliers start: 57 outliers final: 21 residues processed: 374 average time/residue: 0.1400 time to fit residues: 79.5034 Evaluate side-chains 356 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 330 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 253 PHE Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain J residue 253 PHE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain L residue 253 PHE Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 58 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 110 optimal weight: 0.0060 chunk 17 optimal weight: 5.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.144029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.109405 restraints weight = 20190.064| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.35 r_work: 0.2686 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18726 Z= 0.132 Angle : 0.484 5.623 24852 Z= 0.258 Chirality : 0.042 0.137 2730 Planarity : 0.003 0.028 2904 Dihedral : 12.381 59.897 3494 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.29 % Allowed : 1.03 % Favored : 98.68 % Rotamer: Outliers : 2.55 % Allowed : 13.48 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.18), residues: 2040 helix: 2.39 (0.13), residues: 1404 sheet: 1.11 (0.40), residues: 144 loop : -0.90 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 69 TYR 0.008 0.001 TYR B 67 PHE 0.010 0.001 PHE A 81 TRP 0.007 0.001 TRP E 277 HIS 0.003 0.001 HIS I 75 Details of bonding type rmsd covalent geometry : bond 0.00311 (18678) covalent geometry : angle 0.48298 (24780) SS BOND : bond 0.00203 ( 36) SS BOND : angle 0.77935 ( 72) hydrogen bonds : bond 0.04731 ( 1153) hydrogen bonds : angle 3.51290 ( 3387) Misc. bond : bond 0.00014 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 342 time to evaluate : 0.574 Fit side-chains REVERT: G 52 MET cc_start: 0.9257 (mmt) cc_final: 0.8932 (mmt) REVERT: I 29 VAL cc_start: 0.8840 (t) cc_final: 0.8594 (t) REVERT: I 69 ARG cc_start: 0.8875 (tpt170) cc_final: 0.8520 (tpt90) REVERT: I 204 VAL cc_start: 0.9026 (t) cc_final: 0.8722 (m) REVERT: J 52 MET cc_start: 0.9264 (mmt) cc_final: 0.8944 (mmt) REVERT: K 230 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8170 (mm-30) REVERT: L 204 VAL cc_start: 0.9030 (t) cc_final: 0.8738 (m) REVERT: L 237 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8539 (mm) REVERT: A 69 ARG cc_start: 0.8985 (tpt170) cc_final: 0.8583 (ttm-80) REVERT: B 69 ARG cc_start: 0.8935 (tpt170) cc_final: 0.8524 (ttm-80) REVERT: B 275 LEU cc_start: 0.7298 (mp) cc_final: 0.7043 (mp) REVERT: C 69 ARG cc_start: 0.8854 (tpt170) cc_final: 0.8481 (ttm-80) REVERT: C 275 LEU cc_start: 0.7233 (mp) cc_final: 0.6991 (mp) REVERT: D 238 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8427 (mtmt) REVERT: E 69 ARG cc_start: 0.8938 (tpt170) cc_final: 0.8524 (ttm-80) REVERT: E 275 LEU cc_start: 0.7319 (mp) cc_final: 0.7069 (mp) REVERT: F 275 LEU cc_start: 0.7174 (mp) cc_final: 0.6948 (mp) outliers start: 48 outliers final: 31 residues processed: 363 average time/residue: 0.1356 time to fit residues: 76.0078 Evaluate side-chains 359 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 326 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain L residue 253 PHE Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 90 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 197 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.143400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.112115 restraints weight = 20204.524| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.36 r_work: 0.2718 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18726 Z= 0.142 Angle : 0.483 5.622 24852 Z= 0.257 Chirality : 0.042 0.139 2730 Planarity : 0.003 0.029 2904 Dihedral : 11.613 59.884 3488 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.08 % Allowed : 14.86 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.18), residues: 2040 helix: 2.47 (0.13), residues: 1404 sheet: -0.03 (0.36), residues: 204 loop : -0.90 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 246 TYR 0.009 0.001 TYR D 67 PHE 0.011 0.001 PHE E 81 TRP 0.005 0.001 TRP B 277 HIS 0.003 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00339 (18678) covalent geometry : angle 0.48162 (24780) SS BOND : bond 0.00286 ( 36) SS BOND : angle 0.83740 ( 72) hydrogen bonds : bond 0.04737 ( 1153) hydrogen bonds : angle 3.47200 ( 3387) Misc. bond : bond 0.00016 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 333 time to evaluate : 0.705 Fit side-chains REVERT: G 52 MET cc_start: 0.9183 (mmt) cc_final: 0.8935 (mmt) REVERT: I 69 ARG cc_start: 0.8963 (tpt170) cc_final: 0.8700 (tpt90) REVERT: I 204 VAL cc_start: 0.9066 (t) cc_final: 0.8771 (m) REVERT: J 52 MET cc_start: 0.9206 (mmt) cc_final: 0.8964 (mmt) REVERT: K 230 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8131 (mm-30) REVERT: L 204 VAL cc_start: 0.9062 (t) cc_final: 0.8785 (m) REVERT: L 237 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8691 (mm) REVERT: A 69 ARG cc_start: 0.9015 (tpt170) cc_final: 0.8565 (ttm-80) REVERT: A 233 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7477 (ttt180) REVERT: B 69 ARG cc_start: 0.8953 (tpt170) cc_final: 0.8516 (ttm-80) REVERT: C 69 ARG cc_start: 0.8860 (tpt170) cc_final: 0.8449 (ttm-80) REVERT: D 233 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7449 (ttt180) REVERT: D 238 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8508 (mtmt) REVERT: E 69 ARG cc_start: 0.8957 (tpt170) cc_final: 0.8519 (ttm-80) REVERT: E 275 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.7030 (mp) outliers start: 58 outliers final: 35 residues processed: 367 average time/residue: 0.1389 time to fit residues: 78.1932 Evaluate side-chains 360 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 320 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 253 PHE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain J residue 253 PHE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 51 optimal weight: 0.2980 chunk 129 optimal weight: 1.9990 chunk 139 optimal weight: 0.4980 chunk 45 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 HIS A 59 GLN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.142922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.107598 restraints weight = 20109.781| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.28 r_work: 0.2595 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18726 Z= 0.139 Angle : 0.477 6.206 24852 Z= 0.253 Chirality : 0.042 0.136 2730 Planarity : 0.003 0.030 2904 Dihedral : 10.957 58.750 3486 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.81 % Allowed : 15.71 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.18), residues: 2040 helix: 2.51 (0.13), residues: 1404 sheet: 0.05 (0.37), residues: 204 loop : -0.84 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 246 TYR 0.009 0.001 TYR E 67 PHE 0.012 0.001 PHE C 81 TRP 0.004 0.001 TRP B 277 HIS 0.002 0.001 HIS I 75 Details of bonding type rmsd covalent geometry : bond 0.00334 (18678) covalent geometry : angle 0.47515 (24780) SS BOND : bond 0.00223 ( 36) SS BOND : angle 0.83975 ( 72) hydrogen bonds : bond 0.04618 ( 1153) hydrogen bonds : angle 3.41759 ( 3387) Misc. bond : bond 0.00013 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 339 time to evaluate : 0.632 Fit side-chains REVERT: G 52 MET cc_start: 0.9204 (mmt) cc_final: 0.8941 (mmt) REVERT: I 69 ARG cc_start: 0.8972 (tpt170) cc_final: 0.8698 (tpt90) REVERT: I 204 VAL cc_start: 0.9005 (t) cc_final: 0.8708 (m) REVERT: J 52 MET cc_start: 0.9216 (mmt) cc_final: 0.8952 (mmt) REVERT: K 230 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8273 (mm-30) REVERT: L 204 VAL cc_start: 0.8999 (t) cc_final: 0.8717 (m) REVERT: L 237 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8738 (mm) REVERT: B 233 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7544 (ttt180) REVERT: D 233 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7517 (ttt180) REVERT: E 233 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7592 (ttt180) REVERT: E 275 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.7043 (mp) outliers start: 53 outliers final: 38 residues processed: 369 average time/residue: 0.1398 time to fit residues: 79.2328 Evaluate side-chains 370 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 327 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 253 PHE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain J residue 253 PHE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 19 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.144180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.112329 restraints weight = 20001.377| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.34 r_work: 0.2661 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18726 Z= 0.109 Angle : 0.443 5.613 24852 Z= 0.237 Chirality : 0.040 0.134 2730 Planarity : 0.003 0.030 2904 Dihedral : 10.216 59.901 3486 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.55 % Allowed : 16.19 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.18), residues: 2040 helix: 2.66 (0.13), residues: 1404 sheet: 0.52 (0.39), residues: 174 loop : -0.76 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 69 TYR 0.007 0.001 TYR E 67 PHE 0.010 0.001 PHE D 33 TRP 0.004 0.001 TRP F 277 HIS 0.001 0.000 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00249 (18678) covalent geometry : angle 0.44183 (24780) SS BOND : bond 0.00150 ( 36) SS BOND : angle 0.73228 ( 72) hydrogen bonds : bond 0.04195 ( 1153) hydrogen bonds : angle 3.36469 ( 3387) Misc. bond : bond 0.00008 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 332 time to evaluate : 0.685 Fit side-chains REVERT: G 52 MET cc_start: 0.9161 (mmt) cc_final: 0.8933 (mmt) REVERT: H 232 ASN cc_start: 0.8237 (p0) cc_final: 0.7701 (t0) REVERT: I 69 ARG cc_start: 0.8971 (tpt170) cc_final: 0.8703 (tpt90) REVERT: I 204 VAL cc_start: 0.9045 (t) cc_final: 0.8777 (m) REVERT: I 230 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7945 (mm-30) REVERT: J 52 MET cc_start: 0.9163 (mmt) cc_final: 0.8952 (mmt) REVERT: K 230 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8181 (mm-30) REVERT: L 204 VAL cc_start: 0.9028 (t) cc_final: 0.8776 (m) REVERT: A 233 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7489 (ttt180) REVERT: B 233 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7581 (ttt180) REVERT: E 233 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7580 (ttt180) outliers start: 48 outliers final: 32 residues processed: 361 average time/residue: 0.1439 time to fit residues: 78.8656 Evaluate side-chains 359 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 324 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 63 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 75 HIS I 75 HIS J 100 GLN K 100 GLN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.140637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.108235 restraints weight = 20247.877| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.28 r_work: 0.2663 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18726 Z= 0.214 Angle : 0.545 5.566 24852 Z= 0.287 Chirality : 0.045 0.157 2730 Planarity : 0.004 0.032 2904 Dihedral : 10.961 59.375 3486 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.97 % Allowed : 16.51 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.18), residues: 2040 helix: 2.38 (0.13), residues: 1404 sheet: -0.01 (0.37), residues: 204 loop : -0.87 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 69 TYR 0.012 0.002 TYR E 67 PHE 0.012 0.002 PHE D 53 TRP 0.005 0.001 TRP I 79 HIS 0.005 0.001 HIS K 75 Details of bonding type rmsd covalent geometry : bond 0.00532 (18678) covalent geometry : angle 0.54229 (24780) SS BOND : bond 0.00222 ( 36) SS BOND : angle 1.14629 ( 72) hydrogen bonds : bond 0.05321 ( 1153) hydrogen bonds : angle 3.49112 ( 3387) Misc. bond : bond 0.00030 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 320 time to evaluate : 0.707 Fit side-chains REVERT: G 52 MET cc_start: 0.9188 (mmt) cc_final: 0.8937 (mmt) REVERT: I 69 ARG cc_start: 0.8881 (tpt170) cc_final: 0.8549 (tpt90) REVERT: I 204 VAL cc_start: 0.9079 (t) cc_final: 0.8774 (m) REVERT: I 230 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8066 (mm-30) REVERT: J 52 MET cc_start: 0.9194 (mmt) cc_final: 0.8944 (mmt) REVERT: L 204 VAL cc_start: 0.9077 (t) cc_final: 0.8778 (m) REVERT: L 230 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7961 (mm-30) REVERT: A 233 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7591 (ttt180) REVERT: B 233 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7695 (ttt180) REVERT: D 233 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7583 (ttt180) REVERT: E 233 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7715 (ttt180) outliers start: 56 outliers final: 40 residues processed: 357 average time/residue: 0.1397 time to fit residues: 76.8781 Evaluate side-chains 353 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 309 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 253 PHE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 160 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 35 optimal weight: 0.0370 chunk 188 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 189 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 75 HIS H 99 HIS H 274 HIS I 75 HIS I 99 HIS K 274 HIS L 75 HIS L 274 HIS ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.144053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.111962 restraints weight = 20007.031| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.26 r_work: 0.2683 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18726 Z= 0.105 Angle : 0.441 5.580 24852 Z= 0.237 Chirality : 0.040 0.132 2730 Planarity : 0.003 0.030 2904 Dihedral : 9.955 59.775 3486 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.34 % Allowed : 17.30 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.18), residues: 2040 helix: 2.67 (0.13), residues: 1404 sheet: -0.03 (0.37), residues: 204 loop : -0.93 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 77 TYR 0.006 0.001 TYR B 67 PHE 0.011 0.001 PHE D 33 TRP 0.006 0.001 TRP E 277 HIS 0.015 0.001 HIS L 274 Details of bonding type rmsd covalent geometry : bond 0.00235 (18678) covalent geometry : angle 0.43997 (24780) SS BOND : bond 0.00145 ( 36) SS BOND : angle 0.72028 ( 72) hydrogen bonds : bond 0.04204 ( 1153) hydrogen bonds : angle 3.38470 ( 3387) Misc. bond : bond 0.00012 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 317 time to evaluate : 0.685 Fit side-chains REVERT: H 232 ASN cc_start: 0.8206 (p0) cc_final: 0.7711 (t0) REVERT: H 239 GLU cc_start: 0.8589 (tt0) cc_final: 0.8358 (tt0) REVERT: I 69 ARG cc_start: 0.8933 (tpt170) cc_final: 0.8647 (tpt90) REVERT: I 204 VAL cc_start: 0.9026 (t) cc_final: 0.8767 (m) REVERT: I 230 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7653 (mm-30) REVERT: I 239 GLU cc_start: 0.8623 (tt0) cc_final: 0.8191 (tt0) REVERT: L 204 VAL cc_start: 0.9015 (t) cc_final: 0.8768 (m) REVERT: L 230 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7860 (mm-30) REVERT: A 233 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7471 (ttt180) REVERT: B 233 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7611 (ttt180) REVERT: D 233 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7431 (ttt180) REVERT: E 233 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7629 (ttt180) outliers start: 44 outliers final: 31 residues processed: 351 average time/residue: 0.1425 time to fit residues: 76.1022 Evaluate side-chains 344 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 309 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain H residue 274 HIS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain K residue 274 HIS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain L residue 274 HIS Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 184 optimal weight: 0.9990 chunk 193 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 179 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 151 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 274 HIS I 99 HIS K 274 HIS L 75 HIS L 274 HIS ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.144177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.112065 restraints weight = 20089.279| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.25 r_work: 0.2697 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18726 Z= 0.107 Angle : 0.446 5.595 24852 Z= 0.239 Chirality : 0.040 0.136 2730 Planarity : 0.003 0.030 2904 Dihedral : 9.676 59.370 3486 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.23 % Allowed : 17.46 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.18), residues: 2040 helix: 2.71 (0.13), residues: 1404 sheet: -0.04 (0.37), residues: 204 loop : -0.90 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 77 TYR 0.009 0.001 TYR H 229 PHE 0.010 0.001 PHE D 33 TRP 0.004 0.001 TRP E 277 HIS 0.019 0.001 HIS K 274 Details of bonding type rmsd covalent geometry : bond 0.00244 (18678) covalent geometry : angle 0.44519 (24780) SS BOND : bond 0.00141 ( 36) SS BOND : angle 0.72999 ( 72) hydrogen bonds : bond 0.04178 ( 1153) hydrogen bonds : angle 3.35349 ( 3387) Misc. bond : bond 0.00010 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 321 time to evaluate : 0.721 Fit side-chains REVERT: H 232 ASN cc_start: 0.8216 (p0) cc_final: 0.7758 (t0) REVERT: I 69 ARG cc_start: 0.8908 (tpt170) cc_final: 0.8628 (tpt90) REVERT: I 204 VAL cc_start: 0.9027 (t) cc_final: 0.8778 (m) REVERT: I 230 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7915 (mm-30) REVERT: K 232 ASN cc_start: 0.8201 (p0) cc_final: 0.7673 (t0) REVERT: L 204 VAL cc_start: 0.9006 (t) cc_final: 0.8768 (m) REVERT: A 233 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7434 (ttt180) REVERT: B 233 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7619 (ttt180) REVERT: D 233 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7407 (ttt180) REVERT: E 233 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7603 (ttt180) outliers start: 42 outliers final: 28 residues processed: 347 average time/residue: 0.1394 time to fit residues: 73.4829 Evaluate side-chains 347 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 315 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain L residue 274 HIS Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 143 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 176 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 274 HIS I 99 HIS K 274 HIS L 274 HIS ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.144256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.111919 restraints weight = 20017.439| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.17 r_work: 0.2702 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18726 Z= 0.106 Angle : 0.442 5.577 24852 Z= 0.237 Chirality : 0.040 0.136 2730 Planarity : 0.003 0.030 2904 Dihedral : 9.439 59.552 3486 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.80 % Allowed : 17.89 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.18), residues: 2040 helix: 2.74 (0.13), residues: 1404 sheet: 0.39 (0.39), residues: 174 loop : -0.78 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 77 TYR 0.007 0.001 TYR D 67 PHE 0.010 0.001 PHE D 33 TRP 0.004 0.001 TRP E 277 HIS 0.023 0.001 HIS L 274 Details of bonding type rmsd covalent geometry : bond 0.00243 (18678) covalent geometry : angle 0.44041 (24780) SS BOND : bond 0.00145 ( 36) SS BOND : angle 0.73711 ( 72) hydrogen bonds : bond 0.04099 ( 1153) hydrogen bonds : angle 3.34219 ( 3387) Misc. bond : bond 0.00010 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 313 time to evaluate : 0.643 Fit side-chains REVERT: H 232 ASN cc_start: 0.8220 (p0) cc_final: 0.7786 (t0) REVERT: I 69 ARG cc_start: 0.8893 (tpt170) cc_final: 0.8601 (tpt90) REVERT: I 204 VAL cc_start: 0.9028 (t) cc_final: 0.8781 (m) REVERT: I 230 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7887 (mm-30) REVERT: I 232 ASN cc_start: 0.8126 (p0) cc_final: 0.7753 (t0) REVERT: K 232 ASN cc_start: 0.8201 (p0) cc_final: 0.7749 (t0) REVERT: L 204 VAL cc_start: 0.8993 (t) cc_final: 0.8755 (m) REVERT: L 230 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7819 (mm-30) REVERT: L 232 ASN cc_start: 0.8155 (p0) cc_final: 0.7784 (t0) REVERT: A 233 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7421 (ttt180) REVERT: B 233 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7604 (ttt180) REVERT: D 233 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7386 (ttt180) REVERT: E 233 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7588 (ttt180) outliers start: 34 outliers final: 28 residues processed: 335 average time/residue: 0.1336 time to fit residues: 68.6330 Evaluate side-chains 341 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 309 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 274 HIS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain K residue 274 HIS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 274 HIS I 99 HIS K 274 HIS L 274 HIS ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.142680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.110404 restraints weight = 20142.089| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.30 r_work: 0.2632 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18726 Z= 0.162 Angle : 0.486 5.562 24852 Z= 0.257 Chirality : 0.042 0.138 2730 Planarity : 0.003 0.031 2904 Dihedral : 9.615 59.931 3486 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.86 % Allowed : 17.94 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.18), residues: 2040 helix: 2.65 (0.13), residues: 1404 sheet: 0.01 (0.37), residues: 204 loop : -0.90 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 77 TYR 0.009 0.001 TYR D 67 PHE 0.011 0.001 PHE D 53 TRP 0.004 0.001 TRP A 79 HIS 0.028 0.002 HIS H 274 Details of bonding type rmsd covalent geometry : bond 0.00401 (18678) covalent geometry : angle 0.48455 (24780) SS BOND : bond 0.00194 ( 36) SS BOND : angle 0.92959 ( 72) hydrogen bonds : bond 0.04541 ( 1153) hydrogen bonds : angle 3.36301 ( 3387) Misc. bond : bond 0.00014 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3815.68 seconds wall clock time: 66 minutes 28.45 seconds (3988.45 seconds total)