Starting phenix.real_space_refine on Mon Jun 16 07:01:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xnv_33327/06_2025/7xnv_33327.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnv_33327/06_2025/7xnv_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_33327/06_2025/7xnv_33327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnv_33327/06_2025/7xnv_33327.map" model { file = "/net/cci-nas-00/data/ceres_data/7xnv_33327/06_2025/7xnv_33327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnv_33327/06_2025/7xnv_33327.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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-2': 11, 'MC3:plan-1': 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-2': 11, 'MC3:plan-1': 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-2': 11, 'MC3:plan-1': 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-2': 11, 'MC3:plan-1': 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-2': 11, 'MC3:plan-1': 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-2': 11, 'MC3:plan-1': 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-2': 8, 'MC3:plan-1': 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-2': 8, 'MC3:plan-1': 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-2': 8, 'MC3:plan-1': 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-2': 8, 'MC3:plan-1': 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-2': 8, 'MC3:plan-1': 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-2': 8, 'MC3:plan-1': 8} Unresolved non-hydrogen planarities: 48 Time building chain proxies: 11.52, per 1000 atoms: 0.63 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: 4.16 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.51 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: 5.24 Time building geometry restraints manager: 4.96 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: 0.02 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.490 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.080 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.230 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (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 TRP 0.005 0.001 TRP I 79 HIS 0.004 0.001 HIS I 75 PHE 0.019 0.001 PHE C 198 TYR 0.018 0.002 TYR H 96 ARG 0.023 0.001 ARG C 77 Details of bonding type rmsd hydrogen bonds : bond 0.13170 ( 1153) hydrogen bonds : angle 4.76323 ( 3387) SS BOND : bond 0.00169 ( 36) SS BOND : angle 1.31813 ( 72) covalent geometry : bond 0.00499 (18678) covalent geometry : angle 1.07200 (24780) 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 : 1.760 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: 0.8432 (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: 0.7649 (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: 0.9045 (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: 0.3013 time to fit residues: 180.1387 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 : 1.940 ------------------------------------------------------------------------------- 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 172 optimal weight: 20.0000 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 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 99 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 82 GLN D 99 HIS ** 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.144450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.112485 restraints weight = 20095.816| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.28 r_work: 0.2739 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18726 Z= 0.134 Angle : 0.519 5.588 24852 Z= 0.278 Chirality : 0.042 0.138 2730 Planarity : 0.003 0.024 2904 Dihedral : 13.828 59.998 3525 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.29 % Allowed : 0.69 % Favored : 99.02 % Rotamer: Outliers : 2.97 % Allowed : 13.75 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.18), residues: 2040 helix: 2.15 (0.13), residues: 1374 sheet: 0.36 (0.37), residues: 174 loop : -1.10 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 277 HIS 0.003 0.001 HIS I 75 PHE 0.009 0.001 PHE D 53 TYR 0.011 0.001 TYR H 96 ARG 0.003 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.05228 ( 1153) hydrogen bonds : angle 3.68071 ( 3387) SS BOND : bond 0.00184 ( 36) SS BOND : angle 0.82391 ( 72) covalent geometry : bond 0.00301 (18678) covalent geometry : angle 0.51740 (24780) Misc. bond : bond 0.00051 ( 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 409 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 353 time to evaluate : 1.932 Fit side-chains REVERT: I 69 ARG cc_start: 0.8904 (tpt170) cc_final: 0.8565 (tpt90) REVERT: I 230 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8243 (mm-30) REVERT: K 29 VAL cc_start: 0.8854 (t) cc_final: 0.8654 (t) REVERT: L 34 ARG cc_start: 0.8476 (mtt180) cc_final: 0.8238 (mtt180) REVERT: L 230 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8205 (mm-30) REVERT: L 237 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8305 (mm) REVERT: A 69 ARG cc_start: 0.9051 (tpt170) cc_final: 0.8703 (ttm-80) REVERT: A 230 GLU cc_start: 0.8760 (mp0) cc_final: 0.8554 (mp0) REVERT: B 69 ARG cc_start: 0.9018 (tpt170) cc_final: 0.8667 (ttm-80) REVERT: B 275 LEU cc_start: 0.7345 (mp) cc_final: 0.7056 (mp) REVERT: C 69 ARG cc_start: 0.8993 (tpt170) cc_final: 0.8645 (ttm-80) REVERT: C 238 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8224 (mtmt) REVERT: C 275 LEU cc_start: 0.7261 (mp) cc_final: 0.6952 (mp) REVERT: D 238 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8350 (mtmt) REVERT: E 69 ARG cc_start: 0.9020 (tpt170) cc_final: 0.8665 (ttm-80) REVERT: E 275 LEU cc_start: 0.7470 (mp) cc_final: 0.7195 (mp) REVERT: F 238 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8368 (mtmt) REVERT: F 275 LEU cc_start: 0.7228 (mp) cc_final: 0.6939 (mp) outliers start: 56 outliers final: 20 residues processed: 380 average time/residue: 0.3141 time to fit residues: 179.9490 Evaluate side-chains 352 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 328 time to evaluate : 1.981 ------------------------------------------------------------------------------- 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 20 THR 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 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 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 170 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 78 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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** K 100 GLN 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 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 = 0.3472 r_free = 0.3472 target = 0.141881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.106976 restraints weight = 20092.579| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.25 r_work: 0.2610 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18726 Z= 0.193 Angle : 0.549 5.539 24852 Z= 0.290 Chirality : 0.045 0.148 2730 Planarity : 0.004 0.032 2904 Dihedral : 12.838 59.792 3494 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.29 % Allowed : 1.42 % Favored : 98.28 % Rotamer: Outliers : 2.55 % Allowed : 14.07 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.18), residues: 2040 helix: 2.19 (0.13), residues: 1404 sheet: -0.12 (0.37), residues: 204 loop : -0.88 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 277 HIS 0.005 0.001 HIS I 75 PHE 0.011 0.001 PHE A 53 TYR 0.010 0.002 TYR G 67 ARG 0.004 0.001 ARG A 246 Details of bonding type rmsd hydrogen bonds : bond 0.05462 ( 1153) hydrogen bonds : angle 3.61395 ( 3387) SS BOND : bond 0.00278 ( 36) SS BOND : angle 1.03416 ( 72) covalent geometry : bond 0.00479 (18678) covalent geometry : angle 0.54726 (24780) Misc. bond : bond 0.00022 ( 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 377 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 329 time to evaluate : 1.931 Fit side-chains REVERT: G 52 MET cc_start: 0.9225 (mmt) cc_final: 0.8948 (mmt) REVERT: H 230 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8117 (mm-30) REVERT: I 69 ARG cc_start: 0.8888 (tpt170) cc_final: 0.8592 (tpt90) REVERT: I 204 VAL cc_start: 0.9008 (t) cc_final: 0.8697 (m) REVERT: I 230 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8015 (mm-30) REVERT: J 52 MET cc_start: 0.9228 (mmt) cc_final: 0.8961 (mmt) REVERT: L 204 VAL cc_start: 0.9022 (t) cc_final: 0.8715 (m) REVERT: L 230 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7976 (mm-30) REVERT: L 237 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8640 (mm) REVERT: A 69 ARG cc_start: 0.8992 (tpt170) cc_final: 0.8562 (ttm-80) REVERT: B 69 ARG cc_start: 0.8952 (tpt170) cc_final: 0.8522 (ttm-80) REVERT: B 275 LEU cc_start: 0.7352 (mp) cc_final: 0.7088 (mp) REVERT: C 69 ARG cc_start: 0.8886 (tpt170) cc_final: 0.8483 (ttm-80) REVERT: C 275 LEU cc_start: 0.7279 (mp) cc_final: 0.6990 (mp) REVERT: D 238 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8518 (mtmt) REVERT: E 69 ARG cc_start: 0.8944 (tpt170) cc_final: 0.8506 (ttm-80) REVERT: E 275 LEU cc_start: 0.7416 (mp) cc_final: 0.7141 (mp) REVERT: F 275 LEU cc_start: 0.7215 (mp) cc_final: 0.6952 (mp) outliers start: 48 outliers final: 34 residues processed: 348 average time/residue: 0.2973 time to fit residues: 157.1568 Evaluate side-chains 354 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 318 time to evaluate : 1.856 ------------------------------------------------------------------------------- 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 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 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 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 82 GLN 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 91 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 130 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 75 HIS L 99 HIS 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.143253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.108671 restraints weight = 20056.481| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.29 r_work: 0.2625 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18726 Z= 0.129 Angle : 0.469 5.606 24852 Z= 0.251 Chirality : 0.041 0.135 2730 Planarity : 0.003 0.029 2904 Dihedral : 11.629 59.463 3486 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.13 % Allowed : 15.23 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.18), residues: 2040 helix: 2.44 (0.13), residues: 1404 sheet: -0.11 (0.36), residues: 204 loop : -0.85 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 277 HIS 0.002 0.001 HIS L 75 PHE 0.008 0.001 PHE A 53 TYR 0.008 0.001 TYR A 67 ARG 0.002 0.000 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.04648 ( 1153) hydrogen bonds : angle 3.46792 ( 3387) SS BOND : bond 0.00200 ( 36) SS BOND : angle 0.79108 ( 72) covalent geometry : bond 0.00305 (18678) covalent geometry : angle 0.46735 (24780) Misc. bond : bond 0.00012 ( 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 409 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 350 time to evaluate : 1.999 Fit side-chains REVERT: G 52 MET cc_start: 0.9191 (mmt) cc_final: 0.8933 (mmt) REVERT: H 230 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8171 (mm-30) REVERT: I 69 ARG cc_start: 0.8925 (tpt170) cc_final: 0.8647 (tpt90) REVERT: I 204 VAL cc_start: 0.8980 (t) cc_final: 0.8687 (m) REVERT: I 230 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8064 (mm-30) REVERT: J 52 MET cc_start: 0.9210 (mmt) cc_final: 0.8960 (mmt) REVERT: L 204 VAL cc_start: 0.9000 (t) cc_final: 0.8713 (m) REVERT: L 230 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8075 (mm-30) REVERT: A 69 ARG cc_start: 0.9025 (tpt170) cc_final: 0.8560 (ttm-80) REVERT: A 233 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7477 (ttt180) REVERT: B 233 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7509 (ttt180) REVERT: B 275 LEU cc_start: 0.7271 (mp) cc_final: 0.7066 (mp) REVERT: C 69 ARG cc_start: 0.8922 (tpt170) cc_final: 0.8497 (ttm-80) REVERT: C 275 LEU cc_start: 0.7239 (mp) cc_final: 0.7009 (mp) REVERT: D 233 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7463 (ttt180) REVERT: E 233 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7541 (ttt180) REVERT: E 275 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7086 (mp) REVERT: F 275 LEU cc_start: 0.7216 (mp) cc_final: 0.6983 (mp) outliers start: 59 outliers final: 28 residues processed: 384 average time/residue: 0.3013 time to fit residues: 174.8500 Evaluate side-chains 362 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 329 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 I residue 253 PHE 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 L residue 253 PHE Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 233 ARG 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 B residue 73 ILE 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 233 ARG Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 82 GLN 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 271 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 58 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 0.1980 chunk 42 optimal weight: 0.8980 chunk 180 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 140 optimal weight: 20.0000 chunk 158 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 75 HIS A 59 GLN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN ** 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 = 0.3477 r_free = 0.3477 target = 0.142471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.109649 restraints weight = 20407.936| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.45 r_work: 0.2660 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18726 Z= 0.144 Angle : 0.483 5.581 24852 Z= 0.256 Chirality : 0.042 0.139 2730 Planarity : 0.003 0.031 2904 Dihedral : 11.096 59.786 3486 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.13 % Allowed : 16.40 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.18), residues: 2040 helix: 2.46 (0.13), residues: 1404 sheet: -0.02 (0.37), residues: 204 loop : -0.80 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 79 HIS 0.003 0.001 HIS L 75 PHE 0.010 0.001 PHE F 81 TYR 0.009 0.001 TYR F 67 ARG 0.002 0.000 ARG C 246 Details of bonding type rmsd hydrogen bonds : bond 0.04721 ( 1153) hydrogen bonds : angle 3.44301 ( 3387) SS BOND : bond 0.00186 ( 36) SS BOND : angle 0.89162 ( 72) covalent geometry : bond 0.00350 (18678) covalent geometry : angle 0.48097 (24780) Misc. bond : bond 0.00016 ( 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 397 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 338 time to evaluate : 1.960 Fit side-chains REVERT: G 52 MET cc_start: 0.9185 (mmt) cc_final: 0.8920 (mmt) REVERT: H 230 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8163 (mm-30) REVERT: I 69 ARG cc_start: 0.8943 (tpt170) cc_final: 0.8657 (tpt90) REVERT: I 204 VAL cc_start: 0.9044 (t) cc_final: 0.8754 (m) REVERT: I 230 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8107 (mm-30) REVERT: J 52 MET cc_start: 0.9188 (mmt) cc_final: 0.8932 (mmt) REVERT: L 204 VAL cc_start: 0.9037 (t) cc_final: 0.8748 (m) REVERT: A 233 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7451 (ttt180) REVERT: B 233 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7591 (ttt180) REVERT: C 69 ARG cc_start: 0.8902 (tpt170) cc_final: 0.8458 (ttm-80) REVERT: D 233 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7513 (ttt180) REVERT: E 233 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7634 (ttt180) outliers start: 59 outliers final: 43 residues processed: 373 average time/residue: 0.3001 time to fit residues: 170.3438 Evaluate side-chains 376 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 329 time to evaluate : 1.931 ------------------------------------------------------------------------------- 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 238 LYS Chi-restraints excluded: chain A residue 21 MET 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 82 GLN 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 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 82 GLN Chi-restraints excluded: chain D residue 94 ILE 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 82 GLN 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 94 ILE 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 18 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 152 optimal weight: 0.8980 chunk 201 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.143759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.112206 restraints weight = 20171.889| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.33 r_work: 0.2666 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18726 Z= 0.111 Angle : 0.445 5.610 24852 Z= 0.238 Chirality : 0.040 0.136 2730 Planarity : 0.003 0.030 2904 Dihedral : 10.390 58.637 3486 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.34 % Allowed : 17.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.18), residues: 2040 helix: 2.62 (0.13), residues: 1404 sheet: 0.44 (0.39), residues: 174 loop : -0.75 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 277 HIS 0.001 0.000 HIS I 99 PHE 0.010 0.001 PHE D 33 TYR 0.007 0.001 TYR E 67 ARG 0.002 0.000 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 1153) hydrogen bonds : angle 3.37685 ( 3387) SS BOND : bond 0.00242 ( 36) SS BOND : angle 0.74564 ( 72) covalent geometry : bond 0.00257 (18678) covalent geometry : angle 0.44375 (24780) Misc. bond : bond 0.00009 ( 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 376 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 332 time to evaluate : 1.957 Fit side-chains REVERT: I 69 ARG cc_start: 0.8942 (tpt170) cc_final: 0.8672 (tpt90) REVERT: I 204 VAL cc_start: 0.9020 (t) cc_final: 0.8754 (m) REVERT: L 204 VAL cc_start: 0.9012 (t) cc_final: 0.8757 (m) REVERT: A 233 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7485 (ttt180) REVERT: B 233 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7570 (ttt180) REVERT: D 233 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7445 (ttt180) REVERT: E 233 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7610 (ttt180) outliers start: 44 outliers final: 27 residues processed: 358 average time/residue: 0.3047 time to fit residues: 163.8953 Evaluate side-chains 353 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 322 time to evaluate : 1.967 ------------------------------------------------------------------------------- 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 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 19 SER 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 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 233 ARG 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 202 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 139 optimal weight: 0.0470 chunk 74 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 75 HIS H 75 HIS H 99 HIS J 100 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 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 = 0.3459 r_free = 0.3459 target = 0.141016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.108706 restraints weight = 20103.911| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.25 r_work: 0.2688 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18726 Z= 0.203 Angle : 0.533 5.546 24852 Z= 0.281 Chirality : 0.045 0.153 2730 Planarity : 0.004 0.032 2904 Dihedral : 10.839 59.465 3486 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.29 % Allowed : 16.56 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.18), residues: 2040 helix: 2.42 (0.13), residues: 1404 sheet: -0.03 (0.37), residues: 204 loop : -0.82 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 79 HIS 0.007 0.001 HIS G 75 PHE 0.012 0.002 PHE D 53 TYR 0.011 0.002 TYR E 67 ARG 0.004 0.001 ARG I 77 Details of bonding type rmsd hydrogen bonds : bond 0.05180 ( 1153) hydrogen bonds : angle 3.47273 ( 3387) SS BOND : bond 0.00215 ( 36) SS BOND : angle 1.10571 ( 72) covalent geometry : bond 0.00503 (18678) covalent geometry : angle 0.53008 (24780) Misc. bond : bond 0.00025 ( 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 382 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 320 time to evaluate : 2.030 Fit side-chains REVERT: I 69 ARG cc_start: 0.8861 (tpt170) cc_final: 0.8545 (tpt90) REVERT: I 204 VAL cc_start: 0.9076 (t) cc_final: 0.8786 (m) REVERT: J 230 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7879 (mm-30) REVERT: J 239 GLU cc_start: 0.8629 (tt0) cc_final: 0.8220 (tt0) REVERT: L 204 VAL cc_start: 0.9061 (t) cc_final: 0.8775 (m) REVERT: A 233 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7573 (ttt180) REVERT: B 233 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7634 (ttt180) REVERT: D 233 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7553 (ttt180) REVERT: E 233 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7690 (ttt180) outliers start: 62 outliers final: 46 residues processed: 362 average time/residue: 0.3838 time to fit residues: 211.7564 Evaluate side-chains 361 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 311 time to evaluate : 1.965 ------------------------------------------------------------------------------- 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 99 HIS 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 238 LYS Chi-restraints excluded: chain A residue 19 SER 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 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 82 GLN 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 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 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 44 THR Chi-restraints excluded: chain E residue 82 GLN 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 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 115 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 172 optimal weight: 20.0000 chunk 161 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 108 optimal weight: 20.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 75 HIS H 99 HIS H 274 HIS I 75 HIS I 99 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 59 GLN ** 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 = 0.3478 r_free = 0.3478 target = 0.142571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.108239 restraints weight = 20094.551| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.30 r_work: 0.2689 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2064 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= 0.127 Angle : 0.468 5.573 24852 Z= 0.251 Chirality : 0.041 0.136 2730 Planarity : 0.003 0.031 2904 Dihedral : 10.461 59.565 3486 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.81 % Allowed : 17.25 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.18), residues: 2040 helix: 2.56 (0.13), residues: 1404 sheet: -0.07 (0.37), residues: 204 loop : -0.89 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 277 HIS 0.015 0.001 HIS L 274 PHE 0.010 0.001 PHE D 33 TYR 0.009 0.001 TYR A 67 ARG 0.003 0.000 ARG I 77 Details of bonding type rmsd hydrogen bonds : bond 0.04582 ( 1153) hydrogen bonds : angle 3.42266 ( 3387) SS BOND : bond 0.00159 ( 36) SS BOND : angle 0.83150 ( 72) covalent geometry : bond 0.00302 (18678) covalent geometry : angle 0.46681 (24780) 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 374 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 321 time to evaluate : 2.077 Fit side-chains REVERT: I 69 ARG cc_start: 0.8859 (tpt170) cc_final: 0.8577 (tpt90) REVERT: I 204 VAL cc_start: 0.9042 (t) cc_final: 0.8764 (m) REVERT: J 230 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7875 (mm-30) REVERT: L 204 VAL cc_start: 0.9029 (t) cc_final: 0.8754 (m) REVERT: A 233 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7517 (ttt180) REVERT: B 233 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7573 (ttt180) REVERT: D 233 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7489 (ttt180) REVERT: E 233 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7657 (ttt180) outliers start: 53 outliers final: 41 residues processed: 360 average time/residue: 0.3107 time to fit residues: 168.5412 Evaluate side-chains 361 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 316 time to evaluate : 1.794 ------------------------------------------------------------------------------- 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 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 22 ILE 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 A residue 271 GLU 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 82 GLN Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 233 ARG 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 19 SER Chi-restraints excluded: chain D residue 20 THR 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 D residue 264 CYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 43 optimal weight: 0.1980 chunk 189 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 75 HIS H 99 HIS H 274 HIS I 75 HIS I 99 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.143717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.111528 restraints weight = 20197.829| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.24 r_work: 0.2670 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18726 Z= 0.106 Angle : 0.449 5.579 24852 Z= 0.241 Chirality : 0.040 0.137 2730 Planarity : 0.003 0.031 2904 Dihedral : 10.143 59.677 3486 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.55 % Allowed : 17.68 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.18), residues: 2040 helix: 2.65 (0.13), residues: 1404 sheet: -0.09 (0.37), residues: 204 loop : -0.92 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 277 HIS 0.024 0.001 HIS L 274 PHE 0.010 0.001 PHE D 33 TYR 0.007 0.001 TYR A 67 ARG 0.003 0.000 ARG I 77 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 1153) hydrogen bonds : angle 3.38790 ( 3387) SS BOND : bond 0.00148 ( 36) SS BOND : angle 0.74626 ( 72) covalent geometry : bond 0.00239 (18678) covalent geometry : angle 0.44754 (24780) 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 365 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 317 time to evaluate : 1.758 Fit side-chains REVERT: I 69 ARG cc_start: 0.8911 (tpt170) cc_final: 0.8638 (tpt90) REVERT: I 204 VAL cc_start: 0.9033 (t) cc_final: 0.8770 (m) REVERT: J 230 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7904 (mm-30) REVERT: L 204 VAL cc_start: 0.9006 (t) cc_final: 0.8756 (m) REVERT: A 233 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7488 (ttt180) REVERT: B 233 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7557 (ttt180) REVERT: D 233 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7461 (ttt180) REVERT: E 233 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7621 (ttt180) outliers start: 48 outliers final: 34 residues processed: 353 average time/residue: 0.3100 time to fit residues: 164.4783 Evaluate side-chains 348 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 310 time to evaluate : 1.884 ------------------------------------------------------------------------------- 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 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 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 22 ILE 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 82 GLN Chi-restraints excluded: chain B residue 233 ARG 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 19 SER Chi-restraints excluded: chain D residue 20 THR 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 D residue 264 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 140 optimal weight: 20.0000 chunk 151 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 75 HIS H 99 HIS H 274 HIS I 99 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.142087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.108347 restraints weight = 20108.593| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.34 r_work: 0.2660 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2111 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= 0.166 Angle : 0.493 5.548 24852 Z= 0.261 Chirality : 0.042 0.139 2730 Planarity : 0.003 0.032 2904 Dihedral : 10.288 59.348 3486 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.60 % Allowed : 17.78 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.18), residues: 2040 helix: 2.55 (0.13), residues: 1404 sheet: -0.08 (0.37), residues: 204 loop : -0.91 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.021 0.001 HIS L 274 PHE 0.011 0.001 PHE A 53 TYR 0.009 0.001 TYR A 67 ARG 0.003 0.000 ARG I 77 Details of bonding type rmsd hydrogen bonds : bond 0.04695 ( 1153) hydrogen bonds : angle 3.41190 ( 3387) SS BOND : bond 0.00196 ( 36) SS BOND : angle 0.96077 ( 72) covalent geometry : bond 0.00410 (18678) covalent geometry : angle 0.49082 (24780) Misc. bond : bond 0.00016 ( 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 354 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 305 time to evaluate : 1.893 Fit side-chains REVERT: I 69 ARG cc_start: 0.8867 (tpt170) cc_final: 0.8554 (tpt90) REVERT: I 204 VAL cc_start: 0.9043 (t) cc_final: 0.8764 (m) REVERT: J 230 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7993 (mm-30) REVERT: L 204 VAL cc_start: 0.9024 (t) cc_final: 0.8753 (m) REVERT: A 233 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7594 (ttt180) REVERT: B 233 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7612 (ttt180) REVERT: D 233 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7541 (ttt180) REVERT: E 233 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7666 (ttt180) outliers start: 49 outliers final: 42 residues processed: 340 average time/residue: 0.2957 time to fit residues: 153.0008 Evaluate side-chains 346 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 300 time to evaluate : 2.004 ------------------------------------------------------------------------------- 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 238 LYS Chi-restraints excluded: chain H residue 274 HIS 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 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 22 ILE 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 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 82 GLN Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 233 ARG 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 C residue 271 GLU Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 20 THR 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 D residue 264 CYS 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 94 ILE 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 183 optimal weight: 0.1980 chunk 110 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 115 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 75 HIS H 99 HIS H 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.143793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.110764 restraints weight = 19997.612| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.26 r_work: 0.2698 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18726 Z= 0.104 Angle : 0.447 5.552 24852 Z= 0.239 Chirality : 0.040 0.135 2730 Planarity : 0.003 0.031 2904 Dihedral : 9.990 59.985 3486 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.39 % Allowed : 18.05 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.18), residues: 2040 helix: 2.67 (0.13), residues: 1404 sheet: -0.11 (0.37), residues: 204 loop : -0.90 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 277 HIS 0.024 0.001 HIS L 274 PHE 0.011 0.001 PHE D 33 TYR 0.007 0.001 TYR A 67 ARG 0.003 0.000 ARG I 77 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 1153) hydrogen bonds : angle 3.38147 ( 3387) SS BOND : bond 0.00148 ( 36) SS BOND : angle 0.73999 ( 72) covalent geometry : bond 0.00231 (18678) covalent geometry : angle 0.44577 (24780) Misc. bond : bond 0.00010 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8096.49 seconds wall clock time: 142 minutes 2.71 seconds (8522.71 seconds total)