Starting phenix.real_space_refine on Thu Mar 5 05:16:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qeq_13937/03_2026/7qeq_13937.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qeq_13937/03_2026/7qeq_13937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qeq_13937/03_2026/7qeq_13937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qeq_13937/03_2026/7qeq_13937.map" model { file = "/net/cci-nas-00/data/ceres_data/7qeq_13937/03_2026/7qeq_13937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qeq_13937/03_2026/7qeq_13937.cif" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 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 168 5.16 5 C 12792 2.51 5 N 2976 2.21 5 O 3377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19313 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "B" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "D" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "E" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "F" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "G" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "H" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "I" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "J" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "K" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "L" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1536 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 182} Chain breaks: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Time building chain proxies: 5.01, per 1000 atoms: 0.26 Number of scatterers: 19313 At special positions: 0 Unit cell: (99.45, 109.65, 157.25, 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 168 16.00 O 3377 8.00 N 2976 7.00 C 12792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 180 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 180 " distance=2.04 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 169 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 180 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 169 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 180 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 169 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 180 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 180 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 174 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 180 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 169 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 180 " distance=2.04 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 174 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 169 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 180 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 174 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 169 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 180 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 174 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 169 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 921.5 milliseconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 76.2% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 4.175A pdb=" N THR A 8 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 39 removed outlier: 4.323A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 103 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 217 Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 43 Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 103 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 217 Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 43 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 103 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL C 144 " --> pdb=" O ILE C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 217 Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 43 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 103 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL D 144 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 217 Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 18 through 39 removed outlier: 4.323A pdb=" N LEU E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 43 Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 103 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL E 144 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 217 Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 43 Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 103 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL F 144 " --> pdb=" O ILE F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 217 Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 43 Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 103 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL G 144 " --> pdb=" O ILE G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 217 Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 43 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 103 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 217 Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 43 Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 103 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 130 through 159 removed outlier: 3.579A pdb=" N VAL I 144 " --> pdb=" O ILE I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 217 Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 43 Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 103 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL J 144 " --> pdb=" O ILE J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 217 Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 43 Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 103 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL K 144 " --> pdb=" O ILE K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 217 Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 18 through 39 removed outlier: 4.322A pdb=" N LEU L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 43 Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 103 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 130 through 159 removed outlier: 3.580A pdb=" N VAL L 144 " --> pdb=" O ILE L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 1404 hydrogen bonds defined for protein. 4104 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: 3.33 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5463 1.34 - 1.46: 5103 1.46 - 1.58: 8658 1.58 - 1.70: 0 1.70 - 1.81: 240 Bond restraints: 19464 Sorted by residual: bond pdb=" C1 LMT H 305 " pdb=" C2 LMT H 305 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" C1 LMT L 303 " pdb=" C2 LMT L 303 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.16e+00 bond pdb=" C1 LMT K 303 " pdb=" C2 LMT K 303 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.15e+00 bond pdb=" C1 LMT A 305 " pdb=" C2 LMT A 305 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" C1 LMT J 303 " pdb=" C2 LMT J 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.06e+00 ... (remaining 19459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 25413 1.58 - 3.16: 363 3.16 - 4.74: 144 4.74 - 6.31: 156 6.31 - 7.89: 144 Bond angle restraints: 26220 Sorted by residual: angle pdb=" C ASN K 176 " pdb=" CA ASN K 176 " pdb=" CB ASN K 176 " ideal model delta sigma weight residual 116.63 111.76 4.87 1.16e+00 7.43e-01 1.76e+01 angle pdb=" C ASN I 176 " pdb=" CA ASN I 176 " pdb=" CB ASN I 176 " ideal model delta sigma weight residual 116.63 111.76 4.87 1.16e+00 7.43e-01 1.76e+01 angle pdb=" C ASN H 176 " pdb=" CA ASN H 176 " pdb=" CB ASN H 176 " ideal model delta sigma weight residual 116.63 111.76 4.87 1.16e+00 7.43e-01 1.76e+01 angle pdb=" C ASN A 176 " pdb=" CA ASN A 176 " pdb=" CB ASN A 176 " ideal model delta sigma weight residual 116.63 111.77 4.86 1.16e+00 7.43e-01 1.76e+01 angle pdb=" C ASN E 176 " pdb=" CA ASN E 176 " pdb=" CB ASN E 176 " ideal model delta sigma weight residual 116.63 111.77 4.86 1.16e+00 7.43e-01 1.75e+01 ... (remaining 26215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 10470 16.16 - 32.31: 618 32.31 - 48.47: 211 48.47 - 64.63: 41 64.63 - 80.79: 12 Dihedral angle restraints: 11352 sinusoidal: 4680 harmonic: 6672 Sorted by residual: dihedral pdb=" CB GLU J 209 " pdb=" CG GLU J 209 " pdb=" CD GLU J 209 " pdb=" OE1 GLU J 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.79 80.79 1 3.00e+01 1.11e-03 8.96e+00 dihedral pdb=" CB GLU F 209 " pdb=" CG GLU F 209 " pdb=" CD GLU F 209 " pdb=" OE1 GLU F 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.79 80.79 1 3.00e+01 1.11e-03 8.96e+00 dihedral pdb=" CB GLU I 209 " pdb=" CG GLU I 209 " pdb=" CD GLU I 209 " pdb=" OE1 GLU I 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.78 80.78 1 3.00e+01 1.11e-03 8.96e+00 ... (remaining 11349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1776 0.026 - 0.052: 701 0.052 - 0.078: 339 0.078 - 0.104: 112 0.104 - 0.130: 24 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CA THR K 86 " pdb=" N THR K 86 " pdb=" C THR K 86 " pdb=" CB THR K 86 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA THR I 86 " pdb=" N THR I 86 " pdb=" C THR I 86 " pdb=" CB THR I 86 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA THR C 86 " pdb=" N THR C 86 " pdb=" C THR C 86 " pdb=" CB THR C 86 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 2949 not shown) Planarity restraints: 3096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP F 172 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.56e-01 pdb=" N PRO F 173 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO F 173 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 173 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP G 172 " -0.014 5.00e-02 4.00e+02 2.16e-02 7.49e-01 pdb=" N PRO G 173 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO G 173 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO G 173 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 172 " 0.014 5.00e-02 4.00e+02 2.16e-02 7.49e-01 pdb=" N PRO D 173 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO D 173 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 173 " 0.011 5.00e-02 4.00e+02 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 584 2.72 - 3.27: 19723 3.27 - 3.81: 31203 3.81 - 4.36: 38405 4.36 - 4.90: 65044 Nonbonded interactions: 154959 Sorted by model distance: nonbonded pdb=" O ILE H 71 " pdb=" OH TYR H 158 " model vdw 2.181 3.040 nonbonded pdb=" O ILE C 71 " pdb=" OH TYR C 158 " model vdw 2.181 3.040 nonbonded pdb=" O ILE I 71 " pdb=" OH TYR I 158 " model vdw 2.181 3.040 nonbonded pdb=" O ILE F 71 " pdb=" OH TYR F 158 " model vdw 2.181 3.040 nonbonded pdb=" O ILE A 71 " pdb=" OH TYR A 158 " model vdw 2.181 3.040 ... (remaining 154954 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'B' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'C' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'D' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'E' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'F' and (resid 4 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) selection = (chain 'G' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'H' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'I' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'J' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'K' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'L' and (resid 4 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) } 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: 8.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.260 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 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 0.050 19500 Z= 0.240 Angle : 0.868 7.892 26292 Z= 0.374 Chirality : 0.037 0.130 2952 Planarity : 0.002 0.022 3096 Dihedral : 12.392 80.787 6924 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.18 % Allowed : 6.51 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.17), residues: 2220 helix: 2.03 (0.12), residues: 1500 sheet: 1.45 (0.39), residues: 204 loop : -2.18 (0.21), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 165 TYR 0.008 0.001 TYR I 65 PHE 0.013 0.001 PHE E 51 TRP 0.008 0.001 TRP G 24 HIS 0.001 0.000 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00488 (19464) covalent geometry : angle 0.86733 (26220) SS BOND : bond 0.00283 ( 36) SS BOND : angle 1.16452 ( 72) hydrogen bonds : bond 0.24536 ( 1404) hydrogen bonds : angle 6.59046 ( 4104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 332 time to evaluate : 0.740 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 354 average time/residue: 0.4853 time to fit residues: 197.5352 Evaluate side-chains 290 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN B 57 GLN D 206 ASN E 57 GLN F 206 ASN G 57 GLN H 206 ASN J 57 GLN K 206 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.142556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.084690 restraints weight = 23752.701| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.69 r_work: 0.2826 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19500 Z= 0.163 Angle : 0.590 6.625 26292 Z= 0.332 Chirality : 0.043 0.156 2952 Planarity : 0.004 0.019 3096 Dihedral : 8.883 49.033 2808 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.92 % Allowed : 11.88 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.17), residues: 2220 helix: 3.10 (0.12), residues: 1548 sheet: 2.82 (0.42), residues: 132 loop : -1.36 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 165 TYR 0.015 0.002 TYR F 65 PHE 0.014 0.002 PHE G 51 TRP 0.008 0.001 TRP F 24 HIS 0.003 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00315 (19464) covalent geometry : angle 0.58756 (26220) SS BOND : bond 0.00322 ( 36) SS BOND : angle 1.15920 ( 72) hydrogen bonds : bond 0.07357 ( 1404) hydrogen bonds : angle 4.35537 ( 4104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 314 time to evaluate : 0.500 Fit side-chains outliers start: 39 outliers final: 21 residues processed: 332 average time/residue: 0.5254 time to fit residues: 197.9012 Evaluate side-chains 307 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 286 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 132 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 80 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 214 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN C 57 GLN E 57 GLN G 57 GLN I 57 GLN J 57 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.141415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.082896 restraints weight = 23849.124| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.68 r_work: 0.2791 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19500 Z= 0.188 Angle : 0.614 7.371 26292 Z= 0.340 Chirality : 0.045 0.210 2952 Planarity : 0.003 0.026 3096 Dihedral : 8.577 49.958 2808 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.25 % Allowed : 12.38 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.28 (0.17), residues: 2220 helix: 3.29 (0.12), residues: 1536 sheet: 2.48 (0.42), residues: 132 loop : -1.47 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 75 TYR 0.019 0.002 TYR E 65 PHE 0.019 0.002 PHE J 51 TRP 0.010 0.002 TRP G 172 HIS 0.003 0.000 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00418 (19464) covalent geometry : angle 0.61029 (26220) SS BOND : bond 0.00542 ( 36) SS BOND : angle 1.40563 ( 72) hydrogen bonds : bond 0.07024 ( 1404) hydrogen bonds : angle 4.28529 ( 4104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 328 time to evaluate : 0.512 Fit side-chains REVERT: B 94 HIS cc_start: 0.6189 (OUTLIER) cc_final: 0.5958 (t-90) REVERT: D 217 TYR cc_start: 0.5951 (m-80) cc_final: 0.5673 (m-80) outliers start: 66 outliers final: 31 residues processed: 364 average time/residue: 0.4974 time to fit residues: 206.8959 Evaluate side-chains 340 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 308 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 213 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 80 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 205 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN C 57 GLN E 57 GLN E 73 HIS G 57 GLN I 57 GLN I 73 HIS J 57 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.143123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.084851 restraints weight = 23774.316| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.66 r_work: 0.2825 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19500 Z= 0.153 Angle : 0.581 7.304 26292 Z= 0.314 Chirality : 0.044 0.193 2952 Planarity : 0.003 0.017 3096 Dihedral : 8.066 54.124 2808 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.30 % Allowed : 13.86 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.57 (0.17), residues: 2220 helix: 3.61 (0.12), residues: 1536 sheet: 2.50 (0.43), residues: 132 loop : -1.65 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 216 TYR 0.014 0.002 TYR I 65 PHE 0.016 0.002 PHE C 51 TRP 0.009 0.001 TRP B 133 HIS 0.002 0.000 HIS I 73 Details of bonding type rmsd covalent geometry : bond 0.00330 (19464) covalent geometry : angle 0.57855 (26220) SS BOND : bond 0.00403 ( 36) SS BOND : angle 1.20358 ( 72) hydrogen bonds : bond 0.06099 ( 1404) hydrogen bonds : angle 4.08038 ( 4104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 336 time to evaluate : 0.604 Fit side-chains REVERT: B 132 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7065 (mm) REVERT: E 132 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7154 (mm) REVERT: I 132 LEU cc_start: 0.7488 (tt) cc_final: 0.7040 (mm) REVERT: L 132 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7203 (mm) outliers start: 67 outliers final: 36 residues processed: 376 average time/residue: 0.5172 time to fit residues: 222.1425 Evaluate side-chains 364 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 325 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 151 MET Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 132 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 92 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 153 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.143040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.084423 restraints weight = 23717.178| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.68 r_work: 0.2833 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19500 Z= 0.139 Angle : 0.567 7.516 26292 Z= 0.302 Chirality : 0.043 0.194 2952 Planarity : 0.003 0.018 3096 Dihedral : 7.611 57.239 2808 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.01 % Allowed : 14.45 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.80 (0.17), residues: 2220 helix: 3.76 (0.12), residues: 1548 sheet: 2.51 (0.43), residues: 132 loop : -1.64 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 216 TYR 0.013 0.002 TYR I 65 PHE 0.014 0.001 PHE G 51 TRP 0.008 0.001 TRP H 133 HIS 0.002 0.000 HIS H 16 Details of bonding type rmsd covalent geometry : bond 0.00293 (19464) covalent geometry : angle 0.56527 (26220) SS BOND : bond 0.00347 ( 36) SS BOND : angle 1.10341 ( 72) hydrogen bonds : bond 0.05615 ( 1404) hydrogen bonds : angle 3.95408 ( 4104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 339 time to evaluate : 0.694 Fit side-chains REVERT: A 133 TRP cc_start: 0.7315 (OUTLIER) cc_final: 0.7084 (t60) REVERT: B 132 LEU cc_start: 0.7422 (tt) cc_final: 0.7037 (mm) REVERT: E 132 LEU cc_start: 0.7526 (tt) cc_final: 0.7195 (mm) REVERT: H 132 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7221 (mm) REVERT: I 132 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7032 (mm) REVERT: L 132 LEU cc_start: 0.7526 (tt) cc_final: 0.7196 (mm) outliers start: 61 outliers final: 30 residues processed: 375 average time/residue: 0.5050 time to fit residues: 218.3349 Evaluate side-chains 362 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 329 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 85 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 112 optimal weight: 2.9990 chunk 40 optimal weight: 0.0030 chunk 0 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 97 optimal weight: 0.0270 chunk 54 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.4848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.144234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.086327 restraints weight = 23680.557| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.67 r_work: 0.2869 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19500 Z= 0.119 Angle : 0.536 7.313 26292 Z= 0.282 Chirality : 0.042 0.190 2952 Planarity : 0.003 0.020 3096 Dihedral : 6.993 58.595 2808 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.63 % Allowed : 16.52 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.00 (0.18), residues: 2220 helix: 3.87 (0.12), residues: 1560 sheet: 2.65 (0.44), residues: 132 loop : -1.58 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 216 TYR 0.009 0.002 TYR G 158 PHE 0.011 0.001 PHE J 51 TRP 0.008 0.001 TRP B 133 HIS 0.002 0.000 HIS F 16 Details of bonding type rmsd covalent geometry : bond 0.00238 (19464) covalent geometry : angle 0.53462 (26220) SS BOND : bond 0.00246 ( 36) SS BOND : angle 0.91085 ( 72) hydrogen bonds : bond 0.04923 ( 1404) hydrogen bonds : angle 3.82096 ( 4104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 353 time to evaluate : 0.853 Fit side-chains REVERT: A 133 TRP cc_start: 0.7264 (OUTLIER) cc_final: 0.7012 (t60) REVERT: B 132 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7051 (mm) REVERT: B 133 TRP cc_start: 0.7110 (OUTLIER) cc_final: 0.6543 (t60) REVERT: E 132 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7141 (mm) REVERT: F 132 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7197 (mm) REVERT: I 132 LEU cc_start: 0.7413 (tt) cc_final: 0.7016 (mm) REVERT: L 132 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7126 (mm) outliers start: 33 outliers final: 14 residues processed: 374 average time/residue: 0.4872 time to fit residues: 210.0162 Evaluate side-chains 346 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 326 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 162 SER Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 132 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 79 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 179 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.143269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.085031 restraints weight = 23709.606| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.66 r_work: 0.2837 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19500 Z= 0.134 Angle : 0.563 8.345 26292 Z= 0.296 Chirality : 0.042 0.192 2952 Planarity : 0.003 0.019 3096 Dihedral : 6.864 58.199 2808 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.99 % Allowed : 17.46 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.99 (0.17), residues: 2220 helix: 3.87 (0.12), residues: 1560 sheet: 2.50 (0.43), residues: 132 loop : -1.56 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 75 TYR 0.013 0.002 TYR I 65 PHE 0.014 0.001 PHE C 51 TRP 0.008 0.001 TRP B 133 HIS 0.001 0.000 HIS L 73 Details of bonding type rmsd covalent geometry : bond 0.00282 (19464) covalent geometry : angle 0.56054 (26220) SS BOND : bond 0.00333 ( 36) SS BOND : angle 1.07316 ( 72) hydrogen bonds : bond 0.05219 ( 1404) hydrogen bonds : angle 3.85261 ( 4104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 334 time to evaluate : 0.772 Fit side-chains REVERT: A 133 TRP cc_start: 0.7281 (OUTLIER) cc_final: 0.7016 (t60) REVERT: B 132 LEU cc_start: 0.7435 (tt) cc_final: 0.7103 (mm) REVERT: C 132 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7151 (mm) REVERT: E 132 LEU cc_start: 0.7446 (tt) cc_final: 0.7152 (mm) REVERT: I 132 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7007 (mm) REVERT: L 132 LEU cc_start: 0.7453 (tt) cc_final: 0.7158 (mm) outliers start: 20 outliers final: 14 residues processed: 351 average time/residue: 0.4919 time to fit residues: 199.6994 Evaluate side-chains 350 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 333 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 TRP Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 19 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 92 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 209 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 211 optimal weight: 0.0060 chunk 11 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.144276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.086431 restraints weight = 23863.830| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.68 r_work: 0.2867 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19500 Z= 0.120 Angle : 0.548 8.807 26292 Z= 0.284 Chirality : 0.042 0.190 2952 Planarity : 0.003 0.019 3096 Dihedral : 6.386 59.848 2808 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.04 % Allowed : 18.00 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.11 (0.17), residues: 2220 helix: 4.06 (0.12), residues: 1548 sheet: 2.60 (0.44), residues: 132 loop : -1.73 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 75 TYR 0.010 0.002 TYR G 65 PHE 0.015 0.001 PHE E 29 TRP 0.015 0.001 TRP B 134 HIS 0.001 0.000 HIS J 16 Details of bonding type rmsd covalent geometry : bond 0.00245 (19464) covalent geometry : angle 0.54638 (26220) SS BOND : bond 0.00251 ( 36) SS BOND : angle 0.93710 ( 72) hydrogen bonds : bond 0.04754 ( 1404) hydrogen bonds : angle 3.75288 ( 4104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 360 time to evaluate : 0.610 Fit side-chains REVERT: A 140 ILE cc_start: 0.8565 (pt) cc_final: 0.8304 (mp) REVERT: B 132 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7087 (mm) REVERT: D 212 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6599 (t80) REVERT: E 132 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7160 (mm) REVERT: G 132 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7127 (mm) REVERT: H 140 ILE cc_start: 0.8567 (pt) cc_final: 0.8320 (mp) REVERT: I 132 LEU cc_start: 0.7348 (tt) cc_final: 0.7009 (mm) REVERT: I 140 ILE cc_start: 0.8493 (pt) cc_final: 0.8232 (mp) REVERT: L 132 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7167 (mm) outliers start: 21 outliers final: 13 residues processed: 371 average time/residue: 0.4767 time to fit residues: 203.9524 Evaluate side-chains 359 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 341 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 116 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 141 optimal weight: 0.4980 chunk 148 optimal weight: 0.8980 chunk 170 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.143528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.085418 restraints weight = 23673.035| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.67 r_work: 0.2842 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19500 Z= 0.131 Angle : 0.569 9.086 26292 Z= 0.297 Chirality : 0.042 0.191 2952 Planarity : 0.003 0.019 3096 Dihedral : 6.252 59.475 2808 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.84 % Allowed : 18.49 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.06 (0.17), residues: 2220 helix: 3.95 (0.12), residues: 1560 sheet: 2.48 (0.43), residues: 132 loop : -1.59 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 75 TYR 0.013 0.002 TYR I 65 PHE 0.014 0.001 PHE C 51 TRP 0.036 0.001 TRP A 134 HIS 0.001 0.000 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00276 (19464) covalent geometry : angle 0.56716 (26220) SS BOND : bond 0.00321 ( 36) SS BOND : angle 1.05654 ( 72) hydrogen bonds : bond 0.05025 ( 1404) hydrogen bonds : angle 3.79810 ( 4104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 344 time to evaluate : 0.643 Fit side-chains REVERT: B 132 LEU cc_start: 0.7405 (tt) cc_final: 0.7092 (mm) REVERT: D 212 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6614 (t80) REVERT: E 132 LEU cc_start: 0.7449 (tt) cc_final: 0.7173 (mm) REVERT: H 212 TYR cc_start: 0.7246 (OUTLIER) cc_final: 0.6654 (t80) REVERT: I 132 LEU cc_start: 0.7358 (tt) cc_final: 0.7022 (mm) REVERT: K 212 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.6627 (t80) REVERT: L 132 LEU cc_start: 0.7467 (tt) cc_final: 0.7180 (mm) outliers start: 17 outliers final: 15 residues processed: 353 average time/residue: 0.4876 time to fit residues: 198.8952 Evaluate side-chains 358 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 340 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 204 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 182 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.143775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.085793 restraints weight = 23867.577| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.67 r_work: 0.2848 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19500 Z= 0.126 Angle : 0.571 10.523 26292 Z= 0.295 Chirality : 0.042 0.191 2952 Planarity : 0.003 0.019 3096 Dihedral : 6.093 59.391 2808 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.79 % Allowed : 18.69 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.09 (0.17), residues: 2220 helix: 4.04 (0.12), residues: 1548 sheet: 2.53 (0.43), residues: 132 loop : -1.73 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 216 TYR 0.026 0.002 TYR J 212 PHE 0.014 0.001 PHE B 29 TRP 0.039 0.001 TRP A 134 HIS 0.001 0.000 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00262 (19464) covalent geometry : angle 0.56979 (26220) SS BOND : bond 0.00289 ( 36) SS BOND : angle 1.00028 ( 72) hydrogen bonds : bond 0.04904 ( 1404) hydrogen bonds : angle 3.78066 ( 4104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 352 time to evaluate : 0.651 Fit side-chains REVERT: A 140 ILE cc_start: 0.8583 (pt) cc_final: 0.8301 (mp) REVERT: B 132 LEU cc_start: 0.7387 (tt) cc_final: 0.7076 (mm) REVERT: D 212 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6606 (t80) REVERT: E 132 LEU cc_start: 0.7447 (tt) cc_final: 0.7169 (mm) REVERT: H 140 ILE cc_start: 0.8594 (pt) cc_final: 0.8301 (mp) REVERT: H 212 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.6630 (t80) REVERT: I 132 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7010 (mm) REVERT: I 140 ILE cc_start: 0.8453 (pt) cc_final: 0.8081 (mp) REVERT: K 212 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6610 (t80) REVERT: L 132 LEU cc_start: 0.7474 (tt) cc_final: 0.7191 (mm) outliers start: 16 outliers final: 14 residues processed: 359 average time/residue: 0.4770 time to fit residues: 197.8234 Evaluate side-chains 359 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 341 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 215 ILE Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain K residue 19 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 18 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 181 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.142804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.084415 restraints weight = 23733.294| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.67 r_work: 0.2816 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19500 Z= 0.149 Angle : 0.598 10.534 26292 Z= 0.312 Chirality : 0.044 0.193 2952 Planarity : 0.003 0.020 3096 Dihedral : 6.117 59.608 2808 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.04 % Allowed : 18.44 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.05 (0.17), residues: 2220 helix: 4.01 (0.12), residues: 1548 sheet: 2.38 (0.42), residues: 132 loop : -1.69 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 75 TYR 0.016 0.002 TYR I 65 PHE 0.015 0.001 PHE C 51 TRP 0.040 0.001 TRP A 134 HIS 0.002 0.000 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00329 (19464) covalent geometry : angle 0.59565 (26220) SS BOND : bond 0.00422 ( 36) SS BOND : angle 1.22695 ( 72) hydrogen bonds : bond 0.05366 ( 1404) hydrogen bonds : angle 3.86751 ( 4104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12756.39 seconds wall clock time: 216 minutes 28.11 seconds (12988.11 seconds total)