Starting phenix.real_space_refine on Sun Feb 8 06:05:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z8m_73900/02_2026/9z8m_73900_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z8m_73900/02_2026/9z8m_73900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z8m_73900/02_2026/9z8m_73900_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z8m_73900/02_2026/9z8m_73900_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z8m_73900/02_2026/9z8m_73900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z8m_73900/02_2026/9z8m_73900.map" } resolution = 2.7 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= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 96 5.16 5 C 13680 2.51 5 N 2808 2.21 5 O 3108 1.98 5 H 16800 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36516 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2844 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2844 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2844 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2844 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "E" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2844 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2844 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "G" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2844 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "H" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2844 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "I" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2844 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "J" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2844 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "K" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2844 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "L" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2844 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 199 Unusual residues: {'MC3': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 537 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 14} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 199 Unusual residues: {'MC3': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 537 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 14} Unresolved non-hydrogen planarities: 107 Chain: "C" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 199 Unusual residues: {'MC3': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 537 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 14} Unresolved non-hydrogen planarities: 107 Chain: "D" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 199 Unusual residues: {'MC3': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 537 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 14} Unresolved non-hydrogen planarities: 107 Chain: "E" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 199 Unusual residues: {'MC3': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 537 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 14} Unresolved non-hydrogen planarities: 107 Chain: "F" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 199 Unusual residues: {'MC3': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 537 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 14} Unresolved non-hydrogen planarities: 107 Chain: "G" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 199 Unusual residues: {'MC3': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 537 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 14} Unresolved non-hydrogen planarities: 107 Chain: "H" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 199 Unusual residues: {'MC3': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 537 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 14} Unresolved non-hydrogen planarities: 107 Chain: "I" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 199 Unusual residues: {'MC3': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 537 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 14} Unresolved non-hydrogen planarities: 107 Chain: "J" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 199 Unusual residues: {'MC3': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 537 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 14} Unresolved non-hydrogen planarities: 107 Chain: "K" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 199 Unusual residues: {'MC3': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 537 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 14} Unresolved non-hydrogen planarities: 107 Chain: "L" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 199 Unusual residues: {'MC3': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 537 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 14} Unresolved non-hydrogen planarities: 107 Time building chain proxies: 7.14, per 1000 atoms: 0.20 Number of scatterers: 36516 At special positions: 0 Unit cell: (97.818, 99.462, 155.358, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 24 15.00 O 3108 8.00 N 2808 7.00 C 13680 6.00 H 16800 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 189 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 178 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 189 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 183 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 178 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 189 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 183 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 189 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 183 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 178 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 189 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 183 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 178 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 189 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 178 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 189 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 183 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 178 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 189 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 183 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 178 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 189 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 183 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 178 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 189 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 183 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 178 " 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: 2.93 Conformation dependent library (CDL) restraints added in 1.2 seconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4176 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 12 sheets defined 78.3% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 4 through 18 removed outlier: 3.628A pdb=" N ARG A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 104 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 141 through 169 Processing helix chain 'A' and resid 193 through 222 Processing helix chain 'B' and resid 5 through 18 removed outlier: 3.628A pdb=" N ARG B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 32 Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 104 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 141 through 169 Processing helix chain 'B' and resid 193 through 222 Processing helix chain 'C' and resid 5 through 18 removed outlier: 3.628A pdb=" N ARG C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 32 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 104 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 141 through 169 Processing helix chain 'C' and resid 193 through 222 Processing helix chain 'D' and resid 5 through 18 removed outlier: 3.628A pdb=" N ARG D 9 " --> pdb=" O SER D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 32 Processing helix chain 'D' and resid 33 through 40 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 104 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 141 through 169 Processing helix chain 'D' and resid 193 through 222 Processing helix chain 'E' and resid 5 through 18 removed outlier: 3.628A pdb=" N ARG E 9 " --> pdb=" O SER E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 33 through 40 Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 104 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 141 through 169 Processing helix chain 'E' and resid 193 through 222 Processing helix chain 'F' and resid 5 through 18 removed outlier: 3.628A pdb=" N ARG F 9 " --> pdb=" O SER F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 32 Processing helix chain 'F' and resid 33 through 40 Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 104 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 141 through 169 Processing helix chain 'F' and resid 193 through 222 Processing helix chain 'G' and resid 5 through 18 removed outlier: 3.629A pdb=" N ARG G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 32 Processing helix chain 'G' and resid 33 through 40 Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 73 through 104 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 141 through 169 Processing helix chain 'G' and resid 193 through 222 Processing helix chain 'H' and resid 5 through 18 removed outlier: 3.628A pdb=" N ARG H 9 " --> pdb=" O SER H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 32 Processing helix chain 'H' and resid 33 through 40 Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 73 through 104 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 141 through 169 Processing helix chain 'H' and resid 193 through 222 Processing helix chain 'I' and resid 5 through 18 removed outlier: 3.629A pdb=" N ARG I 9 " --> pdb=" O SER I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 32 Processing helix chain 'I' and resid 33 through 40 Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 73 through 104 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 141 through 169 Processing helix chain 'I' and resid 193 through 222 Processing helix chain 'J' and resid 5 through 18 removed outlier: 3.629A pdb=" N ARG J 9 " --> pdb=" O SER J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 32 Processing helix chain 'J' and resid 33 through 40 Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 73 through 104 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 141 through 169 Processing helix chain 'J' and resid 193 through 222 Processing helix chain 'K' and resid 5 through 18 removed outlier: 3.628A pdb=" N ARG K 9 " --> pdb=" O SER K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 32 Processing helix chain 'K' and resid 33 through 40 Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 73 through 104 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 141 through 169 Processing helix chain 'K' and resid 193 through 222 Processing helix chain 'L' and resid 5 through 18 removed outlier: 3.628A pdb=" N ARG L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 32 Processing helix chain 'L' and resid 33 through 40 Processing helix chain 'L' and resid 40 through 45 Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 73 through 104 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 141 through 169 Processing helix chain 'L' and resid 193 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.590A pdb=" N THR A 53 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.590A pdb=" N THR B 53 " --> pdb=" O PHE B 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.589A pdb=" N THR C 53 " --> pdb=" O PHE C 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.589A pdb=" N THR D 53 " --> pdb=" O PHE D 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.590A pdb=" N THR E 53 " --> pdb=" O PHE E 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.590A pdb=" N THR F 53 " --> pdb=" O PHE F 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.589A pdb=" N THR G 53 " --> pdb=" O PHE G 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.590A pdb=" N THR H 53 " --> pdb=" O PHE H 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.590A pdb=" N THR I 53 " --> pdb=" O PHE I 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.590A pdb=" N THR J 53 " --> pdb=" O PHE J 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.590A pdb=" N THR K 53 " --> pdb=" O PHE K 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.590A pdb=" N THR L 53 " --> pdb=" O PHE L 190 " (cutoff:3.500A) 1357 hydrogen bonds defined for protein. 4035 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: 8.14 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16788 1.03 - 1.23: 66 1.23 - 1.42: 7710 1.42 - 1.61: 12132 1.61 - 1.81: 108 Bond restraints: 36804 Sorted by residual: bond pdb=" C20 MC3 C 509 " pdb=" C21 MC3 C 509 " ideal model delta sigma weight residual 1.524 1.472 0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" C20 MC3 J 509 " pdb=" C21 MC3 J 509 " ideal model delta sigma weight residual 1.524 1.472 0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" C17 MC3 I 509 " pdb=" C18 MC3 I 509 " ideal model delta sigma weight residual 1.523 1.471 0.052 2.00e-02 2.50e+03 6.68e+00 bond pdb=" C20 MC3 I 509 " pdb=" C21 MC3 I 509 " ideal model delta sigma weight residual 1.524 1.473 0.051 2.00e-02 2.50e+03 6.63e+00 bond pdb=" C20 MC3 G 509 " pdb=" C21 MC3 G 509 " ideal model delta sigma weight residual 1.524 1.473 0.051 2.00e-02 2.50e+03 6.60e+00 ... (remaining 36799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 64047 2.00 - 4.00: 465 4.00 - 6.01: 12 6.01 - 8.01: 0 8.01 - 10.01: 24 Bond angle restraints: 64548 Sorted by residual: angle pdb=" O3P MC3 K 516 " pdb=" P MC3 K 516 " pdb=" O4P MC3 K 516 " ideal model delta sigma weight residual 93.26 103.27 -10.01 3.00e+00 1.11e-01 1.11e+01 angle pdb=" O3P MC3 G 516 " pdb=" P MC3 G 516 " pdb=" O4P MC3 G 516 " ideal model delta sigma weight residual 93.26 103.24 -9.98 3.00e+00 1.11e-01 1.11e+01 angle pdb=" O3P MC3 I 516 " pdb=" P MC3 I 516 " pdb=" O4P MC3 I 516 " ideal model delta sigma weight residual 93.26 103.23 -9.97 3.00e+00 1.11e-01 1.10e+01 angle pdb=" O3P MC3 C 516 " pdb=" P MC3 C 516 " pdb=" O4P MC3 C 516 " ideal model delta sigma weight residual 93.26 103.23 -9.97 3.00e+00 1.11e-01 1.10e+01 angle pdb=" O3P MC3 E 516 " pdb=" P MC3 E 516 " pdb=" O4P MC3 E 516 " ideal model delta sigma weight residual 93.26 103.23 -9.97 3.00e+00 1.11e-01 1.10e+01 ... (remaining 64543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 15967 17.57 - 35.14: 1522 35.14 - 52.71: 531 52.71 - 70.28: 136 70.28 - 87.85: 60 Dihedral angle restraints: 18216 sinusoidal: 10068 harmonic: 8148 Sorted by residual: dihedral pdb=" C2 MC3 L 506 " pdb=" C31 MC3 L 506 " pdb=" O2 MC3 L 506 " pdb=" C32 MC3 L 506 " ideal model delta sinusoidal sigma weight residual 177.42 -95.55 -87.03 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" C2 MC3 D 515 " pdb=" C31 MC3 D 515 " pdb=" O2 MC3 D 515 " pdb=" C32 MC3 D 515 " ideal model delta sinusoidal sigma weight residual 177.42 -95.56 -87.02 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" C2 MC3 A 515 " pdb=" C31 MC3 A 515 " pdb=" O2 MC3 A 515 " pdb=" C32 MC3 A 515 " ideal model delta sinusoidal sigma weight residual 177.42 -95.57 -87.01 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 18213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1902 0.028 - 0.055: 543 0.055 - 0.083: 356 0.083 - 0.111: 54 0.111 - 0.138: 25 Chirality restraints: 2880 Sorted by residual: chirality pdb=" CA HIS K 95 " pdb=" N HIS K 95 " pdb=" C HIS K 95 " pdb=" CB HIS K 95 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA HIS E 95 " pdb=" N HIS E 95 " pdb=" C HIS E 95 " pdb=" CB HIS E 95 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA HIS J 95 " pdb=" N HIS J 95 " pdb=" C HIS J 95 " pdb=" CB HIS J 95 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 2877 not shown) Planarity restraints: 5148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR K 87 " 0.017 5.00e-02 4.00e+02 2.63e-02 1.11e+00 pdb=" N PRO K 88 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO K 88 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO K 88 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR L 87 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO L 88 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO L 88 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO L 88 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 87 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO F 88 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " 0.015 5.00e-02 4.00e+02 ... (remaining 5145 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.42: 15196 2.42 - 2.97: 77108 2.97 - 3.51: 94377 3.51 - 4.06: 124902 4.06 - 4.60: 185800 Nonbonded interactions: 497383 Sorted by model distance: nonbonded pdb="HE22 GLN G 49 " pdb=" HG SER L 192 " model vdw 1.879 2.100 nonbonded pdb=" HG SER E 192 " pdb="HE22 GLN F 49 " model vdw 1.886 2.100 nonbonded pdb=" HG SER B 192 " pdb="HE22 GLN C 49 " model vdw 1.887 2.100 nonbonded pdb=" HG SER H 192 " pdb="HE22 GLN I 49 " model vdw 1.891 2.100 nonbonded pdb=" HG SER I 192 " pdb="HE22 GLN J 49 " model vdw 1.895 2.100 ... (remaining 497378 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 501 or (resid 502 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 \ or name C43 or name C44)) or (resid 503 and (name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C4 \ 2 or name C43 or name C44)) or (resid 504 and (name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42)) or (resid 505 and \ (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43)) or (resid 506 and (name C34 or name C35 \ or name C36)) or (resid 507 and (name C34 or name C35)) or (resid 508 and (name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ ame C40 or name C41 or name C42)) or resid 510 or (resid 511 and (name C34 or na \ me C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 o \ r name C42 or name C43)) or resid 512 or (resid 513 and (name C35 or name C36 or \ name C37 or name C38 or name C39)) or (resid 514 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42) \ ))) selection = (chain 'B' and (resid 4 through 501 or (resid 502 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 \ or name C43 or name C44)) or (resid 503 and (name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C4 \ 2 or name C43 or name C44)) or (resid 504 and (name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42)) or (resid 505 and \ (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43)) or (resid 506 and (name C34 or name C35 \ or name C36)) or (resid 507 and (name C34 or name C35)) or (resid 508 and (name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ ame C40 or name C41 or name C42)) or resid 510 or (resid 511 and (name C34 or na \ me C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 o \ r name C42 or name C43)) or resid 512 or (resid 513 and (name C35 or name C36 or \ name C37 or name C38 or name C39)) or (resid 514 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42) \ ))) selection = (chain 'C' and (resid 4 through 501 or (resid 502 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 \ or name C43 or name C44)) or (resid 503 and (name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C4 \ 2 or name C43 or name C44)) or (resid 504 and (name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42)) or (resid 505 and \ (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43)) or (resid 506 and (name C34 or name C35 \ or name C36)) or (resid 507 and (name C34 or name C35)) or (resid 508 and (name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ ame C40 or name C41 or name C42)) or resid 510 or (resid 511 and (name C34 or na \ me C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 o \ r name C42 or name C43)) or resid 512 or (resid 513 and (name C35 or name C36 or \ name C37 or name C38 or name C39)) or (resid 514 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42) \ ))) selection = (chain 'D' and (resid 4 through 501 or (resid 502 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 \ or name C43 or name C44)) or (resid 503 and (name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C4 \ 2 or name C43 or name C44)) or (resid 504 and (name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42)) or (resid 505 and \ (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43)) or (resid 506 and (name C34 or name C35 \ or name C36)) or (resid 507 and (name C34 or name C35)) or (resid 508 and (name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ ame C40 or name C41 or name C42)) or resid 510 or (resid 511 and (name C34 or na \ me C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 o \ r name C42 or name C43)) or resid 512 or (resid 513 and (name C35 or name C36 or \ name C37 or name C38 or name C39)) or (resid 514 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42) \ ))) selection = (chain 'E' and (resid 4 through 501 or (resid 502 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 \ or name C43 or name C44)) or (resid 503 and (name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C4 \ 2 or name C43 or name C44)) or (resid 504 and (name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42)) or (resid 505 and \ (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43)) or (resid 506 and (name C34 or name C35 \ or name C36)) or (resid 507 and (name C34 or name C35)) or (resid 508 and (name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ ame C40 or name C41 or name C42)) or resid 510 or (resid 511 and (name C34 or na \ me C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 o \ r name C42 or name C43)) or resid 512 or (resid 513 and (name C35 or name C36 or \ name C37 or name C38 or name C39)) or (resid 514 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42) \ ))) selection = (chain 'F' and (resid 4 through 222 or (resid 501 and (name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 \ or name C42 or name C43 or name C44)) or resid 502 through 505 or (resid 506 and \ (name C34 or name C35 or name C36)) or (resid 507 and (name C34 or name C35)) o \ r (resid 508 and (name C33 or name C34 or name C35 or name C36 or name C37 or na \ me C38 or name C39 or name C40 or name C41 or name C42)) or resid 510 through 51 \ 1 or (resid 512 and (name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C4 \ 4)) or (resid 513 and (name C35 or name C36 or name C37 or name C38 or name C39) \ ) or resid 514)) selection = (chain 'G' and (resid 4 through 501 or (resid 502 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 \ or name C43 or name C44)) or (resid 503 and (name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C4 \ 2 or name C43 or name C44)) or (resid 504 and (name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42)) or (resid 505 and \ (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43)) or (resid 506 and (name C34 or name C35 \ or name C36)) or (resid 507 and (name C34 or name C35)) or (resid 508 and (name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ ame C40 or name C41 or name C42)) or resid 510 or (resid 511 and (name C34 or na \ me C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 o \ r name C42 or name C43)) or resid 512 or (resid 513 and (name C35 or name C36 or \ name C37 or name C38 or name C39)) or (resid 514 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42) \ ))) selection = (chain 'H' and (resid 4 through 501 or (resid 502 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 \ or name C43 or name C44)) or (resid 503 and (name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C4 \ 2 or name C43 or name C44)) or (resid 504 and (name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42)) or (resid 505 and \ (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43)) or (resid 506 and (name C34 or name C35 \ or name C36)) or (resid 507 and (name C34 or name C35)) or (resid 508 and (name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ ame C40 or name C41 or name C42)) or resid 510 or (resid 511 and (name C34 or na \ me C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 o \ r name C42 or name C43)) or resid 512 or (resid 513 and (name C35 or name C36 or \ name C37 or name C38 or name C39)) or (resid 514 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42) \ ))) selection = (chain 'I' and (resid 4 through 501 or (resid 502 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 \ or name C43 or name C44)) or (resid 503 and (name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C4 \ 2 or name C43 or name C44)) or (resid 504 and (name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42)) or (resid 505 and \ (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43)) or (resid 506 and (name C34 or name C35 \ or name C36)) or (resid 507 and (name C34 or name C35)) or (resid 508 and (name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ ame C40 or name C41 or name C42)) or resid 510 or (resid 511 and (name C34 or na \ me C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 o \ r name C42 or name C43)) or resid 512 or (resid 513 and (name C35 or name C36 or \ name C37 or name C38 or name C39)) or (resid 514 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42) \ ))) selection = (chain 'J' and (resid 4 through 501 or (resid 502 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 \ or name C43 or name C44)) or (resid 503 and (name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C4 \ 2 or name C43 or name C44)) or (resid 504 and (name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42)) or (resid 505 and \ (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43)) or (resid 506 and (name C34 or name C35 \ or name C36)) or (resid 507 and (name C34 or name C35)) or (resid 508 and (name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ ame C40 or name C41 or name C42)) or resid 510 or (resid 511 and (name C34 or na \ me C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 o \ r name C42 or name C43)) or resid 512 or (resid 513 and (name C35 or name C36 or \ name C37 or name C38 or name C39)) or (resid 514 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42) \ ))) selection = (chain 'K' and (resid 4 through 501 or (resid 502 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 \ or name C43 or name C44)) or (resid 503 and (name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C4 \ 2 or name C43 or name C44)) or (resid 504 and (name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42)) or (resid 505 and \ (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43)) or (resid 506 and (name C34 or name C35 \ or name C36)) or (resid 507 and (name C34 or name C35)) or (resid 508 and (name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ ame C40 or name C41 or name C42)) or resid 510 or (resid 511 and (name C34 or na \ me C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 o \ r name C42 or name C43)) or resid 512 or (resid 513 and (name C35 or name C36 or \ name C37 or name C38 or name C39)) or (resid 514 and (name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42) \ ))) selection = (chain 'L' and (resid 4 through 222 or (resid 501 and (name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 \ or name C42 or name C43 or name C44)) or resid 502 through 505 or (resid 506 and \ (name C34 or name C35 or name C36)) or (resid 507 and (name C34 or name C35)) o \ r (resid 508 and (name C33 or name C34 or name C35 or name C36 or name C37 or na \ me C38 or name C39 or name C40 or name C41 or name C42)) or resid 510 through 51 \ 1 or (resid 512 and (name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C4 \ 4)) or (resid 513 and (name C35 or name C36 or name C37 or name C38 or name C39) \ ) or resid 514)) } 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: 5.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 34.150 Find NCS groups from input model: 0.580 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:9.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 0.052 20040 Z= 0.252 Angle : 0.597 10.010 26544 Z= 0.269 Chirality : 0.036 0.138 2880 Planarity : 0.003 0.026 3048 Dihedral : 16.970 87.849 7692 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.67 % Allowed : 19.33 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.47 (0.18), residues: 2160 helix: 1.48 (0.13), residues: 1644 sheet: 0.19 (0.37), residues: 204 loop : -0.98 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 76 TYR 0.017 0.001 TYR I 220 PHE 0.008 0.001 PHE H 190 TRP 0.002 0.001 TRP G 78 HIS 0.002 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00510 (20004) covalent geometry : angle 0.59687 (26472) SS BOND : bond 0.00097 ( 36) SS BOND : angle 0.52132 ( 72) hydrogen bonds : bond 0.18356 ( 1357) hydrogen bonds : angle 7.76504 ( 4035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Evaluate side-chains 327 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 315 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7281 (mt-10) REVERT: B 218 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7314 (mt-10) REVERT: C 218 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7332 (mt-10) REVERT: D 218 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7314 (mt-10) REVERT: E 218 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7316 (mt-10) REVERT: F 218 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7344 (mt-10) REVERT: G 218 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7326 (mt-10) REVERT: H 218 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7308 (mt-10) REVERT: I 218 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7231 (mt-10) REVERT: J 218 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7319 (mt-10) REVERT: K 218 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7312 (mt-10) REVERT: L 218 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7312 (mt-10) outliers start: 12 outliers final: 22 residues processed: 315 average time/residue: 1.0361 time to fit residues: 375.6637 Evaluate side-chains 278 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 256 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 87 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.0570 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.0020 chunk 77 optimal weight: 0.0370 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.199883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.142185 restraints weight = 50321.008| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.30 r_work: 0.3392 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 20040 Z= 0.130 Angle : 0.488 4.987 26544 Z= 0.259 Chirality : 0.037 0.111 2880 Planarity : 0.004 0.032 3048 Dihedral : 12.928 80.369 4100 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.28 % Allowed : 20.72 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.08 (0.18), residues: 2160 helix: 2.74 (0.13), residues: 1656 sheet: 0.13 (0.35), residues: 204 loop : -0.78 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 33 TYR 0.008 0.001 TYR J 66 PHE 0.008 0.001 PHE L 190 TRP 0.005 0.001 TRP A 25 HIS 0.004 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00253 (20004) covalent geometry : angle 0.48746 (26472) SS BOND : bond 0.00231 ( 36) SS BOND : angle 0.51002 ( 72) hydrogen bonds : bond 0.05599 ( 1357) hydrogen bonds : angle 5.09380 ( 4035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Evaluate side-chains 327 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 304 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 GLN cc_start: 0.7243 (tp40) cc_final: 0.6993 (tt0) REVERT: B 218 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7334 (mt-10) REVERT: C 164 GLN cc_start: 0.7257 (tp40) cc_final: 0.7013 (tt0) REVERT: D 164 GLN cc_start: 0.7310 (tp40) cc_final: 0.7106 (tt0) REVERT: E 164 GLN cc_start: 0.7214 (tp40) cc_final: 0.6946 (tt0) REVERT: E 218 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7341 (mt-10) REVERT: F 164 GLN cc_start: 0.7249 (tp40) cc_final: 0.6989 (tt0) REVERT: G 164 GLN cc_start: 0.7354 (tp40) cc_final: 0.7102 (tt0) REVERT: G 218 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7329 (mt-10) REVERT: H 33 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8338 (mtm180) REVERT: H 164 GLN cc_start: 0.7271 (tp40) cc_final: 0.7005 (tt0) REVERT: I 164 GLN cc_start: 0.7242 (tp40) cc_final: 0.6989 (tt0) REVERT: I 218 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7306 (mt-10) REVERT: J 164 GLN cc_start: 0.7342 (tp40) cc_final: 0.7087 (tt0) REVERT: J 218 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7329 (mt-10) REVERT: K 33 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8337 (mtm180) REVERT: K 164 GLN cc_start: 0.7275 (tp40) cc_final: 0.7003 (tt0) REVERT: L 164 GLN cc_start: 0.7247 (tp40) cc_final: 0.7003 (tt0) REVERT: L 218 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7325 (mt-10) outliers start: 23 outliers final: 16 residues processed: 315 average time/residue: 0.9765 time to fit residues: 361.1789 Evaluate side-chains 311 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 293 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain K residue 33 ARG Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain L residue 93 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 56 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 212 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 116 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 66 optimal weight: 0.4980 chunk 170 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.196656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144735 restraints weight = 50121.718| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 0.89 r_work: 0.3408 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20040 Z= 0.131 Angle : 0.503 5.735 26544 Z= 0.254 Chirality : 0.038 0.119 2880 Planarity : 0.004 0.028 3048 Dihedral : 11.079 72.334 4068 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.61 % Allowed : 19.06 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.54 (0.18), residues: 2160 helix: 3.11 (0.12), residues: 1668 sheet: 0.07 (0.34), residues: 204 loop : -0.90 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 33 TYR 0.015 0.001 TYR A 220 PHE 0.015 0.001 PHE E 190 TRP 0.003 0.001 TRP A 25 HIS 0.002 0.001 HIS L 74 Details of bonding type rmsd covalent geometry : bond 0.00304 (20004) covalent geometry : angle 0.50270 (26472) SS BOND : bond 0.00173 ( 36) SS BOND : angle 0.64393 ( 72) hydrogen bonds : bond 0.03956 ( 1357) hydrogen bonds : angle 4.35670 ( 4035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Evaluate side-chains 354 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 289 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.8054 (t80) cc_final: 0.7698 (t80) REVERT: B 164 GLN cc_start: 0.7505 (tp40) cc_final: 0.7260 (tt0) REVERT: C 164 GLN cc_start: 0.7429 (tp40) cc_final: 0.7157 (tt0) REVERT: C 204 MET cc_start: 0.8600 (mmm) cc_final: 0.8383 (mmm) REVERT: D 164 GLN cc_start: 0.7458 (tp40) cc_final: 0.7233 (tt0) REVERT: D 220 TYR cc_start: 0.8074 (t80) cc_final: 0.7716 (t80) REVERT: E 164 GLN cc_start: 0.7450 (tp40) cc_final: 0.7198 (tt0) REVERT: F 164 GLN cc_start: 0.7443 (tp40) cc_final: 0.7161 (tt0) REVERT: F 204 MET cc_start: 0.8605 (mmm) cc_final: 0.8321 (mmm) REVERT: G 164 GLN cc_start: 0.7471 (tp40) cc_final: 0.7187 (tt0) REVERT: H 164 GLN cc_start: 0.7402 (tp40) cc_final: 0.7117 (tt0) REVERT: H 220 TYR cc_start: 0.8109 (t80) cc_final: 0.7791 (t80) REVERT: I 164 GLN cc_start: 0.7527 (tp40) cc_final: 0.7284 (tt0) REVERT: J 164 GLN cc_start: 0.7448 (tp40) cc_final: 0.7181 (tt0) REVERT: K 164 GLN cc_start: 0.7423 (tp40) cc_final: 0.7132 (tt0) REVERT: K 220 TYR cc_start: 0.8120 (t80) cc_final: 0.7799 (t80) REVERT: L 164 GLN cc_start: 0.7499 (tp40) cc_final: 0.7256 (tt0) outliers start: 65 outliers final: 33 residues processed: 321 average time/residue: 0.8559 time to fit residues: 327.9167 Evaluate side-chains 316 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 283 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 147 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 197 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 94 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 108 optimal weight: 50.0000 chunk 66 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 158 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 132 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN C 171 GLN F 171 GLN G 171 GLN I 171 GLN J 171 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.194802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.149817 restraints weight = 48352.379| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 0.86 r_work: 0.3363 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 20040 Z= 0.115 Angle : 0.472 4.470 26544 Z= 0.239 Chirality : 0.036 0.115 2880 Planarity : 0.003 0.030 3048 Dihedral : 10.260 71.250 4068 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.61 % Allowed : 20.61 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.85 (0.18), residues: 2160 helix: 3.40 (0.12), residues: 1656 sheet: 0.11 (0.34), residues: 204 loop : -1.02 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 33 TYR 0.009 0.001 TYR E 146 PHE 0.013 0.001 PHE E 190 TRP 0.003 0.001 TRP A 25 HIS 0.002 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00253 (20004) covalent geometry : angle 0.47169 (26472) SS BOND : bond 0.00141 ( 36) SS BOND : angle 0.64244 ( 72) hydrogen bonds : bond 0.03401 ( 1357) hydrogen bonds : angle 4.13543 ( 4035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Evaluate side-chains 354 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 289 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.8013 (t80) cc_final: 0.7528 (t80) REVERT: C 43 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: F 43 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: I 204 MET cc_start: 0.8726 (mmm) cc_final: 0.8466 (mmp) outliers start: 65 outliers final: 40 residues processed: 316 average time/residue: 0.9123 time to fit residues: 344.1545 Evaluate side-chains 313 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 271 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 222 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 222 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 147 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 199 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 144 optimal weight: 50.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 GLN L 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.191998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.146390 restraints weight = 48472.562| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.03 r_work: 0.3280 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20040 Z= 0.169 Angle : 0.525 11.984 26544 Z= 0.265 Chirality : 0.038 0.182 2880 Planarity : 0.004 0.028 3048 Dihedral : 10.617 71.121 4068 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.17 % Allowed : 20.50 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.82 (0.18), residues: 2160 helix: 3.38 (0.12), residues: 1656 sheet: 0.14 (0.34), residues: 204 loop : -1.08 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 180 TYR 0.011 0.002 TYR J 66 PHE 0.017 0.002 PHE L 190 TRP 0.005 0.001 TRP C 181 HIS 0.003 0.001 HIS L 74 Details of bonding type rmsd covalent geometry : bond 0.00392 (20004) covalent geometry : angle 0.52399 (26472) SS BOND : bond 0.00251 ( 36) SS BOND : angle 0.81470 ( 72) hydrogen bonds : bond 0.03627 ( 1357) hydrogen bonds : angle 4.12823 ( 4035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Evaluate side-chains 332 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 275 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.8032 (t80) cc_final: 0.7545 (t80) REVERT: B 204 MET cc_start: 0.8766 (mmm) cc_final: 0.8510 (mmp) REVERT: E 204 MET cc_start: 0.8764 (mmm) cc_final: 0.8446 (mmp) REVERT: I 204 MET cc_start: 0.8792 (mmm) cc_final: 0.8470 (mmp) REVERT: L 204 MET cc_start: 0.8763 (mmm) cc_final: 0.8507 (mmp) outliers start: 57 outliers final: 46 residues processed: 299 average time/residue: 0.8114 time to fit residues: 295.4386 Evaluate side-chains 313 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 267 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 222 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 222 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 37 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 159 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 99 optimal weight: 0.6980 chunk 204 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN D 171 GLN H 171 GLN K 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.193129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.141136 restraints weight = 50156.786| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.16 r_work: 0.3362 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20040 Z= 0.181 Angle : 0.529 9.581 26544 Z= 0.268 Chirality : 0.038 0.190 2880 Planarity : 0.004 0.030 3048 Dihedral : 10.780 69.765 4068 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.00 % Allowed : 19.22 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.79 (0.17), residues: 2160 helix: 3.31 (0.12), residues: 1668 sheet: 0.14 (0.34), residues: 204 loop : -0.97 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 76 TYR 0.012 0.002 TYR E 220 PHE 0.017 0.002 PHE B 190 TRP 0.005 0.001 TRP J 181 HIS 0.003 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00423 (20004) covalent geometry : angle 0.52721 (26472) SS BOND : bond 0.00278 ( 36) SS BOND : angle 0.90753 ( 72) hydrogen bonds : bond 0.03591 ( 1357) hydrogen bonds : angle 4.11758 ( 4035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Evaluate side-chains 342 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 288 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 TYR cc_start: 0.8018 (t80) cc_final: 0.7511 (t80) REVERT: B 204 MET cc_start: 0.8730 (mmm) cc_final: 0.8402 (mmp) REVERT: C 43 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: E 204 MET cc_start: 0.8711 (mmm) cc_final: 0.8375 (mmp) REVERT: F 43 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: I 204 MET cc_start: 0.8730 (mmm) cc_final: 0.8405 (mmp) REVERT: L 204 MET cc_start: 0.8715 (mmm) cc_final: 0.8390 (mmp) outliers start: 54 outliers final: 44 residues processed: 314 average time/residue: 0.7715 time to fit residues: 294.9079 Evaluate side-chains 318 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 272 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 222 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 222 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 101 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 18 optimal weight: 50.0000 chunk 73 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 114 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.188345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144768 restraints weight = 48412.300| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.06 r_work: 0.3229 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 20040 Z= 0.273 Angle : 0.606 4.883 26544 Z= 0.309 Chirality : 0.043 0.133 2880 Planarity : 0.005 0.034 3048 Dihedral : 11.806 68.773 4068 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.72 % Allowed : 18.22 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.43 (0.18), residues: 2160 helix: 3.05 (0.12), residues: 1668 sheet: 0.06 (0.34), residues: 204 loop : -1.08 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 76 TYR 0.015 0.003 TYR C 220 PHE 0.021 0.003 PHE B 190 TRP 0.008 0.002 TRP C 181 HIS 0.004 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00655 (20004) covalent geometry : angle 0.60403 (26472) SS BOND : bond 0.00454 ( 36) SS BOND : angle 1.11553 ( 72) hydrogen bonds : bond 0.04142 ( 1357) hydrogen bonds : angle 4.24598 ( 4035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Evaluate side-chains 370 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 303 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 204 MET cc_start: 0.8782 (mmm) cc_final: 0.8431 (mmp) REVERT: I 204 MET cc_start: 0.8791 (mmm) cc_final: 0.8443 (mmp) outliers start: 67 outliers final: 50 residues processed: 336 average time/residue: 0.6821 time to fit residues: 279.5263 Evaluate side-chains 345 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 295 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 222 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 222 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 175 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 212 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 180 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.192188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.140308 restraints weight = 50181.677| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.26 r_work: 0.3312 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 20040 Z= 0.162 Angle : 0.524 4.451 26544 Z= 0.267 Chirality : 0.038 0.119 2880 Planarity : 0.004 0.031 3048 Dihedral : 11.001 65.273 4068 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.33 % Allowed : 18.56 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.69 (0.18), residues: 2160 helix: 3.24 (0.12), residues: 1668 sheet: 0.07 (0.34), residues: 204 loop : -0.96 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 76 TYR 0.016 0.002 TYR E 92 PHE 0.015 0.002 PHE A 190 TRP 0.006 0.001 TRP D 45 HIS 0.003 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00374 (20004) covalent geometry : angle 0.52240 (26472) SS BOND : bond 0.00223 ( 36) SS BOND : angle 0.92593 ( 72) hydrogen bonds : bond 0.03433 ( 1357) hydrogen bonds : angle 4.09689 ( 4035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Evaluate side-chains 354 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 294 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: A 220 TYR cc_start: 0.7871 (t80) cc_final: 0.7595 (t80) REVERT: B 204 MET cc_start: 0.8761 (mmm) cc_final: 0.8408 (mmp) REVERT: E 204 MET cc_start: 0.8755 (mmm) cc_final: 0.8386 (mmp) REVERT: H 43 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: I 204 MET cc_start: 0.8757 (mmm) cc_final: 0.8397 (mmp) REVERT: K 43 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: L 204 MET cc_start: 0.8739 (mmm) cc_final: 0.8386 (mmp) outliers start: 60 outliers final: 47 residues processed: 323 average time/residue: 0.7196 time to fit residues: 284.9592 Evaluate side-chains 345 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 295 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 222 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 222 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 118 optimal weight: 0.1980 chunk 127 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 195 optimal weight: 0.0170 chunk 209 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.190930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.146858 restraints weight = 48428.204| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.04 r_work: 0.3264 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20040 Z= 0.131 Angle : 0.507 4.455 26544 Z= 0.259 Chirality : 0.037 0.195 2880 Planarity : 0.004 0.028 3048 Dihedral : 10.497 61.968 4068 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.39 % Allowed : 18.50 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.84 (0.18), residues: 2160 helix: 3.38 (0.12), residues: 1668 sheet: -0.20 (0.33), residues: 204 loop : -0.88 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 76 TYR 0.016 0.002 TYR I 92 PHE 0.014 0.001 PHE A 190 TRP 0.005 0.001 TRP D 45 HIS 0.002 0.000 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00298 (20004) covalent geometry : angle 0.50573 (26472) SS BOND : bond 0.00199 ( 36) SS BOND : angle 0.87033 ( 72) hydrogen bonds : bond 0.03193 ( 1357) hydrogen bonds : angle 4.02861 ( 4035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Evaluate side-chains 359 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 298 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: H 43 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: K 43 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7735 (mp0) outliers start: 61 outliers final: 49 residues processed: 330 average time/residue: 0.7395 time to fit residues: 297.2757 Evaluate side-chains 348 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 296 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 219 ILE Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 222 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 13 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 180 optimal weight: 40.0000 chunk 74 optimal weight: 0.8980 chunk 90 optimal weight: 50.0000 chunk 143 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.192810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.141177 restraints weight = 50403.142| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.26 r_work: 0.3327 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20040 Z= 0.138 Angle : 0.503 4.460 26544 Z= 0.257 Chirality : 0.037 0.120 2880 Planarity : 0.004 0.026 3048 Dihedral : 10.050 59.184 4068 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.83 % Allowed : 18.94 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.94 (0.17), residues: 2160 helix: 3.46 (0.12), residues: 1668 sheet: -0.19 (0.33), residues: 204 loop : -0.83 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 33 TYR 0.018 0.002 TYR L 220 PHE 0.015 0.001 PHE A 190 TRP 0.004 0.001 TRP D 45 HIS 0.002 0.000 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00316 (20004) covalent geometry : angle 0.50124 (26472) SS BOND : bond 0.00204 ( 36) SS BOND : angle 0.87007 ( 72) hydrogen bonds : bond 0.03110 ( 1357) hydrogen bonds : angle 4.00035 ( 4035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue MET 102 is missing expected H atoms. Skipping. Evaluate side-chains 349 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 298 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: A 220 TYR cc_start: 0.7849 (t80) cc_final: 0.7408 (t80) REVERT: B 204 MET cc_start: 0.8717 (mmm) cc_final: 0.8406 (mmp) REVERT: E 204 MET cc_start: 0.8714 (mmm) cc_final: 0.8402 (mmp) REVERT: I 204 MET cc_start: 0.8754 (mmm) cc_final: 0.8453 (mmp) REVERT: L 204 MET cc_start: 0.8719 (mmm) cc_final: 0.8412 (mmp) outliers start: 51 outliers final: 45 residues processed: 321 average time/residue: 0.7124 time to fit residues: 281.5606 Evaluate side-chains 341 residues out of total 1980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 295 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 222 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 123 optimal weight: 0.0470 chunk 202 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 141 optimal weight: 0.3980 chunk 126 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.190091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.142592 restraints weight = 48536.168| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 0.89 r_work: 0.3300 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20040 Z= 0.131 Angle : 0.512 18.778 26544 Z= 0.261 Chirality : 0.037 0.147 2880 Planarity : 0.003 0.026 3048 Dihedral : 9.867 59.912 4068 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.67 % Allowed : 18.83 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.97 (0.17), residues: 2160 helix: 3.48 (0.12), residues: 1668 sheet: -0.24 (0.33), residues: 204 loop : -0.83 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 180 TYR 0.016 0.002 TYR I 92 PHE 0.014 0.001 PHE A 190 TRP 0.004 0.001 TRP A 45 HIS 0.002 0.000 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00300 (20004) covalent geometry : angle 0.51060 (26472) SS BOND : bond 0.00193 ( 36) SS BOND : angle 0.85579 ( 72) hydrogen bonds : bond 0.03062 ( 1357) hydrogen bonds : angle 3.97647 ( 4035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12072.95 seconds wall clock time: 204 minutes 55.73 seconds (12295.73 seconds total)