Starting phenix.real_space_refine on Sun Feb 8 08:31:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z9g_73942/02_2026/9z9g_73942_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z9g_73942/02_2026/9z9g_73942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z9g_73942/02_2026/9z9g_73942_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z9g_73942/02_2026/9z9g_73942_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z9g_73942/02_2026/9z9g_73942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z9g_73942/02_2026/9z9g_73942.map" } resolution = 2.5 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= 0.042 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 12 5.49 5 S 96 5.16 5 C 13788 2.51 5 N 2868 2.21 5 O 3828 1.98 5 H 17820 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 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: 38412 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "B" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "C" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "D" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "E" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "F" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "G" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "H" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "I" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "K" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "L" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 168 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 168 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 114 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 168 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 114 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 168 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 114 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 168 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 114 Chain: "F" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 168 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 114 Chain: "G" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 168 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 114 Chain: "H" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 168 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 114 Chain: "I" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 168 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 114 Chain: "J" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 168 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 114 Chain: "K" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 168 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 114 Chain: "L" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 168 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 653 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 14, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 114 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "H" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "J" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "K" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "L" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Time building chain proxies: 7.33, per 1000 atoms: 0.19 Number of scatterers: 38412 At special positions: 0 Unit cell: (100.2, 101.803, 145.09, 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 12 15.00 O 3828 8.00 N 2868 7.00 C 13788 6.00 H 17820 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: 3.48 Conformation dependent library (CDL) restraints added in 978.1 milliseconds 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 79.2% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 removed outlier: 3.640A pdb=" N HIS A 17 " --> pdb=" O ASN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 33 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 100 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 141 through 169 Processing helix chain 'A' and resid 193 through 223 Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.641A pdb=" N HIS B 17 " --> pdb=" O ASN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 33 Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 100 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 141 through 169 Processing helix chain 'B' and resid 193 through 223 Processing helix chain 'C' and resid 4 through 17 removed outlier: 3.640A pdb=" N HIS C 17 " --> pdb=" O ASN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 33 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 100 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 141 through 169 Processing helix chain 'C' and resid 193 through 223 Processing helix chain 'D' and resid 4 through 17 removed outlier: 3.640A pdb=" N HIS D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 33 Processing helix chain 'D' and resid 33 through 40 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 100 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 141 through 169 Processing helix chain 'D' and resid 193 through 223 Processing helix chain 'E' and resid 4 through 17 removed outlier: 3.640A pdb=" N HIS E 17 " --> pdb=" O ASN E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 33 Processing helix chain 'E' and resid 33 through 40 Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 100 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 141 through 169 Processing helix chain 'E' and resid 193 through 223 Processing helix chain 'F' and resid 4 through 17 removed outlier: 3.640A pdb=" N HIS F 17 " --> pdb=" O ASN F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 33 Processing helix chain 'F' and resid 33 through 40 Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 100 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 141 through 169 Processing helix chain 'F' and resid 193 through 223 Processing helix chain 'G' and resid 4 through 17 removed outlier: 3.640A pdb=" N HIS G 17 " --> pdb=" O ASN G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 33 Processing helix chain 'G' and resid 33 through 40 Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 73 through 100 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 141 through 169 Processing helix chain 'G' and resid 193 through 223 Processing helix chain 'H' and resid 4 through 17 removed outlier: 3.640A pdb=" N HIS H 17 " --> pdb=" O ASN H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 33 Processing helix chain 'H' and resid 33 through 40 Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 73 through 100 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 141 through 169 Processing helix chain 'H' and resid 193 through 223 Processing helix chain 'I' and resid 4 through 17 removed outlier: 3.640A pdb=" N HIS I 17 " --> pdb=" O ASN I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 33 Processing helix chain 'I' and resid 33 through 40 Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 46 through 48 No H-bonds generated for 'chain 'I' and resid 46 through 48' Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 73 through 100 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 141 through 169 Processing helix chain 'I' and resid 193 through 223 Processing helix chain 'J' and resid 4 through 17 removed outlier: 3.640A pdb=" N HIS J 17 " --> pdb=" O ASN J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 33 Processing helix chain 'J' and resid 33 through 40 Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 46 through 48 No H-bonds generated for 'chain 'J' and resid 46 through 48' Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 73 through 100 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 141 through 169 Processing helix chain 'J' and resid 193 through 223 Processing helix chain 'K' and resid 4 through 17 removed outlier: 3.640A pdb=" N HIS K 17 " --> pdb=" O ASN K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 33 Processing helix chain 'K' and resid 33 through 40 Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 46 through 48 No H-bonds generated for 'chain 'K' and resid 46 through 48' Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 73 through 100 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 141 through 169 Processing helix chain 'K' and resid 193 through 223 Processing helix chain 'L' and resid 4 through 17 removed outlier: 3.640A pdb=" N HIS L 17 " --> pdb=" O ASN L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 33 Processing helix chain 'L' and resid 33 through 40 Processing helix chain 'L' and resid 40 through 45 Processing helix chain 'L' and resid 46 through 48 No H-bonds generated for 'chain 'L' and resid 46 through 48' Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 73 through 100 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 141 through 169 Processing helix chain 'L' and resid 193 through 223 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.524A 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: 3.524A 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: 3.524A 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: 3.524A 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: 3.524A 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: 3.524A 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: 3.524A 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: 3.524A 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: 3.524A 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: 3.524A 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: 3.524A 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: 3.524A pdb=" N THR L 53 " --> pdb=" O PHE L 190 " (cutoff:3.500A) 1332 hydrogen bonds defined for protein. 3960 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: 9.06 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 17808 1.03 - 1.23: 24 1.23 - 1.42: 8004 1.42 - 1.62: 12060 1.62 - 1.81: 108 Bond restraints: 38004 Sorted by residual: bond pdb=" ND1 HIS K 98 " pdb=" HD1 HIS K 98 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" ND1 HIS C 95 " pdb=" HD1 HIS C 95 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" ND1 HIS L 95 " pdb=" HD1 HIS L 95 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" ND1 HIS C 98 " pdb=" HD1 HIS C 98 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" ND1 HIS I 98 " pdb=" HD1 HIS I 98 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 37999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 64857 2.28 - 4.56: 2109 4.56 - 6.85: 6 6.85 - 9.13: 0 9.13 - 11.41: 12 Bond angle restraints: 66984 Sorted by residual: angle pdb=" O3P MC3 G 502 " pdb=" P MC3 G 502 " pdb=" O4P MC3 G 502 " ideal model delta sigma weight residual 93.26 104.67 -11.41 3.00e+00 1.11e-01 1.45e+01 angle pdb=" O3P MC3 D 508 " pdb=" P MC3 D 508 " pdb=" O4P MC3 D 508 " ideal model delta sigma weight residual 93.26 104.67 -11.41 3.00e+00 1.11e-01 1.45e+01 angle pdb=" O3P MC3 B 508 " pdb=" P MC3 B 508 " pdb=" O4P MC3 B 508 " ideal model delta sigma weight residual 93.26 104.67 -11.41 3.00e+00 1.11e-01 1.45e+01 angle pdb=" O3P MC3 K 508 " pdb=" P MC3 K 508 " pdb=" O4P MC3 K 508 " ideal model delta sigma weight residual 93.26 104.67 -11.41 3.00e+00 1.11e-01 1.45e+01 angle pdb=" O3P MC3 J 508 " pdb=" P MC3 J 508 " pdb=" O4P MC3 J 508 " ideal model delta sigma weight residual 93.26 104.64 -11.38 3.00e+00 1.11e-01 1.44e+01 ... (remaining 66979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.56: 16181 14.56 - 29.11: 1423 29.11 - 43.67: 516 43.67 - 58.22: 360 58.22 - 72.78: 72 Dihedral angle restraints: 18552 sinusoidal: 10296 harmonic: 8256 Sorted by residual: dihedral pdb=" CA ALA B 40 " pdb=" C ALA B 40 " pdb=" N ALA B 41 " pdb=" CA ALA B 41 " ideal model delta harmonic sigma weight residual -180.00 -164.10 -15.90 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ALA A 40 " pdb=" C ALA A 40 " pdb=" N ALA A 41 " pdb=" CA ALA A 41 " ideal model delta harmonic sigma weight residual -180.00 -164.11 -15.89 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ALA J 40 " pdb=" C ALA J 40 " pdb=" N ALA J 41 " pdb=" CA ALA J 41 " ideal model delta harmonic sigma weight residual -180.00 -164.11 -15.89 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 18549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2108 0.041 - 0.081: 570 0.081 - 0.122: 150 0.122 - 0.163: 16 0.163 - 0.204: 12 Chirality restraints: 2856 Sorted by residual: chirality pdb=" CA VAL H 147 " pdb=" N VAL H 147 " pdb=" C VAL H 147 " pdb=" CB VAL H 147 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL J 147 " pdb=" N VAL J 147 " pdb=" C VAL J 147 " pdb=" CB VAL J 147 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA VAL A 147 " pdb=" N VAL A 147 " pdb=" C VAL A 147 " pdb=" CB VAL A 147 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 2853 not shown) Planarity restraints: 5184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 221 " 0.012 2.00e-02 2.50e+03 2.45e-02 5.99e+00 pdb=" C HIS B 221 " -0.042 2.00e-02 2.50e+03 pdb=" O HIS B 221 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 222 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS I 221 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C HIS I 221 " 0.042 2.00e-02 2.50e+03 pdb=" O HIS I 221 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU I 222 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS L 221 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C HIS L 221 " -0.042 2.00e-02 2.50e+03 pdb=" O HIS L 221 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU L 222 " 0.014 2.00e-02 2.50e+03 ... (remaining 5181 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 9179 2.33 - 2.89: 82943 2.89 - 3.46: 99849 3.46 - 4.03: 139662 4.03 - 4.60: 212002 Nonbonded interactions: 543635 Sorted by model distance: nonbonded pdb=" HD1 HIS C 74 " pdb=" O HOH C 611 " model vdw 1.758 2.450 nonbonded pdb=" HD1 HIS L 74 " pdb=" O HOH L 611 " model vdw 1.758 2.450 nonbonded pdb=" HD1 HIS B 74 " pdb=" O HOH B 611 " model vdw 1.758 2.450 nonbonded pdb=" HD1 HIS E 74 " pdb=" O HOH E 611 " model vdw 1.758 2.450 nonbonded pdb=" HD1 HIS A 74 " pdb=" O HOH A 611 " model vdw 1.758 2.450 ... (remaining 543630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 501 or (resid 502 and (name C15 or name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 503 through 505 or (resid 506 and (name C16 or name C17 o \ r name C18 or name C19 or name C20 or name C21 or name C22)) or resid 507 throug \ h 509 or (resid 510 and (name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or nam \ e C24)) or resid 511 or (resid 512 and (name C13 or name C14 or name C15 or name \ C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or \ name C23)) or (resid 513 and (name C14 or name C15 or name C16 or name C17 or na \ me C18 or name C19 or name C20 or name C21)) or (resid 514 and (name C14 or name \ C15 or name C16 or name C17 or name C18 or name C19 or name C20)) or resid 515) \ ) selection = (chain 'B' and (resid 2 through 223 or (resid 501 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23)) or resid 502 or (resid 503 and (name C14 or name C15 o \ r name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C \ 22 or name C23)) or resid 504 or (resid 505 and (name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or nam \ e C23)) or resid 506 or (resid 507 and (name C14 or name C15 or name C16 or name \ C17 or name C18 or name C19 or name C20 or name C21)) or (resid 508 and (name C \ 13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20)) or (resid 509 and (name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)) or resid 510 through 513 \ or (resid 514 and (name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C20)) or (resid 515 and (name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22)))) selection = (chain 'C' and (resid 2 through 223 or (resid 501 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23)) or resid 502 or (resid 503 and (name C14 or name C15 o \ r name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C \ 22 or name C23)) or resid 504 or (resid 505 and (name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or nam \ e C23)) or resid 506 or (resid 507 and (name C14 or name C15 or name C16 or name \ C17 or name C18 or name C19 or name C20 or name C21)) or (resid 508 and (name C \ 13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20)) or (resid 509 and (name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)) or resid 510 through 513 \ or (resid 514 and (name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C20)) or (resid 515 and (name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22)))) selection = (chain 'D' and (resid 2 through 223 or (resid 501 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23)) or resid 502 or (resid 503 and (name C14 or name C15 o \ r name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C \ 22 or name C23)) or resid 504 or (resid 505 and (name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or nam \ e C23)) or resid 506 or (resid 507 and (name C14 or name C15 or name C16 or name \ C17 or name C18 or name C19 or name C20 or name C21)) or (resid 508 and (name C \ 13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20)) or (resid 509 and (name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)) or resid 510 through 513 \ or (resid 514 and (name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C20)) or (resid 515 and (name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22)))) selection = (chain 'E' and (resid 2 through 223 or (resid 501 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23)) or resid 502 or (resid 503 and (name C14 or name C15 o \ r name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C \ 22 or name C23)) or resid 504 or (resid 505 and (name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or nam \ e C23)) or resid 506 or (resid 507 and (name C14 or name C15 or name C16 or name \ C17 or name C18 or name C19 or name C20 or name C21)) or (resid 508 and (name C \ 13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20)) or (resid 509 and (name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)) or resid 510 through 513 \ or (resid 514 and (name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C20)) or (resid 515 and (name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22)))) selection = (chain 'F' and (resid 2 through 223 or (resid 501 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23)) or resid 502 or (resid 503 and (name C14 or name C15 o \ r name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C \ 22 or name C23)) or resid 504 or (resid 505 and (name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or nam \ e C23)) or resid 506 or (resid 507 and (name C14 or name C15 or name C16 or name \ C17 or name C18 or name C19 or name C20 or name C21)) or (resid 508 and (name C \ 13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20)) or (resid 509 and (name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)) or resid 510 through 513 \ or (resid 514 and (name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C20)) or (resid 515 and (name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22)))) selection = (chain 'G' and (resid 2 through 501 or (resid 502 and (name C15 or name C16 or n \ ame C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24)) or resid 503 through 505 or (resid 506 and (name C16 or name C17 o \ r name C18 or name C19 or name C20 or name C21 or name C22)) or resid 507 throug \ h 509 or (resid 510 and (name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or nam \ e C24)) or resid 511 or (resid 512 and (name C13 or name C14 or name C15 or name \ C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or \ name C23)) or (resid 513 and (name C14 or name C15 or name C16 or name C17 or na \ me C18 or name C19 or name C20 or name C21)) or (resid 514 and (name C14 or name \ C15 or name C16 or name C17 or name C18 or name C19 or name C20)) or resid 515) \ ) selection = (chain 'H' and (resid 2 through 223 or (resid 501 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23)) or resid 502 or (resid 503 and (name C14 or name C15 o \ r name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C \ 22 or name C23)) or resid 504 or (resid 505 and (name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or nam \ e C23)) or resid 506 or (resid 507 and (name C14 or name C15 or name C16 or name \ C17 or name C18 or name C19 or name C20 or name C21)) or (resid 508 and (name C \ 13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20)) or (resid 509 and (name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)) or resid 510 through 513 \ or (resid 514 and (name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C20)) or (resid 515 and (name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22)))) selection = (chain 'I' and (resid 2 through 223 or (resid 501 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23)) or resid 502 or (resid 503 and (name C14 or name C15 o \ r name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C \ 22 or name C23)) or resid 504 or (resid 505 and (name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or nam \ e C23)) or resid 506 or (resid 507 and (name C14 or name C15 or name C16 or name \ C17 or name C18 or name C19 or name C20 or name C21)) or (resid 508 and (name C \ 13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20)) or (resid 509 and (name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)) or resid 510 through 513 \ or (resid 514 and (name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C20)) or (resid 515 and (name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22)))) selection = (chain 'J' and (resid 2 through 223 or (resid 501 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23)) or resid 502 or (resid 503 and (name C14 or name C15 o \ r name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C \ 22 or name C23)) or resid 504 or (resid 505 and (name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or nam \ e C23)) or resid 506 or (resid 507 and (name C14 or name C15 or name C16 or name \ C17 or name C18 or name C19 or name C20 or name C21)) or (resid 508 and (name C \ 13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20)) or (resid 509 and (name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)) or resid 510 through 513 \ or (resid 514 and (name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C20)) or (resid 515 and (name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22)))) selection = (chain 'K' and (resid 2 through 223 or (resid 501 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23)) or resid 502 or (resid 503 and (name C14 or name C15 o \ r name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C \ 22 or name C23)) or resid 504 or (resid 505 and (name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or nam \ e C23)) or resid 506 or (resid 507 and (name C14 or name C15 or name C16 or name \ C17 or name C18 or name C19 or name C20 or name C21)) or (resid 508 and (name C \ 13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20)) or (resid 509 and (name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)) or resid 510 through 513 \ or (resid 514 and (name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C20)) or (resid 515 and (name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22)))) selection = (chain 'L' and (resid 2 through 223 or (resid 501 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 \ or name C22 or name C23)) or resid 502 or (resid 503 and (name C14 or name C15 o \ r name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C \ 22 or name C23)) or resid 504 or (resid 505 and (name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or nam \ e C23)) or resid 506 or (resid 507 and (name C14 or name C15 or name C16 or name \ C17 or name C18 or name C19 or name C20 or name C21)) or (resid 508 and (name C \ 13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20)) or (resid 509 and (name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)) or resid 510 through 513 \ or (resid 514 and (name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C20)) or (resid 515 and (name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22)))) } 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: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.280 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 35.710 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 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 : 0.004 0.048 20220 Z= 0.246 Angle : 1.087 11.412 26784 Z= 0.501 Chirality : 0.042 0.204 2856 Planarity : 0.004 0.037 3096 Dihedral : 14.803 72.776 7728 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.62 % Allowed : 10.49 % Favored : 88.89 % 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: 0.21 (0.16), residues: 2148 helix: 0.62 (0.12), residues: 1620 sheet: -0.05 (0.31), residues: 204 loop : -1.68 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 9 TYR 0.007 0.001 TYR E 176 PHE 0.014 0.002 PHE G 190 TRP 0.006 0.001 TRP K 181 HIS 0.004 0.001 HIS F 17 Details of bonding type rmsd covalent geometry : bond 0.00433 (20184) covalent geometry : angle 1.08763 (26712) SS BOND : bond 0.00055 ( 36) SS BOND : angle 0.91548 ( 72) hydrogen bonds : bond 0.12238 ( 1332) hydrogen bonds : angle 6.81456 ( 3960) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 236 time to evaluate : 1.203 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: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.6052 (mp0) cc_final: 0.5848 (mp0) REVERT: A 47 ASP cc_start: 0.6709 (p0) cc_final: 0.6435 (p0) REVERT: A 68 ARG cc_start: 0.7144 (ttm170) cc_final: 0.5935 (ttm170) REVERT: A 171 GLN cc_start: 0.7914 (tt0) cc_final: 0.7518 (tm-30) REVERT: A 172 LEU cc_start: 0.7001 (mp) cc_final: 0.6749 (tp) REVERT: A 173 LYS cc_start: 0.7158 (mttt) cc_final: 0.6847 (mtmm) REVERT: A 179 ASP cc_start: 0.8038 (p0) cc_final: 0.7838 (p0) REVERT: B 47 ASP cc_start: 0.6630 (p0) cc_final: 0.6245 (p0) REVERT: B 51 ASP cc_start: 0.7153 (m-30) cc_final: 0.6721 (m-30) REVERT: B 62 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7279 (tt0) REVERT: B 68 ARG cc_start: 0.7167 (ttm170) cc_final: 0.6279 (ttm170) REVERT: B 171 GLN cc_start: 0.7993 (tt0) cc_final: 0.7427 (tm-30) REVERT: B 172 LEU cc_start: 0.6934 (mp) cc_final: 0.6671 (tp) REVERT: B 173 LYS cc_start: 0.7132 (mttt) cc_final: 0.6851 (mtmm) REVERT: B 213 LEU cc_start: 0.6699 (tp) cc_final: 0.6473 (tm) REVERT: B 217 LEU cc_start: 0.6773 (mt) cc_final: 0.6569 (mt) REVERT: C 68 ARG cc_start: 0.7005 (ttm170) cc_final: 0.6422 (ttm170) REVERT: C 171 GLN cc_start: 0.7897 (tt0) cc_final: 0.7375 (tm-30) REVERT: C 172 LEU cc_start: 0.6917 (mp) cc_final: 0.6583 (tp) REVERT: C 173 LYS cc_start: 0.7076 (mttt) cc_final: 0.6700 (mtmm) REVERT: D 47 ASP cc_start: 0.6695 (p0) cc_final: 0.6416 (p0) REVERT: D 68 ARG cc_start: 0.7175 (ttm170) cc_final: 0.5992 (ttm170) REVERT: D 171 GLN cc_start: 0.7894 (tt0) cc_final: 0.7438 (tm-30) REVERT: D 172 LEU cc_start: 0.6999 (mp) cc_final: 0.6723 (tp) REVERT: D 173 LYS cc_start: 0.7055 (mttt) cc_final: 0.6754 (mtmm) REVERT: E 47 ASP cc_start: 0.6717 (p0) cc_final: 0.6374 (p0) REVERT: E 51 ASP cc_start: 0.7266 (m-30) cc_final: 0.6818 (m-30) REVERT: E 68 ARG cc_start: 0.7177 (ttm170) cc_final: 0.6289 (ttm170) REVERT: E 171 GLN cc_start: 0.8000 (tt0) cc_final: 0.7481 (tm-30) REVERT: E 172 LEU cc_start: 0.6912 (mp) cc_final: 0.6669 (tp) REVERT: E 173 LYS cc_start: 0.7091 (mttt) cc_final: 0.6807 (mtmm) REVERT: E 213 LEU cc_start: 0.6725 (tp) cc_final: 0.6491 (tm) REVERT: E 217 LEU cc_start: 0.6862 (mt) cc_final: 0.6651 (mt) REVERT: F 47 ASP cc_start: 0.6583 (p0) cc_final: 0.6361 (p0) REVERT: F 68 ARG cc_start: 0.7043 (ttm170) cc_final: 0.6424 (ttm170) REVERT: F 171 GLN cc_start: 0.7894 (tt0) cc_final: 0.7374 (tm-30) REVERT: F 172 LEU cc_start: 0.6878 (mp) cc_final: 0.6567 (tp) REVERT: F 173 LYS cc_start: 0.7066 (mttt) cc_final: 0.6689 (mtmm) REVERT: F 179 ASP cc_start: 0.8044 (p0) cc_final: 0.7828 (p0) REVERT: G 47 ASP cc_start: 0.6566 (p0) cc_final: 0.6245 (p0) REVERT: G 68 ARG cc_start: 0.7182 (ttm170) cc_final: 0.5960 (ttm170) REVERT: G 171 GLN cc_start: 0.7901 (tt0) cc_final: 0.7445 (tm-30) REVERT: G 172 LEU cc_start: 0.7006 (mp) cc_final: 0.6740 (tp) REVERT: G 173 LYS cc_start: 0.7061 (mttt) cc_final: 0.6762 (mtmm) REVERT: H 47 ASP cc_start: 0.6709 (p0) cc_final: 0.6368 (p0) REVERT: H 51 ASP cc_start: 0.7220 (m-30) cc_final: 0.6758 (m-30) REVERT: H 68 ARG cc_start: 0.7174 (ttm170) cc_final: 0.6290 (ttm170) REVERT: H 171 GLN cc_start: 0.7999 (tt0) cc_final: 0.7468 (tm-30) REVERT: H 172 LEU cc_start: 0.6901 (mp) cc_final: 0.6665 (tp) REVERT: H 173 LYS cc_start: 0.7084 (mttt) cc_final: 0.6801 (mtmm) REVERT: H 213 LEU cc_start: 0.6722 (tp) cc_final: 0.6491 (tm) REVERT: H 217 LEU cc_start: 0.6849 (mt) cc_final: 0.6636 (mt) REVERT: I 47 ASP cc_start: 0.6598 (p0) cc_final: 0.6382 (p0) REVERT: I 68 ARG cc_start: 0.7031 (ttm170) cc_final: 0.6443 (ttm170) REVERT: I 171 GLN cc_start: 0.7899 (tt0) cc_final: 0.7390 (tm-30) REVERT: I 172 LEU cc_start: 0.6890 (mp) cc_final: 0.6530 (tp) REVERT: I 173 LYS cc_start: 0.7052 (mttt) cc_final: 0.6683 (mtmm) REVERT: I 179 ASP cc_start: 0.8050 (p0) cc_final: 0.7840 (p0) REVERT: J 47 ASP cc_start: 0.6686 (p0) cc_final: 0.6414 (p0) REVERT: J 68 ARG cc_start: 0.7171 (ttm170) cc_final: 0.5943 (ttm170) REVERT: J 171 GLN cc_start: 0.7892 (tt0) cc_final: 0.7452 (tm-30) REVERT: J 172 LEU cc_start: 0.6995 (mp) cc_final: 0.6709 (tp) REVERT: J 173 LYS cc_start: 0.7074 (mttt) cc_final: 0.6770 (mtmm) REVERT: K 47 ASP cc_start: 0.6744 (p0) cc_final: 0.6399 (p0) REVERT: K 51 ASP cc_start: 0.7188 (m-30) cc_final: 0.6766 (m-30) REVERT: K 68 ARG cc_start: 0.7172 (ttm170) cc_final: 0.6280 (ttm170) REVERT: K 171 GLN cc_start: 0.7995 (tt0) cc_final: 0.7445 (tm-30) REVERT: K 172 LEU cc_start: 0.6933 (mp) cc_final: 0.6680 (tp) REVERT: K 173 LYS cc_start: 0.7138 (mttt) cc_final: 0.6861 (mtmm) REVERT: K 213 LEU cc_start: 0.6712 (tp) cc_final: 0.6485 (tm) REVERT: K 217 LEU cc_start: 0.6830 (mt) cc_final: 0.6625 (mt) REVERT: L 47 ASP cc_start: 0.6610 (p0) cc_final: 0.6395 (p0) REVERT: L 68 ARG cc_start: 0.7025 (ttm170) cc_final: 0.6406 (ttm170) REVERT: L 171 GLN cc_start: 0.7893 (tt0) cc_final: 0.7382 (tm-30) REVERT: L 172 LEU cc_start: 0.6888 (mp) cc_final: 0.6566 (tp) REVERT: L 173 LYS cc_start: 0.7081 (mttt) cc_final: 0.6712 (mtmm) REVERT: L 179 ASP cc_start: 0.8051 (p0) cc_final: 0.7845 (p0) outliers start: 12 outliers final: 12 residues processed: 248 average time/residue: 1.1678 time to fit residues: 335.0947 Evaluate side-chains 182 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 149 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.0010 chunk 77 optimal weight: 1.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- 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 = 0.4350 r_free = 0.4350 target = 0.223502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.181688 restraints weight = 40569.925| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 0.82 r_work: 0.3724 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20220 Z= 0.139 Angle : 0.536 4.530 26784 Z= 0.281 Chirality : 0.040 0.126 2856 Planarity : 0.004 0.022 3096 Dihedral : 10.489 86.092 3792 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.87 % Allowed : 10.60 % Favored : 88.53 % 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: 2.44 (0.17), residues: 2148 helix: 2.49 (0.12), residues: 1620 sheet: -0.39 (0.30), residues: 204 loop : -1.72 (0.27), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 180 TYR 0.014 0.002 TYR D 66 PHE 0.018 0.002 PHE J 190 TRP 0.007 0.001 TRP K 181 HIS 0.003 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00298 (20184) covalent geometry : angle 0.53236 (26712) SS BOND : bond 0.00123 ( 36) SS BOND : angle 1.38581 ( 72) hydrogen bonds : bond 0.03703 ( 1332) hydrogen bonds : angle 4.86535 ( 3960) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 1.030 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: A 47 ASP cc_start: 0.8205 (p0) cc_final: 0.7513 (p0) REVERT: A 68 ARG cc_start: 0.8478 (ttm170) cc_final: 0.8145 (ttm170) REVERT: B 47 ASP cc_start: 0.8162 (p0) cc_final: 0.7596 (p0) REVERT: B 51 ASP cc_start: 0.8263 (m-30) cc_final: 0.7981 (m-30) REVERT: B 68 ARG cc_start: 0.8473 (ttm170) cc_final: 0.8094 (ttm170) REVERT: C 68 ARG cc_start: 0.8502 (ttm170) cc_final: 0.8081 (ttm170) REVERT: D 47 ASP cc_start: 0.8232 (p0) cc_final: 0.7761 (p0) REVERT: D 68 ARG cc_start: 0.8496 (ttm170) cc_final: 0.8174 (ttm170) REVERT: E 47 ASP cc_start: 0.8256 (p0) cc_final: 0.7584 (p0) REVERT: E 51 ASP cc_start: 0.8242 (m-30) cc_final: 0.7960 (m-30) REVERT: E 68 ARG cc_start: 0.8481 (ttm170) cc_final: 0.8103 (ttm170) REVERT: F 47 ASP cc_start: 0.8166 (p0) cc_final: 0.7699 (p0) REVERT: F 68 ARG cc_start: 0.8521 (ttm170) cc_final: 0.8109 (ttm170) REVERT: G 47 ASP cc_start: 0.8097 (p0) cc_final: 0.7462 (p0) REVERT: G 68 ARG cc_start: 0.8490 (ttm170) cc_final: 0.8179 (ttm170) REVERT: H 47 ASP cc_start: 0.8273 (p0) cc_final: 0.7622 (p0) REVERT: H 51 ASP cc_start: 0.8231 (m-30) cc_final: 0.7946 (m-30) REVERT: H 68 ARG cc_start: 0.8515 (ttm170) cc_final: 0.8124 (ttm170) REVERT: I 47 ASP cc_start: 0.8160 (p0) cc_final: 0.7711 (p0) REVERT: I 68 ARG cc_start: 0.8515 (ttm170) cc_final: 0.8111 (ttm170) REVERT: J 47 ASP cc_start: 0.8230 (p0) cc_final: 0.7758 (p0) REVERT: J 68 ARG cc_start: 0.8492 (ttm170) cc_final: 0.8176 (ttm170) REVERT: K 47 ASP cc_start: 0.8269 (p0) cc_final: 0.7635 (p0) REVERT: K 51 ASP cc_start: 0.8246 (m-30) cc_final: 0.7974 (m-30) REVERT: K 68 ARG cc_start: 0.8607 (ttm170) cc_final: 0.8195 (ttm170) REVERT: L 47 ASP cc_start: 0.8122 (p0) cc_final: 0.7500 (p0) REVERT: L 62 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8518 (tt0) REVERT: L 68 ARG cc_start: 0.8517 (ttm170) cc_final: 0.8097 (ttm170) outliers start: 17 outliers final: 16 residues processed: 193 average time/residue: 1.3226 time to fit residues: 290.1245 Evaluate side-chains 169 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 149 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 102 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 chunk 199 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN B 58 GLN C 58 GLN D 58 GLN E 58 GLN F 58 GLN G 58 GLN H 58 GLN I 58 GLN J 58 GLN K 58 GLN L 58 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.217167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.186073 restraints weight = 39869.457| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 0.47 r_work: 0.3842 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work: 0.3589 rms_B_bonded: 4.51 restraints_weight: 0.1250 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20220 Z= 0.185 Angle : 0.587 5.614 26784 Z= 0.306 Chirality : 0.041 0.137 2856 Planarity : 0.004 0.023 3096 Dihedral : 8.881 50.152 3792 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.13 % Allowed : 10.19 % Favored : 88.68 % 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: 2.47 (0.18), residues: 2148 helix: 2.53 (0.12), residues: 1620 sheet: -0.33 (0.33), residues: 204 loop : -1.87 (0.27), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 193 TYR 0.017 0.002 TYR A 66 PHE 0.022 0.002 PHE G 190 TRP 0.011 0.002 TRP B 181 HIS 0.003 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00425 (20184) covalent geometry : angle 0.58138 (26712) SS BOND : bond 0.00366 ( 36) SS BOND : angle 1.65089 ( 72) hydrogen bonds : bond 0.04236 ( 1332) hydrogen bonds : angle 5.03724 ( 3960) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.036 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: A 47 ASP cc_start: 0.8541 (p0) cc_final: 0.8097 (p0) REVERT: A 171 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: B 47 ASP cc_start: 0.8357 (p0) cc_final: 0.7698 (p0) REVERT: B 68 ARG cc_start: 0.8511 (ttm170) cc_final: 0.8239 (ttm170) REVERT: C 68 ARG cc_start: 0.8535 (ttm170) cc_final: 0.8126 (ttm170) REVERT: D 43 GLU cc_start: 0.8400 (mp0) cc_final: 0.8190 (mp0) REVERT: D 47 ASP cc_start: 0.8545 (p0) cc_final: 0.7891 (p0) REVERT: D 171 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: E 47 ASP cc_start: 0.8464 (p0) cc_final: 0.7954 (p0) REVERT: E 68 ARG cc_start: 0.8512 (ttm170) cc_final: 0.8241 (ttm170) REVERT: G 47 ASP cc_start: 0.8445 (p0) cc_final: 0.7841 (p0) REVERT: G 171 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: H 47 ASP cc_start: 0.8467 (p0) cc_final: 0.7613 (p0) REVERT: H 68 ARG cc_start: 0.8516 (ttm170) cc_final: 0.8240 (ttm170) REVERT: J 43 GLU cc_start: 0.8405 (mp0) cc_final: 0.8195 (mp0) REVERT: J 47 ASP cc_start: 0.8542 (p0) cc_final: 0.7883 (p0) REVERT: J 171 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: K 47 ASP cc_start: 0.8483 (p0) cc_final: 0.7752 (p0) REVERT: K 68 ARG cc_start: 0.8506 (ttm170) cc_final: 0.8232 (ttm170) REVERT: L 62 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8697 (mt-10) outliers start: 22 outliers final: 17 residues processed: 171 average time/residue: 1.3449 time to fit residues: 259.4014 Evaluate side-chains 160 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 171 GLN Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 149 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 166 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.216293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.181705 restraints weight = 40047.590| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 0.53 r_work: 0.3764 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work: 0.3516 rms_B_bonded: 4.53 restraints_weight: 0.1250 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20220 Z= 0.145 Angle : 0.510 4.221 26784 Z= 0.268 Chirality : 0.038 0.116 2856 Planarity : 0.004 0.041 3096 Dihedral : 7.584 50.269 3792 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.29 % Allowed : 10.55 % Favored : 88.17 % 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: 2.74 (0.18), residues: 2148 helix: 2.76 (0.12), residues: 1620 sheet: -0.20 (0.34), residues: 204 loop : -2.06 (0.26), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 33 TYR 0.015 0.002 TYR G 66 PHE 0.023 0.002 PHE A 190 TRP 0.009 0.002 TRP D 181 HIS 0.001 0.000 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00318 (20184) covalent geometry : angle 0.50486 (26712) SS BOND : bond 0.00239 ( 36) SS BOND : angle 1.45985 ( 72) hydrogen bonds : bond 0.03584 ( 1332) hydrogen bonds : angle 4.78622 ( 3960) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.995 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: A 47 ASP cc_start: 0.8436 (p0) cc_final: 0.8011 (p0) REVERT: A 171 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: B 43 GLU cc_start: 0.8241 (mp0) cc_final: 0.8021 (mp0) REVERT: B 47 ASP cc_start: 0.8343 (p0) cc_final: 0.7693 (p0) REVERT: C 68 ARG cc_start: 0.8564 (ttm170) cc_final: 0.8149 (ttm170) REVERT: D 47 ASP cc_start: 0.8485 (p0) cc_final: 0.8055 (p0) REVERT: D 171 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: E 47 ASP cc_start: 0.8351 (p0) cc_final: 0.8085 (p0) REVERT: F 68 ARG cc_start: 0.8582 (ttm170) cc_final: 0.8189 (ttm170) REVERT: G 47 ASP cc_start: 0.8357 (p0) cc_final: 0.7964 (p0) REVERT: G 171 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: H 62 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8576 (tt0) REVERT: H 68 ARG cc_start: 0.8554 (ttm170) cc_final: 0.8250 (ttm170) REVERT: I 47 ASP cc_start: 0.8473 (p0) cc_final: 0.8172 (p0) REVERT: I 68 ARG cc_start: 0.8544 (ttm170) cc_final: 0.8157 (ttm170) REVERT: J 47 ASP cc_start: 0.8465 (p0) cc_final: 0.8035 (p0) REVERT: J 171 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: K 47 ASP cc_start: 0.8438 (p0) cc_final: 0.7709 (p0) REVERT: L 68 ARG cc_start: 0.8566 (ttm170) cc_final: 0.8094 (ttm170) outliers start: 25 outliers final: 18 residues processed: 186 average time/residue: 1.3649 time to fit residues: 287.3499 Evaluate side-chains 160 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 171 GLN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 149 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 193 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4262 r_free = 0.4262 target = 0.214883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.180657 restraints weight = 40119.033| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 0.51 r_work: 0.3746 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work: 0.3549 rms_B_bonded: 3.84 restraints_weight: 0.1250 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20220 Z= 0.146 Angle : 0.521 4.243 26784 Z= 0.273 Chirality : 0.039 0.118 2856 Planarity : 0.004 0.032 3096 Dihedral : 7.225 53.017 3792 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.90 % Allowed : 9.16 % Favored : 88.94 % 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: 2.76 (0.18), residues: 2148 helix: 2.79 (0.12), residues: 1620 sheet: -0.26 (0.34), residues: 204 loop : -2.09 (0.26), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 33 TYR 0.015 0.001 TYR G 66 PHE 0.021 0.002 PHE D 190 TRP 0.009 0.001 TRP E 181 HIS 0.002 0.000 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00328 (20184) covalent geometry : angle 0.51641 (26712) SS BOND : bond 0.00261 ( 36) SS BOND : angle 1.39743 ( 72) hydrogen bonds : bond 0.03644 ( 1332) hydrogen bonds : angle 4.74978 ( 3960) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.763 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: A 47 ASP cc_start: 0.8437 (p0) cc_final: 0.7842 (p0) REVERT: A 171 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: B 47 ASP cc_start: 0.8387 (p0) cc_final: 0.7746 (p0) REVERT: C 68 ARG cc_start: 0.8531 (ttm170) cc_final: 0.8028 (ttm170) REVERT: D 47 ASP cc_start: 0.8463 (p0) cc_final: 0.7877 (p0) REVERT: D 171 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: E 47 ASP cc_start: 0.8350 (p0) cc_final: 0.7507 (p0) REVERT: G 47 ASP cc_start: 0.8331 (p0) cc_final: 0.7781 (p0) REVERT: G 171 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: H 47 ASP cc_start: 0.8251 (p0) cc_final: 0.7920 (p0) REVERT: H 51 ASP cc_start: 0.8373 (m-30) cc_final: 0.8134 (m-30) REVERT: H 62 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8535 (tt0) REVERT: I 68 ARG cc_start: 0.8513 (ttm170) cc_final: 0.8051 (ttm170) REVERT: J 47 ASP cc_start: 0.8431 (p0) cc_final: 0.7849 (p0) REVERT: J 171 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: K 47 ASP cc_start: 0.8455 (p0) cc_final: 0.7621 (p0) outliers start: 37 outliers final: 28 residues processed: 181 average time/residue: 1.2787 time to fit residues: 263.9617 Evaluate side-chains 174 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 171 GLN Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 187 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 157 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.212954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.178519 restraints weight = 40177.863| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 0.51 r_work: 0.3732 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work: 0.3508 rms_B_bonded: 4.17 restraints_weight: 0.1250 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 20220 Z= 0.173 Angle : 0.544 4.459 26784 Z= 0.288 Chirality : 0.040 0.122 2856 Planarity : 0.004 0.024 3096 Dihedral : 7.622 57.406 3792 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.80 % Allowed : 8.38 % Favored : 89.81 % 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: 2.49 (0.18), residues: 2148 helix: 2.59 (0.12), residues: 1620 sheet: -0.28 (0.34), residues: 204 loop : -2.18 (0.26), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 33 TYR 0.016 0.002 TYR G 66 PHE 0.024 0.002 PHE J 190 TRP 0.010 0.002 TRP E 181 HIS 0.003 0.001 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00390 (20184) covalent geometry : angle 0.53854 (26712) SS BOND : bond 0.00344 ( 36) SS BOND : angle 1.59434 ( 72) hydrogen bonds : bond 0.03816 ( 1332) hydrogen bonds : angle 4.72168 ( 3960) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8527 (p0) cc_final: 0.7893 (p0) REVERT: A 171 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: C 62 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8657 (tt0) REVERT: C 68 ARG cc_start: 0.8577 (ttm170) cc_final: 0.8067 (ttm170) REVERT: D 47 ASP cc_start: 0.8484 (p0) cc_final: 0.7898 (p0) REVERT: D 171 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7574 (tm-30) REVERT: E 47 ASP cc_start: 0.8337 (p0) cc_final: 0.7599 (p0) REVERT: G 47 ASP cc_start: 0.8372 (p0) cc_final: 0.7820 (p0) REVERT: G 171 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: H 47 ASP cc_start: 0.8314 (p0) cc_final: 0.7956 (p0) REVERT: H 51 ASP cc_start: 0.8466 (m-30) cc_final: 0.8218 (m-30) REVERT: H 62 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: J 47 ASP cc_start: 0.8474 (p0) cc_final: 0.7862 (p0) REVERT: J 171 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: K 47 ASP cc_start: 0.8468 (p0) cc_final: 0.7610 (p0) outliers start: 35 outliers final: 26 residues processed: 194 average time/residue: 1.2930 time to fit residues: 287.5424 Evaluate side-chains 172 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 171 GLN Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 187 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 193 optimal weight: 0.9980 chunk 195 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 163 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.213478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.178842 restraints weight = 40374.794| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 0.52 r_work: 0.3737 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work: 0.3523 rms_B_bonded: 4.10 restraints_weight: 0.1250 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20220 Z= 0.130 Angle : 0.496 5.061 26784 Z= 0.259 Chirality : 0.038 0.113 2856 Planarity : 0.003 0.022 3096 Dihedral : 7.051 59.289 3792 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.85 % Allowed : 7.97 % Favored : 90.17 % 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: 2.73 (0.18), residues: 2148 helix: 2.79 (0.12), residues: 1620 sheet: -0.26 (0.34), residues: 204 loop : -2.18 (0.25), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.014 0.001 TYR G 66 PHE 0.020 0.001 PHE D 190 TRP 0.009 0.001 TRP A 181 HIS 0.002 0.001 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00289 (20184) covalent geometry : angle 0.49232 (26712) SS BOND : bond 0.00229 ( 36) SS BOND : angle 1.30513 ( 72) hydrogen bonds : bond 0.03414 ( 1332) hydrogen bonds : angle 4.59281 ( 3960) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8416 (p0) cc_final: 0.7945 (p0) REVERT: A 171 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: B 47 ASP cc_start: 0.8270 (p0) cc_final: 0.7469 (p0) REVERT: C 62 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8636 (tt0) REVERT: C 68 ARG cc_start: 0.8539 (ttm170) cc_final: 0.8032 (ttm170) REVERT: D 47 ASP cc_start: 0.8415 (p0) cc_final: 0.7926 (p0) REVERT: D 171 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: E 47 ASP cc_start: 0.8211 (p0) cc_final: 0.7659 (p0) REVERT: G 47 ASP cc_start: 0.8286 (p0) cc_final: 0.7839 (p0) REVERT: G 171 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: H 47 ASP cc_start: 0.8260 (p0) cc_final: 0.7444 (p0) REVERT: H 62 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: I 62 GLU cc_start: 0.8799 (tt0) cc_final: 0.8503 (tt0) REVERT: J 47 ASP cc_start: 0.8372 (p0) cc_final: 0.7887 (p0) REVERT: J 171 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: K 47 ASP cc_start: 0.8305 (p0) cc_final: 0.7736 (p0) outliers start: 36 outliers final: 30 residues processed: 183 average time/residue: 1.2526 time to fit residues: 262.7206 Evaluate side-chains 184 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 171 GLN Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 187 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 119 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 189 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.213564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.179363 restraints weight = 40319.998| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 0.52 r_work: 0.3745 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work: 0.3522 rms_B_bonded: 4.25 restraints_weight: 0.1250 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 20220 Z= 0.122 Angle : 0.488 5.225 26784 Z= 0.253 Chirality : 0.038 0.113 2856 Planarity : 0.003 0.023 3096 Dihedral : 6.668 59.229 3792 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.54 % Allowed : 7.77 % Favored : 90.69 % 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: 2.83 (0.17), residues: 2148 helix: 2.90 (0.12), residues: 1620 sheet: -0.34 (0.35), residues: 132 loop : -2.00 (0.22), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 33 TYR 0.013 0.001 TYR J 66 PHE 0.020 0.001 PHE A 190 TRP 0.008 0.001 TRP K 181 HIS 0.002 0.001 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00271 (20184) covalent geometry : angle 0.48467 (26712) SS BOND : bond 0.00209 ( 36) SS BOND : angle 1.22287 ( 72) hydrogen bonds : bond 0.03238 ( 1332) hydrogen bonds : angle 4.50686 ( 3960) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8413 (p0) cc_final: 0.7929 (p0) REVERT: A 171 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7579 (tm-30) REVERT: B 47 ASP cc_start: 0.8120 (p0) cc_final: 0.7629 (p0) REVERT: C 68 ARG cc_start: 0.8538 (ttm170) cc_final: 0.8043 (ttm170) REVERT: D 47 ASP cc_start: 0.8420 (p0) cc_final: 0.7915 (p0) REVERT: D 171 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: E 47 ASP cc_start: 0.8209 (p0) cc_final: 0.7660 (p0) REVERT: F 47 ASP cc_start: 0.8249 (p0) cc_final: 0.7707 (p0) REVERT: F 62 GLU cc_start: 0.8717 (tt0) cc_final: 0.8418 (tt0) REVERT: G 47 ASP cc_start: 0.8276 (p0) cc_final: 0.7825 (p0) REVERT: G 171 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: H 47 ASP cc_start: 0.8152 (p0) cc_final: 0.7533 (p0) REVERT: H 62 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8595 (tt0) REVERT: J 47 ASP cc_start: 0.8388 (p0) cc_final: 0.7888 (p0) REVERT: J 171 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: K 47 ASP cc_start: 0.8224 (p0) cc_final: 0.7702 (p0) outliers start: 30 outliers final: 25 residues processed: 178 average time/residue: 1.2107 time to fit residues: 247.2102 Evaluate side-chains 178 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 171 GLN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 149 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 84 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.212433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.178135 restraints weight = 40422.613| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 0.52 r_work: 0.3724 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work: 0.3503 rms_B_bonded: 4.21 restraints_weight: 0.1250 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20220 Z= 0.149 Angle : 0.514 4.500 26784 Z= 0.268 Chirality : 0.039 0.120 2856 Planarity : 0.004 0.023 3096 Dihedral : 7.041 57.935 3792 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.75 % Allowed : 7.82 % Favored : 90.43 % 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: 2.76 (0.17), residues: 2148 helix: 2.84 (0.12), residues: 1620 sheet: -0.30 (0.35), residues: 132 loop : -2.00 (0.22), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.015 0.002 TYR A 66 PHE 0.022 0.002 PHE D 190 TRP 0.009 0.002 TRP H 181 HIS 0.002 0.001 HIS L 74 Details of bonding type rmsd covalent geometry : bond 0.00336 (20184) covalent geometry : angle 0.50936 (26712) SS BOND : bond 0.00276 ( 36) SS BOND : angle 1.41773 ( 72) hydrogen bonds : bond 0.03488 ( 1332) hydrogen bonds : angle 4.55398 ( 3960) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8439 (p0) cc_final: 0.7880 (p0) REVERT: A 171 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: B 47 ASP cc_start: 0.8226 (p0) cc_final: 0.7672 (p0) REVERT: C 68 ARG cc_start: 0.8558 (ttm170) cc_final: 0.8051 (ttm170) REVERT: D 47 ASP cc_start: 0.8460 (p0) cc_final: 0.7963 (p0) REVERT: D 171 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7554 (tm-30) REVERT: E 47 ASP cc_start: 0.8237 (p0) cc_final: 0.7680 (p0) REVERT: F 47 ASP cc_start: 0.8200 (p0) cc_final: 0.7518 (p0) REVERT: F 62 GLU cc_start: 0.8799 (tt0) cc_final: 0.8543 (tt0) REVERT: G 47 ASP cc_start: 0.8322 (p0) cc_final: 0.7875 (p0) REVERT: G 171 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: H 47 ASP cc_start: 0.8115 (p0) cc_final: 0.7579 (p0) REVERT: H 62 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: I 62 GLU cc_start: 0.8816 (tt0) cc_final: 0.8503 (tt0) REVERT: J 47 ASP cc_start: 0.8415 (p0) cc_final: 0.7915 (p0) REVERT: J 171 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: K 47 ASP cc_start: 0.8303 (p0) cc_final: 0.7747 (p0) REVERT: L 47 ASP cc_start: 0.8323 (p0) cc_final: 0.7589 (p0) outliers start: 34 outliers final: 29 residues processed: 183 average time/residue: 1.2315 time to fit residues: 258.9875 Evaluate side-chains 186 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 171 GLN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain J residue 187 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 187 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 100 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 213 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.213612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.179390 restraints weight = 40482.003| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 0.51 r_work: 0.3734 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work: 0.3486 rms_B_bonded: 4.54 restraints_weight: 0.1250 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 20220 Z= 0.113 Angle : 0.474 4.530 26784 Z= 0.246 Chirality : 0.037 0.110 2856 Planarity : 0.003 0.024 3096 Dihedral : 6.587 56.611 3792 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.44 % Allowed : 8.28 % Favored : 90.28 % 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: 2.92 (0.18), residues: 2148 helix: 2.99 (0.12), residues: 1620 sheet: -0.35 (0.35), residues: 132 loop : -2.08 (0.22), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 33 TYR 0.013 0.001 TYR G 66 PHE 0.018 0.001 PHE E 190 TRP 0.008 0.001 TRP A 181 HIS 0.002 0.001 HIS G 74 Details of bonding type rmsd covalent geometry : bond 0.00249 (20184) covalent geometry : angle 0.47116 (26712) SS BOND : bond 0.00174 ( 36) SS BOND : angle 1.18021 ( 72) hydrogen bonds : bond 0.03112 ( 1332) hydrogen bonds : angle 4.44557 ( 3960) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8320 (p0) cc_final: 0.7870 (p0) REVERT: A 171 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: B 47 ASP cc_start: 0.8077 (p0) cc_final: 0.7608 (p0) REVERT: C 62 GLU cc_start: 0.8800 (tt0) cc_final: 0.8499 (tt0) REVERT: C 68 ARG cc_start: 0.8560 (ttm170) cc_final: 0.8053 (ttm170) REVERT: D 47 ASP cc_start: 0.8401 (p0) cc_final: 0.7860 (p0) REVERT: D 171 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: E 47 ASP cc_start: 0.8194 (p0) cc_final: 0.7663 (p0) REVERT: F 47 ASP cc_start: 0.8088 (p0) cc_final: 0.7657 (p0) REVERT: F 62 GLU cc_start: 0.8801 (tt0) cc_final: 0.8530 (tt0) REVERT: G 47 ASP cc_start: 0.8261 (p0) cc_final: 0.7783 (p0) REVERT: G 171 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: H 47 ASP cc_start: 0.8043 (p0) cc_final: 0.7551 (p0) REVERT: I 62 GLU cc_start: 0.8798 (tt0) cc_final: 0.8517 (tt0) REVERT: J 47 ASP cc_start: 0.8354 (p0) cc_final: 0.7812 (p0) REVERT: J 171 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7566 (tm-30) REVERT: K 47 ASP cc_start: 0.8168 (p0) cc_final: 0.7679 (p0) REVERT: L 47 ASP cc_start: 0.8167 (p0) cc_final: 0.7710 (p0) outliers start: 28 outliers final: 23 residues processed: 188 average time/residue: 1.2625 time to fit residues: 272.9996 Evaluate side-chains 179 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain G residue 171 GLN Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 171 GLN Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 149 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 149 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 181 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.212471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.177986 restraints weight = 40351.733| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 0.53 r_work: 0.3713 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work: 0.3487 rms_B_bonded: 4.29 restraints_weight: 0.1250 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20220 Z= 0.145 Angle : 0.511 5.012 26784 Z= 0.266 Chirality : 0.039 0.118 2856 Planarity : 0.003 0.024 3096 Dihedral : 6.885 56.781 3792 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.75 % Allowed : 8.64 % Favored : 89.61 % 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: 2.83 (0.17), residues: 2148 helix: 2.91 (0.12), residues: 1620 sheet: -0.25 (0.35), residues: 132 loop : -2.07 (0.22), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 33 TYR 0.014 0.002 TYR G 66 PHE 0.022 0.002 PHE G 190 TRP 0.008 0.001 TRP A 181 HIS 0.002 0.001 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00328 (20184) covalent geometry : angle 0.50683 (26712) SS BOND : bond 0.00271 ( 36) SS BOND : angle 1.35670 ( 72) hydrogen bonds : bond 0.03388 ( 1332) hydrogen bonds : angle 4.50725 ( 3960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11976.11 seconds wall clock time: 203 minutes 13.08 seconds (12193.08 seconds total)