Starting phenix.real_space_refine on Sun Aug 24 20:11:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b64_15862/08_2025/8b64_15862.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b64_15862/08_2025/8b64_15862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.589 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8b64_15862/08_2025/8b64_15862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b64_15862/08_2025/8b64_15862.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b64_15862/08_2025/8b64_15862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b64_15862/08_2025/8b64_15862.map" } resolution = 2.589 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 7 5.49 5 Mg 34 5.21 5 S 82 5.16 5 C 15257 2.51 5 N 3052 2.21 5 O 3245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21678 Number of models: 1 Model: "" Number of chains: 66 Chain: "a" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "e" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "D" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "b" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "A" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "E" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "X" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 490 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 5, 'TRANS': 57} Chain: "L" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2227 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 267} Chain: "M" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2422 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain: "H" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1943 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 224} Chain: "d" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "B" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "t" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 342 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "S" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "T" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "s" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 342 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "U" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 195 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "u" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 309 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "r" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 342 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "O" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "R" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 303 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "o" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 411 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "n" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "K" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 339 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "N" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "k" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 437 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "j" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "I" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "J" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 339 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "i" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 437 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "g" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "F" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "G" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "f" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "a" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'SPO:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "b" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'SPO': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'SPO:plan-5': 2} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 246 Unusual residues: {'3PE': 1, 'BCL': 1, 'BPH': 1, 'U10': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'U10:plan-6': 3, 'U10:plan-7': 3, 'U10:plan-8': 3, 'U10:plan-9': 3, 'U10:plan-10': 3, 'U10:plan-11': 3, 'U10:plan-4': 2, 'U10:plan-5': 2, 'U10:plan-3': 1} Unresolved non-hydrogen planarities: 92 Chain: "M" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 456 Unusual residues: {' FE': 1, '3PE': 2, 'BCL': 3, 'BPH': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "d" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'3PE': 2, 'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'SPO:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "t" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "S" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'SPO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'SPO:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "T" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "s" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "U" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 2} Unresolved non-hydrogen planarities: 12 Chain: "r" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'SPO:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'SPO:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "o" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "n" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 136 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'SPO:plan-5': 2} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'SPO:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "J" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'SPO:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "i" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'SPO:plan-5': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.85, per 1000 atoms: 0.22 Number of scatterers: 21678 At special positions: 0 Unit cell: (101.077, 126.76, 138.359, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 82 16.00 P 7 15.00 Mg 34 11.99 O 3245 8.00 N 3052 7.00 C 15257 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 842.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4202 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 9 sheets defined 75.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'a' and resid 3 through 10 Processing helix chain 'a' and resid 12 through 38 removed outlier: 3.522A pdb=" N SER a 37 " --> pdb=" O LEU a 33 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR a 38 " --> pdb=" O ILE a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 39 through 42 Processing helix chain 'e' and resid 3 through 10 Processing helix chain 'e' and resid 12 through 38 Processing helix chain 'e' and resid 39 through 41 No H-bonds generated for 'chain 'e' and resid 39 through 41' Processing helix chain 'e' and resid 42 through 52 Processing helix chain 'D' and resid 13 through 46 Processing helix chain 'b' and resid 3 through 10 Processing helix chain 'b' and resid 12 through 37 Processing helix chain 'b' and resid 42 through 52 Processing helix chain 'A' and resid 13 through 46 Processing helix chain 'E' and resid 13 through 46 Processing helix chain 'X' and resid 14 through 53 Proline residue: X 36 - end of helix Processing helix chain 'X' and resid 55 through 60 removed outlier: 3.511A pdb=" N HIS X 59 " --> pdb=" O GLU X 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 10 Processing helix chain 'L' and resid 31 through 57 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 79 through 82 Processing helix chain 'L' and resid 83 through 112 Processing helix chain 'L' and resid 115 through 133 Processing helix chain 'L' and resid 133 through 139 Processing helix chain 'L' and resid 141 through 145 removed outlier: 3.671A pdb=" N TYR L 144 " --> pdb=" O SER L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 163 Processing helix chain 'L' and resid 164 through 165 No H-bonds generated for 'chain 'L' and resid 164 through 165' Processing helix chain 'L' and resid 166 through 169 Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 221 Processing helix chain 'L' and resid 225 through 251 removed outlier: 3.503A pdb=" N SER L 251 " --> pdb=" O CYS L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 263 Processing helix chain 'L' and resid 269 through 274 removed outlier: 4.722A pdb=" N ASP L 274 " --> pdb=" O PRO L 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 29 Processing helix chain 'M' and resid 36 through 40 removed outlier: 3.831A pdb=" N TRP M 40 " --> pdb=" O ILE M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 78 removed outlier: 3.611A pdb=" N GLY M 55 " --> pdb=" O LEU M 51 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR M 56 " --> pdb=" O GLY M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 87 Processing helix chain 'M' and resid 97 through 101 Processing helix chain 'M' and resid 106 through 109 Processing helix chain 'M' and resid 110 through 138 removed outlier: 3.733A pdb=" N LEU M 138 " --> pdb=" O ARG M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 160 removed outlier: 3.546A pdb=" N SER M 150 " --> pdb=" O TRP M 146 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA M 151 " --> pdb=" O ALA M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 167 Processing helix chain 'M' and resid 168 through 172 removed outlier: 3.861A pdb=" N VAL M 171 " --> pdb=" O SER M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 191 removed outlier: 3.901A pdb=" N LEU M 181 " --> pdb=" O ILE M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 196 Processing helix chain 'M' and resid 197 through 224 Processing helix chain 'M' and resid 225 through 228 Processing helix chain 'M' and resid 231 through 238 Processing helix chain 'M' and resid 240 through 255 Processing helix chain 'M' and resid 261 through 285 removed outlier: 3.569A pdb=" N ARG M 265 " --> pdb=" O GLU M 261 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR M 275 " --> pdb=" O ALA M 271 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE M 280 " --> pdb=" O LEU M 276 " (cutoff:3.500A) Processing helix chain 'M' and resid 291 through 299 Processing helix chain 'H' and resid 12 through 35 Processing helix chain 'H' and resid 76 through 83 Processing helix chain 'H' and resid 106 through 111 Processing helix chain 'H' and resid 112 through 116 Processing helix chain 'H' and resid 138 through 140 No H-bonds generated for 'chain 'H' and resid 138 through 140' Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'H' and resid 211 through 216 removed outlier: 4.304A pdb=" N ASP H 216 " --> pdb=" O SER H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 241 Processing helix chain 'd' and resid 3 through 10 Processing helix chain 'd' and resid 12 through 38 Processing helix chain 'd' and resid 42 through 52 Processing helix chain 'B' and resid 13 through 46 Processing helix chain 't' and resid 13 through 38 Processing helix chain 't' and resid 39 through 41 No H-bonds generated for 'chain 't' and resid 39 through 41' Processing helix chain 't' and resid 42 through 52 Processing helix chain 'S' and resid 14 through 46 Processing helix chain 'T' and resid 14 through 46 Processing helix chain 's' and resid 13 through 38 Processing helix chain 's' and resid 42 through 52 Processing helix chain 'U' and resid 21 through 45 Processing helix chain 'u' and resid 16 through 38 Processing helix chain 'u' and resid 42 through 51 Processing helix chain 'r' and resid 13 through 38 Processing helix chain 'r' and resid 42 through 52 Processing helix chain 'O' and resid 13 through 46 Processing helix chain 'R' and resid 13 through 46 Processing helix chain 'o' and resid 6 through 11 removed outlier: 3.701A pdb=" N VAL o 10 " --> pdb=" O LYS o 6 " (cutoff:3.500A) Processing helix chain 'o' and resid 12 through 38 Processing helix chain 'o' and resid 42 through 52 Processing helix chain 'n' and resid 2 through 10 removed outlier: 4.190A pdb=" N TYR n 5 " --> pdb=" O SER n 2 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 38 Processing helix chain 'n' and resid 42 through 52 Processing helix chain 'K' and resid 13 through 46 Processing helix chain 'N' and resid 13 through 46 Processing helix chain 'k' and resid 3 through 10 Processing helix chain 'k' and resid 12 through 37 Processing helix chain 'k' and resid 42 through 52 Processing helix chain 'j' and resid 3 through 10 Processing helix chain 'j' and resid 12 through 38 Processing helix chain 'j' and resid 42 through 52 Processing helix chain 'I' and resid 13 through 46 Processing helix chain 'J' and resid 13 through 46 Processing helix chain 'i' and resid 3 through 10 Processing helix chain 'i' and resid 12 through 38 Processing helix chain 'i' and resid 42 through 52 Processing helix chain 'g' and resid 3 through 10 Processing helix chain 'g' and resid 12 through 38 Processing helix chain 'g' and resid 42 through 52 Processing helix chain 'F' and resid 13 through 46 Processing helix chain 'G' and resid 13 through 46 Processing helix chain 'f' and resid 3 through 10 Processing helix chain 'f' and resid 12 through 38 Processing helix chain 'f' and resid 39 through 41 No H-bonds generated for 'chain 'f' and resid 39 through 41' Processing helix chain 'f' and resid 42 through 52 Processing sheet with id=AA1, first strand: chain 'L' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'L' and resid 65 through 66 Processing sheet with id=AA3, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.462A pdb=" N GLN M 11 " --> pdb=" O SER H 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'H' and resid 5 through 7 removed outlier: 6.968A pdb=" N PHE H 10 " --> pdb=" O PHE H 6 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 63 through 65 Processing sheet with id=AA7, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'H' and resid 134 through 136 removed outlier: 6.155A pdb=" N GLY H 164 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU H 185 " --> pdb=" O GLY H 164 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE H 166 " --> pdb=" O VAL H 183 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL H 183 " --> pdb=" O ILE H 166 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP H 168 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU H 181 " --> pdb=" O ASP H 168 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TRP H 170 " --> pdb=" O ARG H 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 134 through 136 removed outlier: 3.910A pdb=" N GLY H 164 " --> pdb=" O VAL H 155 " (cutoff:3.500A) 1319 hydrogen bonds defined for protein. 3723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.72 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.37: 6366 1.37 - 1.57: 15420 1.57 - 1.77: 431 1.77 - 1.98: 159 1.98 - 2.18: 136 Bond restraints: 22512 Sorted by residual: bond pdb=" C4 U10 L 305 " pdb=" O4 U10 L 305 " ideal model delta sigma weight residual 1.230 1.421 -0.191 2.00e-02 2.50e+03 9.10e+01 bond pdb=" C3 U10 L 305 " pdb=" O3 U10 L 305 " ideal model delta sigma weight residual 1.230 1.418 -0.188 2.00e-02 2.50e+03 8.80e+01 bond pdb=" C23 SPO M 404 " pdb=" C25 SPO M 404 " ideal model delta sigma weight residual 1.448 1.636 -0.188 2.00e-02 2.50e+03 8.80e+01 bond pdb=" C3 U10 M 403 " pdb=" O3 U10 M 403 " ideal model delta sigma weight residual 1.230 1.417 -0.187 2.00e-02 2.50e+03 8.78e+01 bond pdb=" C3 U10 L 303 " pdb=" O3 U10 L 303 " ideal model delta sigma weight residual 1.230 1.415 -0.185 2.00e-02 2.50e+03 8.57e+01 ... (remaining 22507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.58: 30252 10.58 - 21.16: 315 21.16 - 31.74: 196 31.74 - 42.32: 146 42.32 - 52.90: 87 Bond angle restraints: 30996 Sorted by residual: angle pdb=" C34 SPO M 404 " pdb=" C33 SPO M 404 " pdb=" C35 SPO M 404 " ideal model delta sigma weight residual 115.46 62.56 52.90 3.00e+00 1.11e-01 3.11e+02 angle pdb=" C34 SPO d 102 " pdb=" C33 SPO d 102 " pdb=" C35 SPO d 102 " ideal model delta sigma weight residual 115.46 63.19 52.27 3.00e+00 1.11e-01 3.04e+02 angle pdb=" C10 U10 L 305 " pdb=" C9 U10 L 305 " pdb=" C11 U10 L 305 " ideal model delta sigma weight residual 120.00 67.77 52.23 3.00e+00 1.11e-01 3.03e+02 angle pdb=" C25 U10 L 303 " pdb=" C24 U10 L 303 " pdb=" C26 U10 L 303 " ideal model delta sigma weight residual 120.00 67.80 52.20 3.00e+00 1.11e-01 3.03e+02 angle pdb=" C34 SPO i 102 " pdb=" C33 SPO i 102 " pdb=" C35 SPO i 102 " ideal model delta sigma weight residual 115.46 63.31 52.15 3.00e+00 1.11e-01 3.02e+02 ... (remaining 30991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 11426 35.99 - 71.97: 417 71.97 - 107.96: 100 107.96 - 143.94: 4 143.94 - 179.93: 26 Dihedral angle restraints: 11973 sinusoidal: 5480 harmonic: 6493 Sorted by residual: dihedral pdb=" C1 BCL b 102 " pdb=" C2 BCL b 102 " pdb=" C3 BCL b 102 " pdb=" C5 BCL b 102 " ideal model delta sinusoidal sigma weight residual -180.00 -0.07 -179.93 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL a 100 " pdb=" C2 BCL a 100 " pdb=" C3 BCL a 100 " pdb=" C5 BCL a 100 " ideal model delta sinusoidal sigma weight residual -180.00 -0.08 -179.92 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL f 101 " pdb=" C2 BCL f 101 " pdb=" C3 BCL f 101 " pdb=" C5 BCL f 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.09 -179.91 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 11970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2432 0.043 - 0.085: 580 0.085 - 0.128: 91 0.128 - 0.171: 10 0.171 - 0.214: 2 Chirality restraints: 3115 Sorted by residual: chirality pdb=" C2C BPH L 302 " pdb=" C1C BPH L 302 " pdb=" C3C BPH L 302 " pdb=" CMC BPH L 302 " both_signs ideal model delta sigma weight residual False -2.81 -2.60 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C2C BPH M 408 " pdb=" C1C BPH M 408 " pdb=" C3C BPH M 408 " pdb=" CMC BPH M 408 " both_signs ideal model delta sigma weight residual False -2.81 -2.60 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C8 BPH M 408 " pdb=" C10 BPH M 408 " pdb=" C7 BPH M 408 " pdb=" C9 BPH M 408 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 3112 not shown) Planarity restraints: 3837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BPH M 408 " 0.015 2.00e-02 2.50e+03 5.06e-02 5.75e+01 pdb=" C1D BPH M 408 " 0.015 2.00e-02 2.50e+03 pdb=" C2D BPH M 408 " -0.026 2.00e-02 2.50e+03 pdb=" C3D BPH M 408 " -0.046 2.00e-02 2.50e+03 pdb=" C4D BPH M 408 " -0.023 2.00e-02 2.50e+03 pdb=" CAD BPH M 408 " 0.113 2.00e-02 2.50e+03 pdb=" CHA BPH M 408 " -0.048 2.00e-02 2.50e+03 pdb=" CHD BPH M 408 " 0.047 2.00e-02 2.50e+03 pdb=" CMD BPH M 408 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BPH L 302 " -0.016 2.00e-02 2.50e+03 3.97e-02 3.54e+01 pdb=" C1D BPH L 302 " -0.009 2.00e-02 2.50e+03 pdb=" C2D BPH L 302 " 0.021 2.00e-02 2.50e+03 pdb=" C3D BPH L 302 " 0.040 2.00e-02 2.50e+03 pdb=" C4D BPH L 302 " 0.020 2.00e-02 2.50e+03 pdb=" CAD BPH L 302 " -0.089 2.00e-02 2.50e+03 pdb=" CHA BPH L 302 " 0.036 2.00e-02 2.50e+03 pdb=" CHD BPH L 302 " -0.035 2.00e-02 2.50e+03 pdb=" CMD BPH L 302 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BPH M 408 " -0.001 2.00e-02 2.50e+03 1.48e-02 4.91e+00 pdb=" C1B BPH M 408 " 0.010 2.00e-02 2.50e+03 pdb=" C2B BPH M 408 " -0.004 2.00e-02 2.50e+03 pdb=" C3B BPH M 408 " 0.001 2.00e-02 2.50e+03 pdb=" C4B BPH M 408 " -0.012 2.00e-02 2.50e+03 pdb=" CAB BPH M 408 " 0.027 2.00e-02 2.50e+03 pdb=" CHB BPH M 408 " 0.015 2.00e-02 2.50e+03 pdb=" CHC BPH M 408 " -0.011 2.00e-02 2.50e+03 pdb=" CMB BPH M 408 " -0.025 2.00e-02 2.50e+03 ... (remaining 3834 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 145 2.56 - 3.15: 15671 3.15 - 3.73: 35855 3.73 - 4.32: 51642 4.32 - 4.90: 84285 Nonbonded interactions: 187598 Sorted by model distance: nonbonded pdb=" OE2 GLU M 232 " pdb="FE FE M 402 " model vdw 1.980 2.260 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE M 402 " model vdw 2.082 2.340 nonbonded pdb=" NE2 HIS M 217 " pdb="FE FE M 402 " model vdw 2.106 2.340 nonbonded pdb=" OH TYR X 65 " pdb=" O ALA L 145 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR L 255 " pdb=" O LEU L 258 " model vdw 2.220 3.040 ... (remaining 187593 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 49) selection = (chain 'B' and resid 8 through 49) selection = (chain 'D' and resid 8 through 49) selection = (chain 'E' and resid 8 through 49) selection = (chain 'F' and resid 8 through 49) selection = (chain 'G' and resid 8 through 49) selection = (chain 'I' and resid 8 through 49) selection = (chain 'J' and resid 8 through 49) selection = (chain 'K' and resid 8 through 49) selection = (chain 'N' and resid 8 through 49) selection = (chain 'O' and resid 8 through 49) } ncs_group { reference = (chain 'R' and resid 13 through 49) selection = (chain 'S' and resid 13 through 49) selection = (chain 'T' and resid 13 through 49) } ncs_group { reference = (chain 'a' and resid 5 through 44) selection = (chain 'o' and resid 5 through 44) } ncs_group { reference = (chain 'b' and resid 2 through 101) selection = (chain 'd' and resid 2 through 101) selection = (chain 'e' and resid 2 through 101) selection = (chain 'f' and resid 2 through 101) selection = (chain 'g' and resid 2 through 101) selection = (chain 'i' and resid 2 through 101) selection = (chain 'j' and resid 2 through 101) selection = (chain 'k' and resid 2 through 101) selection = (chain 'n' and resid 2 through 101) } ncs_group { reference = (chain 'r' and (resid 12 through 54 or (resid 101 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )))) selection = (chain 's' and resid 12 through 101) selection = (chain 't' and resid 12 through 101) } 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.900 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 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 : 0.024 0.689 22533 Z= 1.606 Angle : 4.456 52.896 30996 Z= 1.492 Chirality : 0.036 0.214 3115 Planarity : 0.004 0.051 3837 Dihedral : 21.085 179.931 7771 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.19 % Allowed : 3.90 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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 aren not related in a simple way. whole: 3.50 (0.18), residues: 2181 helix: 3.09 (0.12), residues: 1485 sheet: -0.67 (0.92), residues: 32 loop : 0.67 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 109 TYR 0.015 0.001 TYR M 301 PHE 0.014 0.001 PHE L 146 TRP 0.014 0.001 TRP L 185 HIS 0.006 0.001 HIS M 180 Details of bonding type rmsd covalent geometry : bond 0.02046 (22512) covalent geometry : angle 4.45555 (30996) hydrogen bonds : bond 0.11721 ( 1317) hydrogen bonds : angle 4.37730 ( 3723) Misc. bond : bond 0.40586 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 283 time to evaluate : 0.460 Fit side-chains REVERT: a 6 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8598 (mtpp) REVERT: b 53 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.4398 (p90) REVERT: X 6 LYS cc_start: 0.7956 (mttm) cc_final: 0.7746 (mttm) REVERT: X 9 ASP cc_start: 0.7555 (t0) cc_final: 0.7277 (t70) REVERT: X 24 ARG cc_start: 0.8412 (mtt-85) cc_final: 0.8188 (mtt90) REVERT: M 166 MET cc_start: 0.9164 (mmm) cc_final: 0.8910 (mmm) REVERT: H 91 GLU cc_start: 0.8050 (tt0) cc_final: 0.7830 (tt0) REVERT: B 9 PHE cc_start: 0.9076 (m-80) cc_final: 0.8873 (m-80) REVERT: r 31 ILE cc_start: 0.7948 (mt) cc_final: 0.7707 (mt) outliers start: 22 outliers final: 8 residues processed: 300 average time/residue: 0.5066 time to fit residues: 173.6261 Evaluate side-chains 264 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 255 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 35 PHE Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain d residue 1 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0770 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN H 135 GLN H 176 GLN t 20 GLN S 21 HIS R 16 GLN o 20 GLN i 20 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.139766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.101955 restraints weight = 21208.608| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.46 r_work: 0.2624 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 22533 Z= 0.227 Angle : 1.520 44.780 30996 Z= 0.539 Chirality : 0.042 0.210 3115 Planarity : 0.005 0.057 3837 Dihedral : 25.242 179.989 3967 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.38 % Allowed : 6.33 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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 aren not related in a simple way. whole: 3.25 (0.17), residues: 2181 helix: 2.85 (0.12), residues: 1509 sheet: -0.47 (1.14), residues: 22 loop : 0.61 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 14 TYR 0.017 0.002 TYR b 53 PHE 0.021 0.002 PHE L 146 TRP 0.019 0.002 TRP M 250 HIS 0.010 0.001 HIS L 153 Details of bonding type rmsd covalent geometry : bond 0.00526 (22512) covalent geometry : angle 1.51966 (30996) hydrogen bonds : bond 0.06672 ( 1317) hydrogen bonds : angle 3.95744 ( 3723) Misc. bond : bond 0.00366 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 258 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6735 (OUTLIER) cc_final: 0.3722 (p90) REVERT: X 6 LYS cc_start: 0.7955 (mttm) cc_final: 0.7369 (mmtm) REVERT: L 275 MET cc_start: 0.8218 (mtp) cc_final: 0.7993 (mtt) REVERT: H 38 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8013 (mm-30) REVERT: H 139 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7999 (mmtm) REVERT: B 15 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6685 (pp20) REVERT: B 40 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8494 (tp) REVERT: r 23 PHE cc_start: 0.7064 (t80) cc_final: 0.6842 (t80) REVERT: I 19 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7448 (tt0) REVERT: I 40 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8521 (mt) outliers start: 44 outliers final: 23 residues processed: 279 average time/residue: 0.5340 time to fit residues: 169.2960 Evaluate side-chains 278 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain e residue 7 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 43 MET Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 135 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN H 135 GLN H 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.138014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.100489 restraints weight = 21081.038| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.39 r_work: 0.2590 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 22533 Z= 0.242 Angle : 1.366 44.475 30996 Z= 0.496 Chirality : 0.044 0.245 3115 Planarity : 0.005 0.060 3837 Dihedral : 24.401 179.996 3962 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.87 % Allowed : 7.26 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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 aren not related in a simple way. whole: 2.92 (0.17), residues: 2181 helix: 2.57 (0.12), residues: 1498 sheet: -0.59 (1.10), residues: 22 loop : 0.59 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG f 15 TYR 0.021 0.002 TYR b 53 PHE 0.024 0.002 PHE L 146 TRP 0.021 0.002 TRP M 250 HIS 0.009 0.002 HIS M 191 Details of bonding type rmsd covalent geometry : bond 0.00585 (22512) covalent geometry : angle 1.36564 (30996) hydrogen bonds : bond 0.07221 ( 1317) hydrogen bonds : angle 3.98705 ( 3723) Misc. bond : bond 0.00274 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 252 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.3751 (p90) REVERT: E 7 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6219 (tp) REVERT: X 6 LYS cc_start: 0.7947 (mttm) cc_final: 0.7357 (mmtm) REVERT: L 82 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7583 (mmmm) REVERT: H 38 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7979 (mm-30) REVERT: H 70 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7924 (mtp180) REVERT: H 139 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7962 (mmtm) REVERT: B 9 PHE cc_start: 0.9062 (m-80) cc_final: 0.8791 (m-80) REVERT: B 40 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8468 (tp) REVERT: I 19 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7453 (tt0) outliers start: 53 outliers final: 22 residues processed: 283 average time/residue: 0.5180 time to fit residues: 166.9878 Evaluate side-chains 270 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain o residue 48 THR Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 43 MET Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 152 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN H 135 GLN H 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.140673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.102802 restraints weight = 21087.113| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.45 r_work: 0.2643 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22533 Z= 0.136 Angle : 1.160 43.487 30996 Z= 0.416 Chirality : 0.037 0.160 3115 Planarity : 0.004 0.036 3837 Dihedral : 23.149 179.995 3960 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.33 % Allowed : 8.23 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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 aren not related in a simple way. whole: 3.33 (0.17), residues: 2181 helix: 2.92 (0.12), residues: 1503 sheet: -0.28 (1.13), residues: 22 loop : 0.64 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f 15 TYR 0.015 0.001 TYR M 301 PHE 0.019 0.001 PHE L 146 TRP 0.016 0.002 TRP M 250 HIS 0.006 0.001 HIS L 153 Details of bonding type rmsd covalent geometry : bond 0.00297 (22512) covalent geometry : angle 1.15991 (30996) hydrogen bonds : bond 0.05632 ( 1317) hydrogen bonds : angle 3.74947 ( 3723) Misc. bond : bond 0.00152 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 259 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6489 (OUTLIER) cc_final: 0.3807 (p90) REVERT: E 7 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6057 (tp) REVERT: X 6 LYS cc_start: 0.7916 (mttm) cc_final: 0.7306 (mmtm) REVERT: X 53 MET cc_start: 0.8252 (mtm) cc_final: 0.7775 (mmp) REVERT: X 56 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8208 (tm-30) REVERT: H 70 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7908 (mtp180) REVERT: B 9 PHE cc_start: 0.9063 (m-80) cc_final: 0.8813 (m-80) REVERT: r 42 ASN cc_start: 0.8623 (t0) cc_final: 0.8364 (t0) REVERT: O 25 MET cc_start: 0.7350 (mmm) cc_final: 0.6446 (mmm) REVERT: N 13 THR cc_start: 0.6860 (OUTLIER) cc_final: 0.6307 (t) REVERT: I 40 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8522 (mt) outliers start: 43 outliers final: 19 residues processed: 283 average time/residue: 0.5251 time to fit residues: 169.7548 Evaluate side-chains 277 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 252 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 43 MET Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 43 MET Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 194 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 192 optimal weight: 0.0980 chunk 70 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN H 135 GLN H 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.138858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.098284 restraints weight = 21012.183| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.32 r_work: 0.2601 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22533 Z= 0.153 Angle : 1.178 43.537 30996 Z= 0.425 Chirality : 0.038 0.177 3115 Planarity : 0.004 0.041 3837 Dihedral : 22.203 179.934 3960 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.92 % Allowed : 7.90 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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 aren not related in a simple way. whole: 3.29 (0.17), residues: 2181 helix: 2.89 (0.12), residues: 1504 sheet: -0.37 (1.12), residues: 22 loop : 0.61 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG f 15 TYR 0.017 0.002 TYR b 53 PHE 0.019 0.001 PHE L 146 TRP 0.017 0.002 TRP M 250 HIS 0.009 0.001 HIS L 153 Details of bonding type rmsd covalent geometry : bond 0.00349 (22512) covalent geometry : angle 1.17786 (30996) hydrogen bonds : bond 0.05984 ( 1317) hydrogen bonds : angle 3.75898 ( 3723) Misc. bond : bond 0.00211 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 258 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6593 (OUTLIER) cc_final: 0.3619 (p90) REVERT: E 7 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6002 (tp) REVERT: E 20 LEU cc_start: 0.9034 (tt) cc_final: 0.8803 (tm) REVERT: X 24 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8141 (mtt-85) REVERT: X 53 MET cc_start: 0.8333 (mtm) cc_final: 0.7826 (mmp) REVERT: X 56 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8216 (tm-30) REVERT: H 70 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7964 (mtp180) REVERT: H 139 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7990 (mmtm) REVERT: B 9 PHE cc_start: 0.9099 (m-80) cc_final: 0.8804 (m-80) REVERT: B 15 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6879 (pp20) REVERT: B 40 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8454 (tp) REVERT: r 42 ASN cc_start: 0.8622 (t0) cc_final: 0.8348 (t0) REVERT: N 13 THR cc_start: 0.6863 (OUTLIER) cc_final: 0.6311 (t) REVERT: I 40 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8551 (mt) outliers start: 54 outliers final: 20 residues processed: 288 average time/residue: 0.5344 time to fit residues: 175.2814 Evaluate side-chains 283 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 43 MET Chi-restraints excluded: chain X residue 24 ARG Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 43 MET Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 39 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 189 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN H 135 GLN H 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.139637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.099146 restraints weight = 21068.832| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.15 r_work: 0.2651 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22533 Z= 0.138 Angle : 1.155 44.798 30996 Z= 0.415 Chirality : 0.037 0.162 3115 Planarity : 0.004 0.052 3837 Dihedral : 21.785 179.948 3960 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.27 % Allowed : 8.93 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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 aren not related in a simple way. whole: 3.37 (0.17), residues: 2181 helix: 2.95 (0.12), residues: 1504 sheet: -0.28 (1.12), residues: 22 loop : 0.63 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG f 15 TYR 0.015 0.001 TYR b 53 PHE 0.019 0.001 PHE L 146 TRP 0.016 0.002 TRP M 250 HIS 0.007 0.001 HIS L 153 Details of bonding type rmsd covalent geometry : bond 0.00312 (22512) covalent geometry : angle 1.15495 (30996) hydrogen bonds : bond 0.05662 ( 1317) hydrogen bonds : angle 3.71151 ( 3723) Misc. bond : bond 0.00190 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 257 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: a 3 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8486 (mttp) REVERT: b 53 TYR cc_start: 0.6552 (OUTLIER) cc_final: 0.3571 (p90) REVERT: E 7 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.5923 (tp) REVERT: X 6 LYS cc_start: 0.8014 (mttm) cc_final: 0.7356 (mmtm) REVERT: X 53 MET cc_start: 0.8254 (mtm) cc_final: 0.7772 (mmp) REVERT: X 56 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: H 70 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7907 (mtp180) REVERT: H 139 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7980 (mmtm) REVERT: B 9 PHE cc_start: 0.9080 (m-80) cc_final: 0.8818 (m-80) REVERT: B 15 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6599 (pp20) REVERT: B 40 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8427 (tp) REVERT: r 31 ILE cc_start: 0.7862 (mt) cc_final: 0.7661 (mt) REVERT: r 42 ASN cc_start: 0.8618 (t0) cc_final: 0.8380 (t0) REVERT: O 25 MET cc_start: 0.7328 (mmm) cc_final: 0.6440 (mmm) REVERT: N 13 THR cc_start: 0.6926 (OUTLIER) cc_final: 0.6403 (t) REVERT: I 40 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8520 (mt) REVERT: i 3 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7026 (mtpt) outliers start: 42 outliers final: 21 residues processed: 281 average time/residue: 0.5275 time to fit residues: 168.5866 Evaluate side-chains 284 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 43 MET Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 43 MET Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 153 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 174 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN H 135 GLN H 176 GLN t 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.096217 restraints weight = 20964.093| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.19 r_work: 0.2600 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22533 Z= 0.199 Angle : 1.156 43.132 30996 Z= 0.425 Chirality : 0.042 0.220 3115 Planarity : 0.004 0.054 3837 Dihedral : 21.980 179.991 3960 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.44 % Allowed : 8.99 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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 aren not related in a simple way. whole: 3.07 (0.17), residues: 2181 helix: 2.71 (0.12), residues: 1504 sheet: -0.45 (1.11), residues: 22 loop : 0.57 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG f 15 TYR 0.019 0.002 TYR b 53 PHE 0.022 0.002 PHE L 146 TRP 0.019 0.002 TRP M 250 HIS 0.009 0.001 HIS L 153 Details of bonding type rmsd covalent geometry : bond 0.00479 (22512) covalent geometry : angle 1.15611 (30996) hydrogen bonds : bond 0.06638 ( 1317) hydrogen bonds : angle 3.86491 ( 3723) Misc. bond : bond 0.00281 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6670 (OUTLIER) cc_final: 0.3498 (p90) REVERT: E 7 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.5773 (tp) REVERT: E 20 LEU cc_start: 0.9047 (tt) cc_final: 0.8827 (tm) REVERT: X 6 LYS cc_start: 0.8019 (mttm) cc_final: 0.7367 (mmtm) REVERT: X 24 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8104 (mtt-85) REVERT: X 53 MET cc_start: 0.8293 (mtm) cc_final: 0.7792 (mmp) REVERT: H 70 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7920 (mtp180) REVERT: H 139 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8051 (mmtm) REVERT: H 148 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8552 (mtt180) REVERT: B 40 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8454 (tp) REVERT: O 25 MET cc_start: 0.7407 (mmm) cc_final: 0.6543 (mmm) REVERT: N 13 THR cc_start: 0.6958 (OUTLIER) cc_final: 0.6396 (t) REVERT: I 19 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7444 (tt0) REVERT: i 3 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7162 (mtpt) outliers start: 45 outliers final: 20 residues processed: 287 average time/residue: 0.5189 time to fit residues: 169.3597 Evaluate side-chains 287 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 258 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 43 MET Chi-restraints excluded: chain X residue 24 ARG Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN H 135 GLN H 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.138575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.101576 restraints weight = 21039.210| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.41 r_work: 0.2603 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22533 Z= 0.161 Angle : 1.116 43.261 30996 Z= 0.407 Chirality : 0.039 0.182 3115 Planarity : 0.004 0.044 3837 Dihedral : 21.719 179.985 3960 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.22 % Allowed : 9.26 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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 aren not related in a simple way. whole: 3.18 (0.17), residues: 2181 helix: 2.79 (0.12), residues: 1504 sheet: -0.37 (1.11), residues: 22 loop : 0.60 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG f 15 TYR 0.017 0.002 TYR b 53 PHE 0.021 0.001 PHE L 146 TRP 0.017 0.002 TRP M 250 HIS 0.008 0.001 HIS L 153 Details of bonding type rmsd covalent geometry : bond 0.00376 (22512) covalent geometry : angle 1.11576 (30996) hydrogen bonds : bond 0.06078 ( 1317) hydrogen bonds : angle 3.79979 ( 3723) Misc. bond : bond 0.00224 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6570 (OUTLIER) cc_final: 0.3547 (p90) REVERT: E 7 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.5743 (tp) REVERT: E 20 LEU cc_start: 0.9036 (tt) cc_final: 0.8809 (tm) REVERT: X 6 LYS cc_start: 0.8015 (mttm) cc_final: 0.7363 (mmtm) REVERT: X 24 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8101 (mtt-85) REVERT: X 53 MET cc_start: 0.8281 (mtm) cc_final: 0.7785 (mmp) REVERT: X 56 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8102 (tm-30) REVERT: H 70 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7941 (mtp180) REVERT: H 139 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7976 (mmtm) REVERT: B 9 PHE cc_start: 0.9071 (m-80) cc_final: 0.8825 (m-80) REVERT: B 15 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6814 (pp20) REVERT: B 40 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8416 (tp) REVERT: O 25 MET cc_start: 0.7379 (mmm) cc_final: 0.6471 (mmm) REVERT: N 13 THR cc_start: 0.6841 (OUTLIER) cc_final: 0.6293 (t) REVERT: i 3 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7135 (mtpt) outliers start: 41 outliers final: 19 residues processed: 280 average time/residue: 0.5788 time to fit residues: 184.5076 Evaluate side-chains 281 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 252 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 43 MET Chi-restraints excluded: chain X residue 24 ARG Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 15 GLU Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 25 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 171 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 135 GLN H 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.136912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.096192 restraints weight = 21036.292| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.32 r_work: 0.2578 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 22533 Z= 0.206 Angle : 1.165 43.053 30996 Z= 0.429 Chirality : 0.042 0.227 3115 Planarity : 0.004 0.054 3837 Dihedral : 21.923 179.994 3960 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.17 % Allowed : 9.26 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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 aren not related in a simple way. whole: 2.94 (0.17), residues: 2181 helix: 2.61 (0.12), residues: 1500 sheet: -0.42 (1.11), residues: 22 loop : 0.54 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG f 15 TYR 0.021 0.002 TYR b 53 PHE 0.022 0.002 PHE L 146 TRP 0.019 0.002 TRP M 250 HIS 0.009 0.002 HIS L 153 Details of bonding type rmsd covalent geometry : bond 0.00500 (22512) covalent geometry : angle 1.16478 (30996) hydrogen bonds : bond 0.06776 ( 1317) hydrogen bonds : angle 3.90548 ( 3723) Misc. bond : bond 0.00283 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 258 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.3529 (p90) REVERT: E 7 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.5588 (tp) REVERT: E 20 LEU cc_start: 0.9066 (tt) cc_final: 0.8834 (tm) REVERT: X 6 LYS cc_start: 0.8030 (mttm) cc_final: 0.7385 (mmtm) REVERT: X 24 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8158 (mtt-85) REVERT: X 53 MET cc_start: 0.8309 (mtm) cc_final: 0.7801 (mmp) REVERT: X 56 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: H 38 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8065 (mm-30) REVERT: H 70 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7944 (mtp180) REVERT: H 139 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8067 (mmtm) REVERT: H 148 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8529 (mtt180) REVERT: B 9 PHE cc_start: 0.9090 (m-80) cc_final: 0.8815 (m-80) REVERT: B 40 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8449 (tp) REVERT: O 25 MET cc_start: 0.7430 (mmm) cc_final: 0.6568 (mmm) REVERT: N 13 THR cc_start: 0.7005 (OUTLIER) cc_final: 0.6788 (m) REVERT: I 19 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7467 (tt0) REVERT: i 3 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7138 (mtpt) outliers start: 40 outliers final: 18 residues processed: 284 average time/residue: 0.6089 time to fit residues: 195.5977 Evaluate side-chains 280 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain X residue 24 ARG Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 15 GLU Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 43 MET Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 83 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 135 GLN H 176 GLN G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.136152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.097948 restraints weight = 21074.865| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.53 r_work: 0.2573 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 22533 Z= 0.254 Angle : 1.220 42.758 30996 Z= 0.454 Chirality : 0.046 0.261 3115 Planarity : 0.005 0.062 3837 Dihedral : 22.239 179.971 3960 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.89 % Allowed : 9.64 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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 aren not related in a simple way. whole: 2.62 (0.17), residues: 2181 helix: 2.36 (0.12), residues: 1508 sheet: -0.60 (1.09), residues: 22 loop : 0.39 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 46 TYR 0.025 0.003 TYR b 53 PHE 0.024 0.002 PHE L 146 TRP 0.028 0.002 TRP n 8 HIS 0.010 0.002 HIS M 191 Details of bonding type rmsd covalent geometry : bond 0.00629 (22512) covalent geometry : angle 1.21996 (30996) hydrogen bonds : bond 0.07320 ( 1317) hydrogen bonds : angle 4.02176 ( 3723) Misc. bond : bond 0.00328 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6826 (OUTLIER) cc_final: 0.3906 (p90) REVERT: E 20 LEU cc_start: 0.9060 (tt) cc_final: 0.8815 (tm) REVERT: X 6 LYS cc_start: 0.8037 (mttm) cc_final: 0.7380 (mmtm) REVERT: X 24 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8128 (mtt-85) REVERT: X 53 MET cc_start: 0.8324 (mtm) cc_final: 0.7790 (mmp) REVERT: L 82 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7489 (mmmm) REVERT: H 70 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7919 (mtp180) REVERT: H 139 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7945 (mmtm) REVERT: B 40 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8428 (tp) REVERT: O 25 MET cc_start: 0.7390 (mmm) cc_final: 0.6575 (mmm) REVERT: I 19 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7429 (tt0) REVERT: i 3 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7133 (mtpt) outliers start: 35 outliers final: 17 residues processed: 272 average time/residue: 0.5981 time to fit residues: 184.0434 Evaluate side-chains 269 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 245 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain X residue 24 ARG Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain i residue 3 LYS Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 43 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 209 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 135 GLN H 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.138971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.098484 restraints weight = 21076.201| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.32 r_work: 0.2629 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22533 Z= 0.142 Angle : 1.103 43.090 30996 Z= 0.402 Chirality : 0.038 0.164 3115 Planarity : 0.004 0.041 3837 Dihedral : 21.603 179.977 3960 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.46 % Allowed : 10.12 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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 aren not related in a simple way. whole: 3.15 (0.17), residues: 2181 helix: 2.81 (0.12), residues: 1499 sheet: -0.21 (1.13), residues: 22 loop : 0.50 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG f 15 TYR 0.019 0.002 TYR a 5 PHE 0.021 0.001 PHE L 146 TRP 0.032 0.002 TRP n 8 HIS 0.007 0.001 HIS M 180 Details of bonding type rmsd covalent geometry : bond 0.00320 (22512) covalent geometry : angle 1.10336 (30996) hydrogen bonds : bond 0.05799 ( 1317) hydrogen bonds : angle 3.79216 ( 3723) Misc. bond : bond 0.00176 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6820.60 seconds wall clock time: 116 minutes 42.82 seconds (7002.82 seconds total)