Starting phenix.real_space_refine on Sat Jul 4 18:18:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b64_15862/07_2026/8b64_15862.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b64_15862/07_2026/8b64_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8b64_15862/07_2026/8b64_15862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b64_15862/07_2026/8b64_15862.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8b64_15862/07_2026/8b64_15862.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b64_15862/07_2026/8b64_15862.cif" model { file = "/net/cci-nas-00/data/ceres_data/8b64_15862/07_2026/8b64_15862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b64_15862/07_2026/8b64_15862.cif" } 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-dev-6108/lib/python3.11/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: 4.74, 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: 1.96 Conformation dependent library (CDL) restraints added in 757.8 milliseconds 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: 0.56 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: 3.67 Time building geometry restraints manager: 2.55 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: 11289 35.99 - 71.97: 381 71.97 - 107.96: 98 107.96 - 143.94: 3 143.94 - 179.93: 26 Dihedral angle restraints: 11797 sinusoidal: 5304 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 11794 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: 1.860 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.560 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 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 : 20.808 179.931 7595 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 are 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/Z covalent geometry : bond 0.02046 / 1.02 (22512) covalent geometry : angle 4.45555 / 1.49 (30996) hydrogen bonds : bond 0.11721 / 7.17 ( 1317) hydrogen bonds : angle 4.37730 / 3.20 ( 3723) Misc. bond : bond 0.40586 / 25.00 ( 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 : 0.740 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: 0.8411 (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: 0.6051 time to fit residues: 208.5140 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 : 0.693 ------------------------------------------------------------------------------- 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... 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 = 0.139787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.102018 restraints weight = 21208.894| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.47 r_work: 0.2620 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 22533 Z= 0.224 Angle : 1.503 44.762 30996 Z= 0.533 Chirality : 0.042 0.211 3115 Planarity : 0.005 0.067 3837 Dihedral : 25.069 179.986 3791 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.60 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 are 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 0.011 0.001 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (22512) covalent geometry : angle 1.50294 / 0.53 (30996) hydrogen bonds : bond 0.06672 / 4.37 ( 1317) hydrogen bonds : angle 3.95789 / 2.86 ( 3723) Misc. bond : bond 0.00226 / 0.13 ( 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 : 0.773 Fit side-chains revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.3731 (p90) REVERT: X 6 LYS cc_start: 0.7954 (mttm) cc_final: 0.7370 (mmtm) REVERT: L 275 MET cc_start: 0.8206 (mtp) cc_final: 0.7980 (mtt) REVERT: H 38 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8022 (mm-30) REVERT: H 139 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8010 (mmtm) REVERT: B 15 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6711 (pp20) REVERT: B 40 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8496 (tp) REVERT: r 23 PHE cc_start: 0.7052 (t80) cc_final: 0.6829 (t80) REVERT: I 19 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7485 (tt0) REVERT: I 40 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8522 (mt) outliers start: 44 outliers final: 23 residues processed: 279 average time/residue: 0.6098 time to fit residues: 194.2201 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 : 0.736 ------------------------------------------------------------------------------- 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: 3.9990 chunk 2 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 158 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 37 optimal weight: 0.0670 chunk 132 optimal weight: 5.9990 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 42 ASN H 135 GLN H 176 GLN i 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.138215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.100321 restraints weight = 21073.346| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.42 r_work: 0.2588 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 22533 Z= 0.238 Angle : 1.360 44.376 30996 Z= 0.493 Chirality : 0.044 0.251 3115 Planarity : 0.005 0.059 3837 Dihedral : 24.222 179.994 3786 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.82 % Allowed : 7.42 % Favored : 89.77 % 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 are not related in a simple way. whole: 2.95 (0.17), residues: 2181 helix: 2.59 (0.12), residues: 1500 sheet: -0.56 (1.11), residues: 22 loop : 0.62 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG f 15 TYR 0.021 0.002 TYR b 53 PHE 0.025 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/Z covalent geometry : bond 0.00580 / 0.24 (22512) covalent geometry : angle 1.36028 / 0.49 (30996) hydrogen bonds : bond 0.07119 / 4.67 ( 1317) hydrogen bonds : angle 3.97376 / 2.86 ( 3723) Misc. bond : bond 0.00317 / 0.18 ( 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 306 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 254 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6818 (OUTLIER) cc_final: 0.3788 (p90) REVERT: E 7 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6213 (tp) REVERT: X 6 LYS cc_start: 0.7974 (mttm) cc_final: 0.7400 (mmtm) REVERT: L 82 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7606 (mmmm) REVERT: H 38 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7976 (mm-30) REVERT: H 70 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7908 (mtp180) REVERT: B 9 PHE cc_start: 0.9060 (m-80) cc_final: 0.8797 (m-80) REVERT: B 40 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8467 (tp) REVERT: I 19 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7495 (tt0) outliers start: 52 outliers final: 21 residues processed: 285 average time/residue: 0.6148 time to fit residues: 200.1185 Evaluate side-chains 269 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 163 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 49 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 58 optimal weight: 0.0470 chunk 97 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 overall best weight: 1.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 42 ASN H 135 GLN H 176 GLN i 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.141129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.100816 restraints weight = 21125.273| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.17 r_work: 0.2677 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22533 Z= 0.122 Angle : 1.149 43.521 30996 Z= 0.410 Chirality : 0.036 0.153 3115 Planarity : 0.003 0.036 3837 Dihedral : 23.181 179.997 3784 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.44 % Allowed : 8.12 % 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 are not related in a simple way. whole: 3.43 (0.17), residues: 2181 helix: 2.99 (0.12), residues: 1503 sheet: -0.24 (1.15), residues: 22 loop : 0.67 (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 0.017 0.001 PHE L 146 TRP 0.015 0.001 TRP M 65 HIS 0.005 0.001 HIS M 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (22512) covalent geometry : angle 1.14902 / 0.41 (30996) hydrogen bonds : bond 0.05369 / 3.51 ( 1317) hydrogen bonds : angle 3.71384 / 2.66 ( 3723) Misc. bond : bond 0.00122 / 0.07 ( 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 303 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6439 (OUTLIER) cc_final: 0.3743 (p90) REVERT: E 7 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6135 (tp) REVERT: X 6 LYS cc_start: 0.7886 (mttm) cc_final: 0.7276 (mmtm) REVERT: X 53 MET cc_start: 0.8215 (mtm) cc_final: 0.7786 (mmp) REVERT: X 56 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: H 70 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7881 (mtp180) REVERT: H 139 LYS cc_start: 0.8321 (mmtm) cc_final: 0.7986 (mmtm) REVERT: B 9 PHE cc_start: 0.9051 (m-80) cc_final: 0.8822 (m-80) REVERT: r 42 ASN cc_start: 0.8559 (t0) cc_final: 0.8356 (t0) REVERT: O 25 MET cc_start: 0.7374 (mmm) cc_final: 0.6448 (mmm) REVERT: N 13 THR cc_start: 0.6896 (OUTLIER) cc_final: 0.6357 (t) REVERT: I 40 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8547 (mt) outliers start: 45 outliers final: 18 residues processed: 282 average time/residue: 0.5964 time to fit residues: 193.2325 Evaluate side-chains 276 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 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 H residue 217 THR Chi-restraints excluded: chain H residue 233 ASP 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 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: 0.0020 chunk 148 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 157 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 60 optimal weight: 0.0980 chunk 15 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 42 ASN M 43 ASN H 135 GLN H 176 GLN i 20 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.144238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.104268 restraints weight = 21191.947| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.32 r_work: 0.2738 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22533 Z= 0.105 Angle : 1.121 43.413 30996 Z= 0.398 Chirality : 0.035 0.144 3115 Planarity : 0.003 0.034 3837 Dihedral : 21.801 179.973 3784 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.84 % Allowed : 8.93 % Favored : 89.23 % 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 are not related in a simple way. whole: 3.70 (0.17), residues: 2181 helix: 3.20 (0.12), residues: 1506 sheet: 0.01 (1.20), residues: 22 loop : 0.74 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG f 15 TYR 0.015 0.001 TYR M 301 PHE 0.015 0.001 PHE L 146 TRP 0.015 0.001 TRP M 65 HIS 0.006 0.001 HIS L 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (22512) covalent geometry : angle 1.12076 / 0.40 (30996) hydrogen bonds : bond 0.04553 / 2.98 ( 1317) hydrogen bonds : angle 3.51043 / 2.50 ( 3723) Misc. bond : bond 0.00103 / 0.06 ( 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 304 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: a 12 ASP cc_start: 0.8235 (t70) cc_final: 0.8008 (t0) REVERT: b 53 TYR cc_start: 0.6166 (OUTLIER) cc_final: 0.3428 (p90) REVERT: E 7 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6027 (tp) REVERT: X 6 LYS cc_start: 0.7835 (mttm) cc_final: 0.7229 (mmtm) REVERT: X 53 MET cc_start: 0.8174 (mtm) cc_final: 0.7729 (mmp) REVERT: X 56 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: H 70 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7848 (mtp180) REVERT: H 77 VAL cc_start: 0.8794 (t) cc_final: 0.8594 (m) REVERT: H 139 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7954 (mmtm) REVERT: B 9 PHE cc_start: 0.9094 (m-80) cc_final: 0.8836 (m-80) REVERT: r 31 ILE cc_start: 0.7684 (mt) cc_final: 0.7469 (mt) REVERT: r 42 ASN cc_start: 0.8493 (t0) cc_final: 0.8240 (t0) REVERT: O 25 MET cc_start: 0.7338 (mmm) cc_final: 0.6369 (mmm) REVERT: N 13 THR cc_start: 0.6875 (OUTLIER) cc_final: 0.6400 (t) REVERT: k 6 LYS cc_start: 0.7847 (mttm) cc_final: 0.7636 (mttp) outliers start: 34 outliers final: 14 residues processed: 288 average time/residue: 0.5762 time to fit residues: 190.9534 Evaluate side-chains 277 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 258 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 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 274 VAL Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain n residue 54 VAL 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 G residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 39 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 chunk 196 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 42 ASN M 43 ASN H 79 ASN H 135 GLN H 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.141296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.103406 restraints weight = 21106.815| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.44 r_work: 0.2674 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22533 Z= 0.132 Angle : 1.145 44.247 30996 Z= 0.410 Chirality : 0.037 0.189 3115 Planarity : 0.003 0.036 3837 Dihedral : 21.353 179.925 3784 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.06 % Allowed : 9.64 % Favored : 88.31 % 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 are not related in a simple way. whole: 3.60 (0.17), residues: 2181 helix: 3.11 (0.12), residues: 1507 sheet: -0.25 (1.16), residues: 22 loop : 0.75 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f 15 TYR 0.014 0.001 TYR b 53 PHE 0.017 0.001 PHE L 146 TRP 0.015 0.001 TRP M 250 HIS 0.008 0.001 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (22512) covalent geometry : angle 1.14499 / 0.41 (30996) hydrogen bonds : bond 0.05330 / 3.49 ( 1317) hydrogen bonds : angle 3.61685 / 2.59 ( 3723) Misc. bond : bond 0.00195 / 0.11 ( 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 297 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 259 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: b 15 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7632 (mtp180) REVERT: b 53 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.3489 (p90) REVERT: E 7 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.5987 (tp) REVERT: X 6 LYS cc_start: 0.7862 (mttm) cc_final: 0.7250 (mmtm) REVERT: X 53 MET cc_start: 0.8213 (mtm) cc_final: 0.7772 (mmp) REVERT: X 56 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: H 70 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7893 (mtp180) REVERT: B 9 PHE cc_start: 0.9067 (m-80) cc_final: 0.8800 (m-80) REVERT: B 15 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6546 (pp20) REVERT: O 25 MET cc_start: 0.7367 (mmm) cc_final: 0.6443 (mmm) REVERT: N 13 THR cc_start: 0.6855 (OUTLIER) cc_final: 0.6323 (t) outliers start: 38 outliers final: 19 residues processed: 281 average time/residue: 0.5858 time to fit residues: 188.9541 Evaluate side-chains 277 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 251 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 15 ARG 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 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 217 THR Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain n residue 54 VAL 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 j residue 1 MET 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: 9.9990 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 42 ASN M 43 ASN H 79 ASN H 135 GLN H 176 GLN r 42 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.138051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.101392 restraints weight = 20967.546| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.48 r_work: 0.2576 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1568 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= 0.202 Angle : 1.150 43.140 30996 Z= 0.423 Chirality : 0.042 0.216 3115 Planarity : 0.004 0.052 3837 Dihedral : 21.459 179.975 3784 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.27 % Allowed : 9.47 % Favored : 88.25 % 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 are not related in a simple way. whole: 3.22 (0.17), residues: 2181 helix: 2.81 (0.12), residues: 1504 sheet: -0.47 (1.11), residues: 22 loop : 0.65 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 46 TYR 0.018 0.002 TYR b 53 PHE 0.021 0.002 PHE L 146 TRP 0.017 0.002 TRP M 250 HIS 0.009 0.002 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.20 (22512) covalent geometry : angle 1.14959 / 0.42 (30996) hydrogen bonds : bond 0.06499 / 4.27 ( 1317) hydrogen bonds : angle 3.82196 / 2.75 ( 3723) Misc. bond : bond 0.00285 / 0.16 ( 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 301 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 259 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: b 15 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7626 (mtp180) REVERT: b 53 TYR cc_start: 0.6650 (OUTLIER) cc_final: 0.3403 (p90) REVERT: E 7 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.5878 (tp) REVERT: X 6 LYS cc_start: 0.7955 (mttm) cc_final: 0.7342 (mmtm) REVERT: X 24 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8130 (mtt-85) REVERT: X 53 MET cc_start: 0.8258 (mtm) cc_final: 0.7771 (mmp) REVERT: X 56 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: H 70 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7928 (mtp180) REVERT: B 9 PHE cc_start: 0.9105 (m-80) cc_final: 0.8810 (m-80) REVERT: B 40 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8438 (tp) REVERT: N 13 THR cc_start: 0.6919 (OUTLIER) cc_final: 0.6709 (m) REVERT: I 19 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7460 (tt0) outliers start: 42 outliers final: 20 residues processed: 280 average time/residue: 0.5995 time to fit residues: 192.0556 Evaluate side-chains 283 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 15 ARG 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 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 217 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP 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 j residue 1 MET 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: 7.9990 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 42 ASN X 60 GLN M 43 ASN H 135 GLN H 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.140054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.102307 restraints weight = 20993.887| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.45 r_work: 0.2612 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22533 Z= 0.156 Angle : 1.110 43.321 30996 Z= 0.404 Chirality : 0.039 0.177 3115 Planarity : 0.004 0.043 3837 Dihedral : 21.258 179.983 3784 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.06 % Allowed : 10.07 % Favored : 87.87 % 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 are not related in a simple way. whole: 3.26 (0.17), residues: 2181 helix: 2.86 (0.12), residues: 1504 sheet: -0.42 (1.11), residues: 22 loop : 0.62 (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 0.020 0.001 PHE L 146 TRP 0.015 0.002 TRP M 250 HIS 0.008 0.001 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (22512) covalent geometry : angle 1.11033 / 0.40 (30996) hydrogen bonds : bond 0.05950 / 3.90 ( 1317) hydrogen bonds : angle 3.75812 / 2.69 ( 3723) Misc. bond : bond 0.00222 / 0.13 ( 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 289 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: b 15 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7639 (mtp180) REVERT: b 53 TYR cc_start: 0.6539 (OUTLIER) cc_final: 0.3492 (p90) REVERT: E 7 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.5782 (tp) REVERT: X 6 LYS cc_start: 0.7937 (mttm) cc_final: 0.7313 (mmtm) REVERT: X 24 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8079 (mtt-85) REVERT: X 53 MET cc_start: 0.8249 (mtm) cc_final: 0.7766 (mmp) REVERT: X 56 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: X 60 GLN cc_start: 0.8465 (mt0) cc_final: 0.8264 (mt0) REVERT: M 108 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8170 (mptt) REVERT: H 70 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7903 (mtp180) REVERT: B 9 PHE cc_start: 0.9090 (m-80) cc_final: 0.8814 (m-80) REVERT: B 40 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8402 (tp) REVERT: O 25 MET cc_start: 0.7364 (mmm) cc_final: 0.6502 (mmm) REVERT: N 13 THR cc_start: 0.6805 (OUTLIER) cc_final: 0.6265 (t) REVERT: i 3 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7048 (mtpt) outliers start: 38 outliers final: 18 residues processed: 271 average time/residue: 0.6211 time to fit residues: 192.5995 Evaluate side-chains 276 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 15 ARG 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 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 108 LYS 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 217 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP 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: 6.9990 chunk 160 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 210 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 42 ASN H 135 GLN H 176 GLN r 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.138576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.102197 restraints weight = 20974.765| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.48 r_work: 0.2583 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1671 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= 0.182 Angle : 1.143 43.187 30996 Z= 0.419 Chirality : 0.040 0.205 3115 Planarity : 0.004 0.051 3837 Dihedral : 21.388 179.991 3784 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.89 % Allowed : 10.18 % Favored : 87.93 % 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 are not related in a simple way. whole: 3.09 (0.17), residues: 2181 helix: 2.72 (0.12), residues: 1504 sheet: -0.45 (1.10), residues: 22 loop : 0.59 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG f 15 TYR 0.019 0.002 TYR b 53 PHE 0.020 0.002 PHE L 146 TRP 0.018 0.002 TRP n 8 HIS 0.009 0.001 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (22512) covalent geometry : angle 1.14298 / 0.42 (30996) hydrogen bonds : bond 0.06441 / 4.22 ( 1317) hydrogen bonds : angle 3.83710 / 2.76 ( 3723) Misc. bond : bond 0.00261 / 0.15 ( 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 287 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 15 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7632 (mtp180) REVERT: b 53 TYR cc_start: 0.6608 (OUTLIER) cc_final: 0.3431 (p90) REVERT: E 7 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.5738 (tp) REVERT: E 20 LEU cc_start: 0.9013 (tt) cc_final: 0.8798 (tm) REVERT: X 6 LYS cc_start: 0.7954 (mttm) cc_final: 0.7296 (mmtm) REVERT: X 24 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8128 (mtt-85) REVERT: X 53 MET cc_start: 0.8265 (mtm) cc_final: 0.7794 (mmp) REVERT: X 56 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7904 (tm-30) REVERT: M 108 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8270 (mptt) REVERT: H 70 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7907 (mtp180) REVERT: B 9 PHE cc_start: 0.9116 (m-80) cc_final: 0.8810 (m-80) REVERT: B 40 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8418 (tp) REVERT: O 25 MET cc_start: 0.7444 (mmm) cc_final: 0.6614 (mmm) outliers start: 35 outliers final: 16 residues processed: 271 average time/residue: 0.5857 time to fit residues: 181.2925 Evaluate side-chains 272 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 248 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 15 ARG 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 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 108 LYS 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 217 THR 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 43 MET Chi-restraints excluded: chain k residue 29 VAL 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: 9.9990 chunk 61 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 198 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3463 r_free = 0.3463 target = 0.138162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.101678 restraints weight = 21052.286| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.50 r_work: 0.2584 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1704 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= 0.179 Angle : 1.134 43.187 30996 Z= 0.416 Chirality : 0.040 0.203 3115 Planarity : 0.004 0.049 3837 Dihedral : 21.327 179.974 3784 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.52 % Allowed : 10.50 % Favored : 87.98 % 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 are not related in a simple way. whole: 3.07 (0.17), residues: 2181 helix: 2.70 (0.12), residues: 1504 sheet: -0.39 (1.12), residues: 22 loop : 0.58 (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 0.021 0.002 PHE L 146 TRP 0.023 0.002 TRP n 8 HIS 0.009 0.001 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (22512) covalent geometry : angle 1.13419 / 0.42 (30996) hydrogen bonds : bond 0.06314 / 4.14 ( 1317) hydrogen bonds : angle 3.83343 / 2.75 ( 3723) Misc. bond : bond 0.00250 / 0.14 ( 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 280 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 252 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: b 15 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7646 (mtp180) REVERT: b 53 TYR cc_start: 0.6603 (OUTLIER) cc_final: 0.3485 (p90) REVERT: E 7 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.5611 (tp) REVERT: X 6 LYS cc_start: 0.8033 (mttm) cc_final: 0.7409 (mmtm) REVERT: X 24 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8148 (mtt-85) REVERT: X 53 MET cc_start: 0.8257 (mtm) cc_final: 0.7782 (mmp) REVERT: X 56 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: H 70 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7915 (mtp180) REVERT: B 40 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8423 (tp) REVERT: O 25 MET cc_start: 0.7472 (mmm) cc_final: 0.6620 (mmm) REVERT: I 19 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7443 (tt0) outliers start: 28 outliers final: 19 residues processed: 268 average time/residue: 0.6143 time to fit residues: 189.6172 Evaluate side-chains 275 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 15 ARG 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 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 217 THR Chi-restraints excluded: chain H residue 233 ASP 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 43 MET Chi-restraints excluded: chain k residue 29 VAL 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: 9.9990 chunk 102 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 79 ASN H 135 GLN H 176 GLN r 42 ASN G 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.138757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.101089 restraints weight = 20993.130| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.58 r_work: 0.2602 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22533 Z= 0.174 Angle : 1.131 43.174 30996 Z= 0.415 Chirality : 0.040 0.198 3115 Planarity : 0.004 0.048 3837 Dihedral : 21.219 179.994 3784 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.73 % Allowed : 10.45 % Favored : 87.82 % 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 are not related in a simple way. whole: 3.08 (0.17), residues: 2181 helix: 2.71 (0.12), residues: 1504 sheet: -0.34 (1.13), residues: 22 loop : 0.56 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG f 15 TYR 0.020 0.002 TYR a 5 PHE 0.021 0.002 PHE L 146 TRP 0.030 0.002 TRP n 8 HIS 0.009 0.001 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (22512) covalent geometry : angle 1.13113 / 0.42 (30996) hydrogen bonds : bond 0.06271 / 4.11 ( 1317) hydrogen bonds : angle 3.81922 / 2.74 ( 3723) Misc. bond : bond 0.00245 / 0.14 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7559.09 seconds wall clock time: 129 minutes 26.27 seconds (7766.27 seconds total)