Starting phenix.real_space_refine on Thu May 22 08:49:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b64_15862/05_2025/8b64_15862.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b64_15862/05_2025/8b64_15862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.589 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b64_15862/05_2025/8b64_15862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b64_15862/05_2025/8b64_15862.map" model { file = "/net/cci-nas-00/data/ceres_data/8b64_15862/05_2025/8b64_15862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b64_15862/05_2025/8b64_15862.cif" } resolution = 2.589 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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-8': 3, 'U10:plan-9': 3, 'U10:plan-3': 1, 'U10:plan-4': 2, 'U10:plan-5': 2, 'U10:plan-6': 3, 'U10:plan-7': 3, 'U10:plan-10': 3, 'U10:plan-11': 3} 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: 12.64, per 1000 atoms: 0.58 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: 6.68 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.64 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: 5.74 Time building geometry restraints manager: 7.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.37: 6366 1.37 - 1.57: 15420 1.57 - 1.77: 431 1.77 - 1.98: 159 1.98 - 2.18: 136 Bond restraints: 22512 Sorted by residual: bond pdb=" C4 U10 L 305 " pdb=" O4 U10 L 305 " ideal model delta sigma weight residual 1.230 1.421 -0.191 2.00e-02 2.50e+03 9.10e+01 bond pdb=" C3 U10 L 305 " pdb=" O3 U10 L 305 " ideal model delta sigma weight residual 1.230 1.418 -0.188 2.00e-02 2.50e+03 8.80e+01 bond pdb=" C23 SPO M 404 " pdb=" C25 SPO M 404 " ideal model delta sigma weight residual 1.448 1.636 -0.188 2.00e-02 2.50e+03 8.80e+01 bond pdb=" C3 U10 M 403 " pdb=" O3 U10 M 403 " ideal model delta sigma weight residual 1.230 1.417 -0.187 2.00e-02 2.50e+03 8.78e+01 bond pdb=" C3 U10 L 303 " pdb=" O3 U10 L 303 " ideal model delta sigma weight residual 1.230 1.415 -0.185 2.00e-02 2.50e+03 8.57e+01 ... (remaining 22507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.58: 30252 10.58 - 21.16: 315 21.16 - 31.74: 196 31.74 - 42.32: 146 42.32 - 52.90: 87 Bond angle restraints: 30996 Sorted by residual: angle pdb=" C34 SPO M 404 " pdb=" C33 SPO M 404 " pdb=" C35 SPO M 404 " ideal model delta sigma weight residual 115.46 62.56 52.90 3.00e+00 1.11e-01 3.11e+02 angle pdb=" C34 SPO d 102 " pdb=" C33 SPO d 102 " pdb=" C35 SPO d 102 " ideal model delta sigma weight residual 115.46 63.19 52.27 3.00e+00 1.11e-01 3.04e+02 angle pdb=" C10 U10 L 305 " pdb=" C9 U10 L 305 " pdb=" C11 U10 L 305 " ideal model delta sigma weight residual 120.00 67.77 52.23 3.00e+00 1.11e-01 3.03e+02 angle pdb=" C25 U10 L 303 " pdb=" C24 U10 L 303 " pdb=" C26 U10 L 303 " ideal model delta sigma weight residual 120.00 67.80 52.20 3.00e+00 1.11e-01 3.03e+02 angle pdb=" C34 SPO i 102 " pdb=" C33 SPO i 102 " pdb=" C35 SPO i 102 " ideal model delta sigma weight residual 115.46 63.31 52.15 3.00e+00 1.11e-01 3.02e+02 ... (remaining 30991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 11426 35.99 - 71.97: 417 71.97 - 107.96: 100 107.96 - 143.94: 4 143.94 - 179.93: 26 Dihedral angle restraints: 11973 sinusoidal: 5480 harmonic: 6493 Sorted by residual: dihedral pdb=" C1 BCL b 102 " pdb=" C2 BCL b 102 " pdb=" C3 BCL b 102 " pdb=" C5 BCL b 102 " ideal model delta sinusoidal sigma weight residual -180.00 -0.07 -179.93 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL a 100 " pdb=" C2 BCL a 100 " pdb=" C3 BCL a 100 " pdb=" C5 BCL a 100 " ideal model delta sinusoidal sigma weight residual -180.00 -0.08 -179.92 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL f 101 " pdb=" C2 BCL f 101 " pdb=" C3 BCL f 101 " pdb=" C5 BCL f 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.09 -179.91 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 11970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2432 0.043 - 0.085: 580 0.085 - 0.128: 91 0.128 - 0.171: 10 0.171 - 0.214: 2 Chirality restraints: 3115 Sorted by residual: chirality pdb=" C2C BPH L 302 " pdb=" C1C BPH L 302 " pdb=" C3C BPH L 302 " pdb=" CMC BPH L 302 " both_signs ideal model delta sigma weight residual False -2.81 -2.60 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C2C BPH M 408 " pdb=" C1C BPH M 408 " pdb=" C3C BPH M 408 " pdb=" CMC BPH M 408 " both_signs ideal model delta sigma weight residual False -2.81 -2.60 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C8 BPH M 408 " pdb=" C10 BPH M 408 " pdb=" C7 BPH M 408 " pdb=" C9 BPH M 408 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 3112 not shown) Planarity restraints: 3837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BPH M 408 " 0.015 2.00e-02 2.50e+03 5.06e-02 5.75e+01 pdb=" C1D BPH M 408 " 0.015 2.00e-02 2.50e+03 pdb=" C2D BPH M 408 " -0.026 2.00e-02 2.50e+03 pdb=" C3D BPH M 408 " -0.046 2.00e-02 2.50e+03 pdb=" C4D BPH M 408 " -0.023 2.00e-02 2.50e+03 pdb=" CAD BPH M 408 " 0.113 2.00e-02 2.50e+03 pdb=" CHA BPH M 408 " -0.048 2.00e-02 2.50e+03 pdb=" CHD BPH M 408 " 0.047 2.00e-02 2.50e+03 pdb=" CMD BPH M 408 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BPH L 302 " -0.016 2.00e-02 2.50e+03 3.97e-02 3.54e+01 pdb=" C1D BPH L 302 " -0.009 2.00e-02 2.50e+03 pdb=" C2D BPH L 302 " 0.021 2.00e-02 2.50e+03 pdb=" C3D BPH L 302 " 0.040 2.00e-02 2.50e+03 pdb=" C4D BPH L 302 " 0.020 2.00e-02 2.50e+03 pdb=" CAD BPH L 302 " -0.089 2.00e-02 2.50e+03 pdb=" CHA BPH L 302 " 0.036 2.00e-02 2.50e+03 pdb=" CHD BPH L 302 " -0.035 2.00e-02 2.50e+03 pdb=" CMD BPH L 302 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB BPH M 408 " -0.001 2.00e-02 2.50e+03 1.48e-02 4.91e+00 pdb=" C1B BPH M 408 " 0.010 2.00e-02 2.50e+03 pdb=" C2B BPH M 408 " -0.004 2.00e-02 2.50e+03 pdb=" C3B BPH M 408 " 0.001 2.00e-02 2.50e+03 pdb=" C4B BPH M 408 " -0.012 2.00e-02 2.50e+03 pdb=" CAB BPH M 408 " 0.027 2.00e-02 2.50e+03 pdb=" CHB BPH M 408 " 0.015 2.00e-02 2.50e+03 pdb=" CHC BPH M 408 " -0.011 2.00e-02 2.50e+03 pdb=" CMB BPH M 408 " -0.025 2.00e-02 2.50e+03 ... (remaining 3834 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 145 2.56 - 3.15: 15671 3.15 - 3.73: 35855 3.73 - 4.32: 51642 4.32 - 4.90: 84285 Nonbonded interactions: 187598 Sorted by model distance: nonbonded pdb=" OE2 GLU M 232 " pdb="FE FE M 402 " model vdw 1.980 2.260 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE M 402 " model vdw 2.082 2.340 nonbonded pdb=" NE2 HIS M 217 " pdb="FE FE M 402 " model vdw 2.106 2.340 nonbonded pdb=" OH TYR X 65 " pdb=" O ALA L 145 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR L 255 " pdb=" O LEU L 258 " model vdw 2.220 3.040 ... (remaining 187593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 49) selection = (chain 'B' and resid 8 through 49) selection = (chain 'D' and resid 8 through 49) selection = (chain 'E' and resid 8 through 49) selection = (chain 'F' and resid 8 through 49) selection = (chain 'G' and resid 8 through 49) selection = (chain 'I' and resid 8 through 49) selection = (chain 'J' and resid 8 through 49) selection = (chain 'K' and resid 8 through 49) selection = (chain 'N' and resid 8 through 49) selection = (chain 'O' and resid 8 through 49) } ncs_group { reference = (chain 'R' and resid 13 through 49) selection = (chain 'S' and resid 13 through 49) selection = (chain 'T' and resid 13 through 49) } ncs_group { reference = (chain 'a' and resid 5 through 44) selection = (chain 'o' and resid 5 through 44) } ncs_group { reference = (chain 'b' and (resid 2 through 54 or resid 101)) selection = (chain 'd' and (resid 2 through 54 or resid 101)) selection = (chain 'e' and (resid 2 through 54 or resid 101)) selection = (chain 'f' and (resid 2 through 54 or resid 101)) selection = (chain 'g' and (resid 2 through 54 or resid 101)) selection = (chain 'i' and (resid 2 through 54 or resid 101)) selection = (chain 'j' and (resid 2 through 54 or resid 101)) selection = (chain 'k' and (resid 2 through 54 or resid 101)) selection = (chain 'n' and (resid 2 through 54 or resid 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 54 or resid 101)) selection = (chain 't' and (resid 12 through 54 or resid 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 45.320 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.100 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:10.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.689 22533 Z= 1.606 Angle : 4.456 52.896 30996 Z= 1.492 Chirality : 0.036 0.214 3115 Planarity : 0.004 0.051 3837 Dihedral : 21.085 179.931 7771 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP L 185 HIS 0.006 0.001 HIS M 180 PHE 0.014 0.001 PHE L 146 TYR 0.015 0.001 TYR M 301 ARG 0.002 0.000 ARG L 109 Details of bonding type rmsd hydrogen bonds : bond 0.11721 ( 1317) hydrogen bonds : angle 4.37730 ( 3723) covalent geometry : bond 0.02046 (22512) covalent geometry : angle 4.45555 (30996) Misc. bond : bond 0.40586 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 283 time to evaluate : 1.940 Fit side-chains REVERT: a 6 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8598 (mtpp) REVERT: b 53 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.4398 (p90) REVERT: X 6 LYS cc_start: 0.7956 (mttm) cc_final: 0.7746 (mttm) REVERT: X 9 ASP cc_start: 0.7555 (t0) cc_final: 0.7277 (t70) REVERT: X 24 ARG cc_start: 0.8412 (mtt-85) cc_final: 0.8188 (mtt90) REVERT: M 166 MET cc_start: 0.9164 (mmm) cc_final: 0.8910 (mmm) REVERT: H 91 GLU cc_start: 0.8050 (tt0) cc_final: 0.7830 (tt0) REVERT: B 9 PHE cc_start: 0.9076 (m-80) cc_final: 0.8873 (m-80) REVERT: r 31 ILE cc_start: 0.7948 (mt) cc_final: 0.7707 (mt) outliers start: 22 outliers final: 8 residues processed: 300 average time/residue: 1.2125 time to fit residues: 419.0421 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 : 1.988 ------------------------------------------------------------------------------- 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 179 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN H 135 GLN H 176 GLN t 20 GLN S 21 HIS R 16 GLN o 20 GLN i 20 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.139867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.102133 restraints weight = 21046.400| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.48 r_work: 0.2622 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 22533 Z= 0.236 Angle : 1.555 44.922 30996 Z= 0.551 Chirality : 0.042 0.218 3115 Planarity : 0.005 0.065 3837 Dihedral : 25.253 179.992 3967 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.54 % Allowed : 6.23 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.17), residues: 2181 helix: 2.82 (0.12), residues: 1505 sheet: -0.49 (1.13), residues: 22 loop : 0.62 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 250 HIS 0.010 0.002 HIS L 153 PHE 0.021 0.002 PHE L 146 TYR 0.018 0.002 TYR b 53 ARG 0.007 0.001 ARG a 14 Details of bonding type rmsd hydrogen bonds : bond 0.06777 ( 1317) hydrogen bonds : angle 3.97453 ( 3723) covalent geometry : bond 0.00552 (22512) covalent geometry : angle 1.55474 (30996) Misc. bond : bond 0.00211 ( 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 303 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 256 time to evaluate : 1.935 Fit side-chains revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6749 (OUTLIER) cc_final: 0.3742 (p90) REVERT: E 7 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6228 (tp) REVERT: X 6 LYS cc_start: 0.7962 (mttm) cc_final: 0.7379 (mmtm) REVERT: L 275 MET cc_start: 0.8206 (mtp) cc_final: 0.7978 (mtt) REVERT: H 38 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8018 (mm-30) REVERT: H 139 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8007 (mmtm) REVERT: B 15 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6713 (pp20) REVERT: B 40 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8496 (tp) REVERT: r 23 PHE cc_start: 0.7058 (t80) cc_final: 0.6834 (t80) REVERT: I 19 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7497 (tt0) REVERT: I 40 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8520 (mt) outliers start: 47 outliers final: 24 residues processed: 279 average time/residue: 1.2977 time to fit residues: 413.9518 Evaluate side-chains 280 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 1.986 ------------------------------------------------------------------------------- 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 7 LEU 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 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 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 192 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 156 optimal weight: 6.9990 chunk 184 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 102 optimal weight: 0.0070 chunk 18 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 overall best weight: 2.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN H 135 GLN H 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.139925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.099381 restraints weight = 20958.167| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.29 r_work: 0.2629 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22533 Z= 0.163 Angle : 1.310 44.348 30996 Z= 0.467 Chirality : 0.039 0.179 3115 Planarity : 0.004 0.072 3837 Dihedral : 24.359 179.989 3962 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.38 % Allowed : 7.74 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.17), residues: 2181 helix: 2.87 (0.12), residues: 1506 sheet: -0.32 (1.14), residues: 22 loop : 0.69 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 250 HIS 0.008 0.001 HIS L 153 PHE 0.020 0.002 PHE L 146 TYR 0.016 0.002 TYR b 53 ARG 0.003 0.001 ARG M 130 Details of bonding type rmsd hydrogen bonds : bond 0.06055 ( 1317) hydrogen bonds : angle 3.79745 ( 3723) covalent geometry : bond 0.00374 (22512) covalent geometry : angle 1.31020 (30996) Misc. bond : bond 0.00242 ( 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 307 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 263 time to evaluate : 1.986 Fit side-chains REVERT: b 53 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.3624 (p90) REVERT: X 6 LYS cc_start: 0.7966 (mttm) cc_final: 0.7405 (mmtm) REVERT: X 56 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: L 82 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7629 (mmmm) REVERT: L 275 MET cc_start: 0.8217 (mtp) cc_final: 0.8015 (mtt) REVERT: H 70 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7902 (mtp180) REVERT: H 139 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7993 (mmtm) REVERT: B 9 PHE cc_start: 0.9066 (m-80) cc_final: 0.8815 (m-80) REVERT: B 40 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8476 (tp) REVERT: O 25 MET cc_start: 0.7439 (mmm) cc_final: 0.6538 (mmm) REVERT: I 19 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7507 (tt0) REVERT: I 40 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8531 (mt) outliers start: 44 outliers final: 17 residues processed: 287 average time/residue: 1.2482 time to fit residues: 411.0085 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 : 2.019 ------------------------------------------------------------------------------- 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 A residue 12 LEU Chi-restraints excluded: chain A residue 40 LEU 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 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 26 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 34 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN H 135 GLN H 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.137468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.098904 restraints weight = 21227.250| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.22 r_work: 0.2574 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22533 Z= 0.207 Angle : 1.239 44.077 30996 Z= 0.452 Chirality : 0.042 0.225 3115 Planarity : 0.005 0.057 3837 Dihedral : 23.642 179.985 3962 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.98 % Allowed : 7.36 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.17), residues: 2181 helix: 2.65 (0.12), residues: 1505 sheet: -0.39 (1.12), residues: 22 loop : 0.50 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 250 HIS 0.009 0.001 HIS L 153 PHE 0.022 0.002 PHE L 146 TYR 0.020 0.002 TYR b 53 ARG 0.005 0.001 ARG F 46 Details of bonding type rmsd hydrogen bonds : bond 0.06796 ( 1317) hydrogen bonds : angle 3.91435 ( 3723) covalent geometry : bond 0.00497 (22512) covalent geometry : angle 1.23927 (30996) Misc. bond : bond 0.00260 ( 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 310 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 255 time to evaluate : 1.977 Fit side-chains revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6756 (OUTLIER) cc_final: 0.3620 (p90) REVERT: E 7 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6160 (tp) REVERT: X 53 MET cc_start: 0.8327 (mtm) cc_final: 0.7841 (mmp) REVERT: L 82 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7649 (mmmm) REVERT: H 38 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8020 (mm-30) REVERT: H 70 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7945 (mtp180) REVERT: H 139 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8015 (mmtm) REVERT: B 9 PHE cc_start: 0.9094 (m-80) cc_final: 0.8797 (m-80) REVERT: B 40 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8487 (tp) REVERT: I 19 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7520 (tt0) outliers start: 55 outliers final: 21 residues processed: 285 average time/residue: 1.2695 time to fit residues: 414.4731 Evaluate side-chains 278 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 250 time to evaluate : 2.044 ------------------------------------------------------------------------------- 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 A residue 12 LEU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain N residue 26 SER 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 43 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 128 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN H 135 GLN H 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.136744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.097353 restraints weight = 21126.882| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.22 r_work: 0.2568 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2452 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 22533 Z= 0.220 Angle : 1.240 44.847 30996 Z= 0.454 Chirality : 0.043 0.241 3115 Planarity : 0.005 0.062 3837 Dihedral : 22.784 179.999 3962 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.65 % Allowed : 8.07 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.17), residues: 2181 helix: 2.57 (0.12), residues: 1505 sheet: -0.50 (1.11), residues: 22 loop : 0.43 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 250 HIS 0.009 0.002 HIS L 153 PHE 0.024 0.002 PHE L 146 TYR 0.022 0.002 TYR b 53 ARG 0.005 0.001 ARG f 15 Details of bonding type rmsd hydrogen bonds : bond 0.06930 ( 1317) hydrogen bonds : angle 3.93280 ( 3723) covalent geometry : bond 0.00538 (22512) covalent geometry : angle 1.24008 (30996) Misc. bond : bond 0.00300 ( 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 303 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 254 time to evaluate : 2.091 Fit side-chains revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.3689 (p90) REVERT: E 7 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.5884 (tp) REVERT: X 6 LYS cc_start: 0.8064 (mttm) cc_final: 0.7434 (mmtm) REVERT: X 24 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8182 (mtt-85) REVERT: X 53 MET cc_start: 0.8372 (mtm) cc_final: 0.7864 (mmt) REVERT: L 82 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7627 (mmmm) REVERT: H 38 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8082 (mm-30) REVERT: H 70 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7947 (mtp180) REVERT: H 139 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8058 (mmtm) REVERT: B 9 PHE cc_start: 0.9119 (m-80) cc_final: 0.8833 (m-80) REVERT: B 40 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8511 (tp) REVERT: S 25 MET cc_start: 0.5887 (tpp) cc_final: 0.5670 (mmt) REVERT: O 25 MET cc_start: 0.7349 (mmm) cc_final: 0.6515 (mmm) REVERT: I 19 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7448 (tt0) outliers start: 49 outliers final: 18 residues processed: 283 average time/residue: 1.3279 time to fit residues: 429.0975 Evaluate side-chains 270 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain X residue 24 ARG Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain k residue 54 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 59 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 70 optimal weight: 0.0670 chunk 38 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 42 ASN X 60 GLN H 135 GLN H 176 GLN G 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.140146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.102180 restraints weight = 21080.255| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.45 r_work: 0.2636 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22533 Z= 0.129 Angle : 1.085 43.365 30996 Z= 0.392 Chirality : 0.036 0.158 3115 Planarity : 0.004 0.039 3837 Dihedral : 22.067 179.973 3960 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.06 % Allowed : 9.20 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.17), residues: 2181 helix: 2.94 (0.12), residues: 1503 sheet: -0.30 (1.11), residues: 22 loop : 0.61 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 65 HIS 0.006 0.001 HIS L 153 PHE 0.019 0.001 PHE L 146 TYR 0.015 0.001 TYR b 53 ARG 0.005 0.000 ARG f 15 Details of bonding type rmsd hydrogen bonds : bond 0.05534 ( 1317) hydrogen bonds : angle 3.72851 ( 3723) covalent geometry : bond 0.00279 (22512) covalent geometry : angle 1.08550 (30996) Misc. bond : bond 0.00136 ( 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 296 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 2.256 Fit side-chains revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6538 (OUTLIER) cc_final: 0.3776 (p90) REVERT: E 7 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.5870 (tp) REVERT: X 6 LYS cc_start: 0.7965 (mttm) cc_final: 0.7298 (mmtm) REVERT: X 53 MET cc_start: 0.8269 (mtm) cc_final: 0.7750 (mmp) REVERT: X 56 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: X 60 GLN cc_start: 0.8502 (mt0) cc_final: 0.8279 (mt0) REVERT: H 70 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7894 (mtp180) REVERT: H 204 ARG cc_start: 0.8720 (ptp-170) cc_final: 0.8510 (ptp-170) REVERT: B 9 PHE cc_start: 0.9088 (m-80) cc_final: 0.8822 (m-80) REVERT: r 31 ILE cc_start: 0.7802 (mt) cc_final: 0.7597 (mt) REVERT: r 42 ASN cc_start: 0.8599 (t0) cc_final: 0.8374 (t0) REVERT: O 25 MET cc_start: 0.7262 (mmm) cc_final: 0.6370 (mmm) outliers start: 38 outliers final: 21 residues processed: 277 average time/residue: 1.2487 time to fit residues: 397.2611 Evaluate side-chains 278 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 2.098 ------------------------------------------------------------------------------- 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 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 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 d residue 1 MET 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 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 149 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 90 optimal weight: 0.0000 chunk 170 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 135 GLN H 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.136547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.098565 restraints weight = 20953.192| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.54 r_work: 0.2569 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 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 : 0.006 0.074 22533 Z= 0.240 Angle : 1.194 42.997 30996 Z= 0.443 Chirality : 0.045 0.257 3115 Planarity : 0.005 0.059 3837 Dihedral : 22.442 179.996 3960 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.27 % Allowed : 8.93 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.17), residues: 2181 helix: 2.55 (0.12), residues: 1507 sheet: -0.48 (1.11), residues: 22 loop : 0.45 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 250 HIS 0.010 0.002 HIS M 191 PHE 0.023 0.002 PHE L 146 TYR 0.022 0.002 TYR b 53 ARG 0.006 0.001 ARG F 46 Details of bonding type rmsd hydrogen bonds : bond 0.07128 ( 1317) hydrogen bonds : angle 3.94581 ( 3723) covalent geometry : bond 0.00588 (22512) covalent geometry : angle 1.19436 (30996) Misc. bond : bond 0.00289 ( 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 296 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 254 time to evaluate : 2.003 Fit side-chains revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6776 (OUTLIER) cc_final: 0.3685 (p90) REVERT: E 7 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.5727 (tp) REVERT: X 6 LYS cc_start: 0.7998 (mttm) cc_final: 0.7345 (mmtm) REVERT: X 24 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8097 (mtt-85) REVERT: X 53 MET cc_start: 0.8326 (mtm) cc_final: 0.7809 (mmt) REVERT: H 70 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7926 (mtp180) REVERT: H 139 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7974 (mmtm) REVERT: B 9 PHE cc_start: 0.9096 (m-80) cc_final: 0.8812 (m-80) REVERT: B 40 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8449 (tp) REVERT: O 25 MET cc_start: 0.7360 (mmm) cc_final: 0.6556 (mmm) REVERT: I 19 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7473 (tt0) outliers start: 42 outliers final: 22 residues processed: 278 average time/residue: 1.3578 time to fit residues: 432.1525 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 : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain X residue 24 ARG Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 17 GLU Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain s residue 30 LEU Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain j residue 54 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 8 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 159 optimal weight: 0.1980 chunk 169 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 135 GLN H 176 GLN G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.138331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.099194 restraints weight = 21170.932| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.27 r_work: 0.2605 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22533 Z= 0.151 Angle : 1.108 43.267 30996 Z= 0.404 Chirality : 0.038 0.199 3115 Planarity : 0.004 0.042 3837 Dihedral : 21.994 179.984 3960 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.89 % Allowed : 9.47 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.17), residues: 2181 helix: 2.81 (0.12), residues: 1504 sheet: -0.35 (1.11), residues: 22 loop : 0.58 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP n 8 HIS 0.007 0.001 HIS L 153 PHE 0.021 0.001 PHE L 146 TYR 0.017 0.002 TYR b 53 ARG 0.005 0.000 ARG f 15 Details of bonding type rmsd hydrogen bonds : bond 0.05977 ( 1317) hydrogen bonds : angle 3.78513 ( 3723) covalent geometry : bond 0.00346 (22512) covalent geometry : angle 1.10787 (30996) Misc. bond : bond 0.00200 ( 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 292 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 257 time to evaluate : 2.111 Fit side-chains revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6550 (OUTLIER) cc_final: 0.3657 (p90) REVERT: E 7 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.5683 (tp) REVERT: X 6 LYS cc_start: 0.8041 (mttm) cc_final: 0.7386 (mmtm) REVERT: X 53 MET cc_start: 0.8308 (mtm) cc_final: 0.7816 (mmt) REVERT: X 56 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: H 70 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7902 (mtp180) REVERT: H 139 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7969 (mmtm) REVERT: B 9 PHE cc_start: 0.9102 (m-80) cc_final: 0.8806 (m-80) REVERT: B 15 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6838 (pp20) REVERT: B 40 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8447 (tp) REVERT: O 25 MET cc_start: 0.7441 (mmm) cc_final: 0.6581 (mmm) outliers start: 35 outliers final: 19 residues processed: 277 average time/residue: 1.2838 time to fit residues: 406.3064 Evaluate side-chains 278 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 252 time to evaluate : 1.977 ------------------------------------------------------------------------------- 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 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain j residue 54 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 175 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 193 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 135 GLN H 176 GLN G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.137044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.099224 restraints weight = 21043.139| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.54 r_work: 0.2575 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 22533 Z= 0.209 Angle : 1.165 42.986 30996 Z= 0.430 Chirality : 0.042 0.227 3115 Planarity : 0.005 0.056 3837 Dihedral : 22.073 179.979 3960 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.22 % Allowed : 9.42 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.17), residues: 2181 helix: 2.58 (0.12), residues: 1510 sheet: -0.47 (1.12), residues: 22 loop : 0.48 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP n 8 HIS 0.009 0.002 HIS L 153 PHE 0.023 0.002 PHE L 146 TYR 0.021 0.002 TYR b 53 ARG 0.007 0.001 ARG f 15 Details of bonding type rmsd hydrogen bonds : bond 0.06776 ( 1317) hydrogen bonds : angle 3.91058 ( 3723) covalent geometry : bond 0.00508 (22512) covalent geometry : angle 1.16469 (30996) Misc. bond : bond 0.00283 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6668 (OUTLIER) cc_final: 0.3719 (p90) REVERT: E 7 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.5570 (tp) REVERT: X 6 LYS cc_start: 0.7998 (mttm) cc_final: 0.7332 (mmtm) REVERT: X 24 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8101 (mtt-85) REVERT: X 53 MET cc_start: 0.8307 (mtm) cc_final: 0.7734 (mmp) REVERT: X 56 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: H 38 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8009 (mm-30) REVERT: H 70 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7918 (mtp180) REVERT: H 139 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7959 (mmtm) REVERT: B 40 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8426 (tp) REVERT: O 25 MET cc_start: 0.7319 (mmm) cc_final: 0.6511 (mmm) REVERT: I 19 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7436 (tt0) REVERT: I 40 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8546 (mt) REVERT: J 13 THR cc_start: 0.7512 (OUTLIER) cc_final: 0.7219 (p) outliers start: 41 outliers final: 21 residues processed: 278 average time/residue: 1.3134 time to fit residues: 417.4498 Evaluate side-chains 282 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain b residue 53 TYR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain X residue 24 ARG Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 15 GLU Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain j residue 54 VAL Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain J residue 13 THR 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 104 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 97 optimal weight: 0.1980 chunk 112 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 135 GLN H 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.141696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.104807 restraints weight = 21164.999| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.45 r_work: 0.2669 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1647 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= 0.120 Angle : 1.074 43.326 30996 Z= 0.388 Chirality : 0.036 0.148 3115 Planarity : 0.003 0.039 3837 Dihedral : 21.443 179.963 3960 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.41 % Allowed : 10.02 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.17), residues: 2181 helix: 2.96 (0.12), residues: 1503 sheet: -0.09 (1.15), residues: 22 loop : 0.62 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP n 8 HIS 0.005 0.001 HIS M 180 PHE 0.018 0.001 PHE L 146 TYR 0.017 0.001 TYR a 5 ARG 0.005 0.000 ARG f 15 Details of bonding type rmsd hydrogen bonds : bond 0.05234 ( 1317) hydrogen bonds : angle 3.70594 ( 3723) covalent geometry : bond 0.00257 (22512) covalent geometry : angle 1.07406 (30996) Misc. bond : bond 0.00141 ( 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 282 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 53 TYR cc_start: 0.6315 (OUTLIER) cc_final: 0.3584 (p90) REVERT: b 54 VAL cc_start: 0.5853 (OUTLIER) cc_final: 0.5618 (p) REVERT: E 19 GLU cc_start: 0.8137 (tp30) cc_final: 0.7721 (tp30) REVERT: X 6 LYS cc_start: 0.7942 (mttm) cc_final: 0.7264 (mmtm) REVERT: X 17 GLU cc_start: 0.8570 (mt-10) cc_final: 0.7717 (mm-30) REVERT: X 24 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8057 (mtt-85) REVERT: X 53 MET cc_start: 0.8243 (mtm) cc_final: 0.7756 (mmt) REVERT: X 56 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: B 9 PHE cc_start: 0.9054 (m-80) cc_final: 0.8846 (m-80) REVERT: r 31 ILE cc_start: 0.7685 (mt) cc_final: 0.7475 (mt) REVERT: O 25 MET cc_start: 0.7285 (mmm) cc_final: 0.6362 (mmm) outliers start: 26 outliers final: 15 residues processed: 274 average time/residue: 1.2389 time to fit residues: 389.1471 Evaluate side-chains 270 residues out of total 1847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 251 time to evaluate : 1.965 ------------------------------------------------------------------------------- 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 X residue 24 ARG Chi-restraints excluded: chain X residue 56 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain S residue 15 GLU Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain j residue 54 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 29 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 135 optimal weight: 20.0000 chunk 195 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 43 ASN H 135 GLN H 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.139648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.099264 restraints weight = 21092.997| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.27 r_work: 0.2634 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22533 Z= 0.135 Angle : 1.088 43.272 30996 Z= 0.395 Chirality : 0.037 0.169 3115 Planarity : 0.004 0.039 3837 Dihedral : 21.330 179.975 3960 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.41 % Allowed : 10.18 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.17), residues: 2181 helix: 2.95 (0.12), residues: 1506 sheet: -0.23 (1.15), residues: 22 loop : 0.63 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP n 8 HIS 0.008 0.001 HIS L 153 PHE 0.019 0.001 PHE L 146 TYR 0.017 0.001 TYR a 5 ARG 0.005 0.000 ARG f 15 Details of bonding type rmsd hydrogen bonds : bond 0.05574 ( 1317) hydrogen bonds : angle 3.72098 ( 3723) covalent geometry : bond 0.00303 (22512) covalent geometry : angle 1.08804 (30996) Misc. bond : bond 0.00187 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15706.76 seconds wall clock time: 270 minutes 35.09 seconds (16235.09 seconds total)