Starting phenix.real_space_refine on Fri Sep 19 03:48:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygl_39255/09_2025/8ygl_39255.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygl_39255/09_2025/8ygl_39255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ygl_39255/09_2025/8ygl_39255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygl_39255/09_2025/8ygl_39255.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygl_39255/09_2025/8ygl_39255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygl_39255/09_2025/8ygl_39255.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.051 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 17 5.49 5 Mg 34 5.21 5 S 66 5.16 5 C 16441 2.51 5 N 3181 2.21 5 O 3482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23222 Number of models: 1 Model: "" Number of chains: 68 Chain: "0" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "1" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "2" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 319 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "3" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "7" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 387 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "8" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "9" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "A" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "B" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "C" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "D" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "E" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "G" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "H" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1980 Classifications: {'peptide': 254} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 235} Chain: "I" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "J" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "L" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2231 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 267} Chain: "M" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2432 Classifications: {'peptide': 304} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 294} Chain: "N" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "P" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "R" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "S" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "T" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "U" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "V" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "W" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "X" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 379 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "Z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "a" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "b" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "0" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "1" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "3" 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: "7" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "9" 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: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 175 Unusual residues: {'BCL': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 53 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "C" 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: "D" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 187 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" 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: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 78 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 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: "J" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 497 Unusual residues: {'BCL': 2, 'BPH': 2, 'PC1': 3, 'U10': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'U10:plan-8': 3, 'U10:plan-9': 4, 'U10:plan-10': 4, 'U10:plan-11': 4, 'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 2} Unresolved non-hydrogen planarities: 84 Chain: "M" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 576 Unusual residues: {'BCL': 2, 'CDL': 2, 'FE2': 1, 'PC1': 3, 'SPO': 1, 'U10': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 28 Chain: "N" 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: "O" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 182 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "P" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" 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: "T" 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: "U" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" 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: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 87 Unusual residues: {'SPO': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'SPO:plan-4': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 15 Chain: "Z" 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: "a" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.77, per 1000 atoms: 0.25 Number of scatterers: 23222 At special positions: 0 Unit cell: (92.9, 132.847, 136.563, 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 66 16.00 P 17 15.00 Mg 34 11.99 O 3482 8.00 N 3181 7.00 C 16441 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=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 900.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4258 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 8 sheets defined 73.9% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain '0' and resid 13 through 46 Processing helix chain '1' and resid 6 through 11 Processing helix chain '1' and resid 12 through 38 removed outlier: 3.529A pdb=" N LYS 1 38 " --> pdb=" O ILE 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 52 Processing helix chain '2' and resid 13 through 46 removed outlier: 3.842A pdb=" N VAL 2 23 " --> pdb=" O GLU 2 19 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 5 No H-bonds generated for 'chain '3' and resid 3 through 5' Processing helix chain '3' and resid 6 through 11 removed outlier: 4.078A pdb=" N VAL 3 10 " --> pdb=" O LYS 3 6 " (cutoff:3.500A) Processing helix chain '3' and resid 12 through 38 Processing helix chain '3' and resid 42 through 51 Processing helix chain '7' and resid 3 through 10 Processing helix chain '7' and resid 12 through 37 Processing helix chain '8' and resid 13 through 46 Processing helix chain '9' and resid 3 through 9 Processing helix chain '9' and resid 12 through 37 Processing helix chain '9' and resid 42 through 51 Processing helix chain 'A' and resid 3 through 9 Processing helix chain 'A' and resid 12 through 38 Processing helix chain 'A' and resid 42 through 51 removed outlier: 3.549A pdb=" N TYR A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 46 Processing helix chain 'C' and resid 18 through 51 Processing helix chain 'D' and resid 3 through 5 No H-bonds generated for 'chain 'D' and resid 3 through 5' Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 12 through 38 Processing helix chain 'D' and resid 42 through 52 Processing helix chain 'E' and resid 13 through 46 Processing helix chain 'F' and resid 3 through 10 removed outlier: 3.579A pdb=" N ILE F 7 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP F 8 " --> pdb=" O TYR F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 38 Processing helix chain 'F' and resid 42 through 52 Processing helix chain 'G' and resid 13 through 46 Processing helix chain 'H' and resid 11 through 35 Processing helix chain 'H' and resid 77 through 84 Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 113 through 117 Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 230 through 248 removed outlier: 3.773A pdb=" N GLY H 244 " --> pdb=" O TYR H 240 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TRP H 245 " --> pdb=" O VAL H 241 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU H 246 " --> pdb=" O ALA H 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 5 No H-bonds generated for 'chain 'I' and resid 3 through 5' Processing helix chain 'I' and resid 6 through 11 Processing helix chain 'I' and resid 12 through 38 removed outlier: 3.563A pdb=" N LYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 52 Processing helix chain 'J' and resid 13 through 46 Processing helix chain 'K' and resid 3 through 5 No H-bonds generated for 'chain 'K' and resid 3 through 5' Processing helix chain 'K' and resid 6 through 11 Processing helix chain 'K' and resid 12 through 37 Processing helix chain 'K' and resid 42 through 52 Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 33 through 58 Processing helix chain 'L' and resid 84 through 113 Processing helix chain 'L' and resid 116 through 134 removed outlier: 3.641A pdb=" N PHE L 124 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 141 Processing helix chain 'L' and resid 142 through 146 removed outlier: 3.797A pdb=" N TYR L 145 " --> pdb=" O SER L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 164 removed outlier: 3.741A pdb=" N ASP L 156 " --> pdb=" O TRP L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 166 No H-bonds generated for 'chain 'L' and resid 165 through 166' Processing helix chain 'L' and resid 167 through 170 Processing helix chain 'L' and resid 171 through 200 Processing helix chain 'L' and resid 209 through 222 removed outlier: 3.600A pdb=" N GLU L 213 " --> pdb=" O THR L 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 251 removed outlier: 3.885A pdb=" N HIS L 231 " --> pdb=" O THR L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 263 Processing helix chain 'L' and resid 264 through 269 removed outlier: 3.883A pdb=" N VAL L 268 " --> pdb=" O TRP L 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 42 removed outlier: 3.555A pdb=" N GLY M 41 " --> pdb=" O TRP M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 79 Processing helix chain 'M' and resid 82 through 89 Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'M' and resid 109 through 140 removed outlier: 3.753A pdb=" N LEU M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 162 removed outlier: 3.807A pdb=" N SER M 152 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 169 removed outlier: 3.536A pdb=" N ILE M 166 " --> pdb=" O PHE M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 174 Processing helix chain 'M' and resid 178 through 193 removed outlier: 3.831A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 226 Processing helix chain 'M' and resid 227 through 230 Processing helix chain 'M' and resid 233 through 240 removed outlier: 3.862A pdb=" N VAL M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 257 Processing helix chain 'M' and resid 264 through 290 removed outlier: 3.512A pdb=" N TRP M 268 " --> pdb=" O GLY M 264 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL M 276 " --> pdb=" O PHE M 272 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR M 277 " --> pdb=" O GLY M 273 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLY M 288 " --> pdb=" O ILE M 284 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR M 289 " --> pdb=" O LEU M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 removed outlier: 3.516A pdb=" N TRP M 297 " --> pdb=" O ASN M 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 46 Processing helix chain 'O' and resid 3 through 10 Processing helix chain 'O' and resid 12 through 37 removed outlier: 3.779A pdb=" N VAL O 18 " --> pdb=" O ARG O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 52 Processing helix chain 'P' and resid 13 through 46 Processing helix chain 'Q' and resid 3 through 10 removed outlier: 3.734A pdb=" N TRP Q 8 " --> pdb=" O TYR Q 5 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL Q 10 " --> pdb=" O ILE Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 38 Processing helix chain 'Q' and resid 42 through 51 Processing helix chain 'R' and resid 13 through 46 Processing helix chain 'S' and resid 3 through 5 No H-bonds generated for 'chain 'S' and resid 3 through 5' Processing helix chain 'S' and resid 6 through 11 Processing helix chain 'S' and resid 12 through 38 removed outlier: 3.561A pdb=" N VAL S 16 " --> pdb=" O ASP S 12 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS S 38 " --> pdb=" O ILE S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 51 Processing helix chain 'T' and resid 13 through 46 Processing helix chain 'U' and resid 3 through 10 Processing helix chain 'U' and resid 12 through 38 removed outlier: 3.505A pdb=" N LYS U 38 " --> pdb=" O ILE U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 51 Processing helix chain 'V' and resid 13 through 46 Processing helix chain 'W' and resid 3 through 5 No H-bonds generated for 'chain 'W' and resid 3 through 5' Processing helix chain 'W' and resid 6 through 11 Processing helix chain 'W' and resid 12 through 38 Processing helix chain 'W' and resid 42 through 52 Processing helix chain 'X' and resid 15 through 51 Processing helix chain 'X' and resid 52 through 58 removed outlier: 6.028A pdb=" N GLN X 55 " --> pdb=" O LEU X 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 46 removed outlier: 4.407A pdb=" N GLN Z 16 " --> pdb=" O LEU Z 12 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLN Z 18 " --> pdb=" O ASP Z 14 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU Z 19 " --> pdb=" O GLU Z 15 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 38 removed outlier: 3.718A pdb=" N VAL a 16 " --> pdb=" O ASP a 12 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL a 18 " --> pdb=" O ARG a 14 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY a 21 " --> pdb=" O PHE a 17 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 51 removed outlier: 3.749A pdb=" N VAL a 46 " --> pdb=" O ASN a 42 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY a 47 " --> pdb=" O TRP a 43 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 15 No H-bonds generated for 'chain 'b' and resid 13 through 15' Processing helix chain 'b' and resid 16 through 46 removed outlier: 4.318A pdb=" N ILE b 44 " --> pdb=" O ILE b 40 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP b 45 " --> pdb=" O ALA b 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 62 through 66 removed outlier: 4.296A pdb=" N GLY H 71 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 91 through 93 Processing sheet with id=AA3, first strand: chain 'H' and resid 135 through 137 removed outlier: 6.766A pdb=" N GLU H 184 " --> pdb=" O SER H 169 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU H 171 " --> pdb=" O TYR H 182 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR H 182 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL H 173 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL H 180 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 135 through 137 removed outlier: 6.489A pdb=" N VAL H 164 " --> pdb=" O ALA H 159 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA H 159 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY H 166 " --> pdb=" O VAL H 157 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL H 209 " --> pdb=" O PRO H 156 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN H 158 " --> pdb=" O VAL H 209 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 145 through 149 removed outlier: 6.906A pdb=" N GLN M 12 " --> pdb=" O THR H 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 25 through 27 removed outlier: 3.982A pdb=" N PHE L 25 " --> pdb=" O VAL L 32 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 66 through 67 Processing sheet with id=AA8, first strand: chain 'M' and resid 35 through 36 1296 hydrogen bonds defined for protein. 3732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.34 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 8734 1.38 - 1.56: 15019 1.56 - 1.74: 68 1.74 - 1.92: 128 1.92 - 2.10: 136 Bond restraints: 24085 Sorted by residual: bond pdb=" C23 U10 M 407 " pdb=" C24 U10 M 407 " ideal model delta sigma weight residual 1.470 1.324 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" C23 U10 M 403 " pdb=" C24 U10 M 403 " ideal model delta sigma weight residual 1.470 1.324 0.146 2.00e-02 2.50e+03 5.31e+01 bond pdb=" C33 U10 M 407 " pdb=" C34 U10 M 407 " ideal model delta sigma weight residual 1.470 1.325 0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" C8 U10 M 407 " pdb=" C9 U10 M 407 " ideal model delta sigma weight residual 1.470 1.325 0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" C13 U10 M 407 " pdb=" C14 U10 M 407 " ideal model delta sigma weight residual 1.470 1.325 0.145 2.00e-02 2.50e+03 5.23e+01 ... (remaining 24080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 30672 2.32 - 4.63: 1832 4.63 - 6.95: 409 6.95 - 9.27: 78 9.27 - 11.58: 34 Bond angle restraints: 33025 Sorted by residual: angle pdb=" ND BCL V 102 " pdb="MG BCL V 102 " pdb=" NC BCL V 102 " ideal model delta sigma weight residual 85.24 80.08 5.15 9.98e-01 1.00e+00 2.67e+01 angle pdb=" ND BCL T 101 " pdb="MG BCL T 101 " pdb=" NC BCL T 101 " ideal model delta sigma weight residual 85.24 80.12 5.12 9.98e-01 1.00e+00 2.63e+01 angle pdb=" ND BCL E 101 " pdb="MG BCL E 101 " pdb=" NC BCL E 101 " ideal model delta sigma weight residual 85.24 80.19 5.05 9.98e-01 1.00e+00 2.56e+01 angle pdb=" ND BCL M 405 " pdb="MG BCL M 405 " pdb=" NC BCL M 405 " ideal model delta sigma weight residual 85.24 80.19 5.04 9.98e-01 1.00e+00 2.56e+01 angle pdb=" ND BCL 8 101 " pdb="MG BCL 8 101 " pdb=" NC BCL 8 101 " ideal model delta sigma weight residual 85.24 80.21 5.03 9.98e-01 1.00e+00 2.54e+01 ... (remaining 33020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 12203 35.79 - 71.57: 656 71.57 - 107.36: 49 107.36 - 143.14: 12 143.14 - 178.93: 14 Dihedral angle restraints: 12934 sinusoidal: 6308 harmonic: 6626 Sorted by residual: dihedral pdb=" CBD BCL 1 101 " pdb=" CGD BCL 1 101 " pdb=" O2D BCL 1 101 " pdb=" CED BCL 1 101 " ideal model delta sinusoidal sigma weight residual -180.00 -14.79 -165.21 1 5.00e+00 4.00e-02 7.55e+02 dihedral pdb=" C1 BCL N 102 " pdb=" CGA BCL N 102 " pdb=" O2A BCL N 102 " pdb=" CBA BCL N 102 " ideal model delta sinusoidal sigma weight residual -180.00 -4.70 -175.30 1 6.00e+00 2.78e-02 5.32e+02 dihedral pdb=" CBD BCL U 101 " pdb=" CGD BCL U 101 " pdb=" O2D BCL U 101 " pdb=" CED BCL U 101 " ideal model delta sinusoidal sigma weight residual -180.00 -70.60 -109.40 1 5.00e+00 4.00e-02 5.12e+02 ... (remaining 12931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.042: 3162 1.042 - 2.085: 0 2.085 - 3.127: 0 3.127 - 4.169: 0 4.169 - 5.212: 6 Chirality restraints: 3168 Sorted by residual: chirality pdb=" C18 BCL E 101 " pdb=" C17 BCL E 101 " pdb=" C19 BCL E 101 " pdb=" C20 BCL E 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.50 5.21 2.00e-01 2.50e+01 6.79e+02 chirality pdb=" C18 BCL J 101 " pdb=" C17 BCL J 101 " pdb=" C19 BCL J 101 " pdb=" C20 BCL J 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.50 5.21 2.00e-01 2.50e+01 6.78e+02 chirality pdb=" C18 BCL C 101 " pdb=" C17 BCL C 101 " pdb=" C19 BCL C 101 " pdb=" C20 BCL C 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.49 5.20 2.00e-01 2.50e+01 6.75e+02 ... (remaining 3165 not shown) Planarity restraints: 4033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL 1 101 " -0.361 1.50e-02 4.44e+03 3.04e-01 2.05e+03 pdb=" C2 BCL 1 101 " 0.524 1.50e-02 4.44e+03 pdb=" C3 BCL 1 101 " 0.114 1.50e-02 4.44e+03 pdb=" C4 BCL 1 101 " -0.093 1.50e-02 4.44e+03 pdb=" C5 BCL 1 101 " -0.185 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL 2 101 " 0.359 1.50e-02 4.44e+03 3.02e-01 2.03e+03 pdb=" C2 BCL 2 101 " -0.525 1.50e-02 4.44e+03 pdb=" C3 BCL 2 101 " -0.111 1.50e-02 4.44e+03 pdb=" C4 BCL 2 101 " 0.104 1.50e-02 4.44e+03 pdb=" C5 BCL 2 101 " 0.173 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL E 101 " 0.355 1.50e-02 4.44e+03 2.98e-01 1.97e+03 pdb=" C2 BCL E 101 " -0.514 1.50e-02 4.44e+03 pdb=" C3 BCL E 101 " -0.109 1.50e-02 4.44e+03 pdb=" C4 BCL E 101 " 0.187 1.50e-02 4.44e+03 pdb=" C5 BCL E 101 " 0.081 1.50e-02 4.44e+03 ... (remaining 4030 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 111 2.50 - 3.10: 15754 3.10 - 3.70: 35340 3.70 - 4.30: 56331 4.30 - 4.90: 91740 Nonbonded interactions: 199276 Sorted by model distance: nonbonded pdb=" OE1 GLN O 20 " pdb=" OH TYR P 24 " model vdw 1.900 3.040 nonbonded pdb=" OG SER M 152 " pdb=" OG1 THR M 277 " model vdw 1.965 3.040 nonbonded pdb=" O CYS L 248 " pdb=" OG1 THR L 252 " model vdw 2.005 3.040 nonbonded pdb=" OH TYR 0 24 " pdb=" OE1 GLN 9 20 " model vdw 2.008 3.040 nonbonded pdb=" OE1 GLN K 20 " pdb=" OH TYR N 24 " model vdw 2.011 3.040 ... (remaining 199271 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 '0' and resid 10 through 48) selection = (chain '2' and resid 10 through 48) selection = (chain '8' and resid 10 through 48) selection = (chain 'B' and resid 10 through 48) selection = (chain 'C' and resid 15 through 53) selection = (chain 'E' and resid 10 through 48) selection = (chain 'G' and resid 10 through 48) selection = (chain 'J' and resid 10 through 48) selection = (chain 'N' and resid 10 through 48) selection = (chain 'P' and resid 10 through 48) selection = (chain 'R' and resid 10 through 48) selection = (chain 'T' and resid 10 through 48) selection = (chain 'V' and resid 10 through 48) selection = (chain 'Z' and resid 10 through 48) } ncs_group { reference = (chain '1' and resid 4 through 52) selection = (chain '3' and resid 4 through 52) selection = (chain '9' and resid 4 through 52) selection = (chain 'A' and resid 4 through 52) selection = (chain 'D' and resid 4 through 52) selection = (chain 'F' and resid 4 through 52) selection = (chain 'I' and resid 4 through 52) selection = (chain 'K' and resid 4 through 52) selection = (chain 'O' and resid 4 through 52) selection = (chain 'Q' and resid 4 through 52) selection = (chain 'S' and resid 4 through 52) selection = (chain 'U' and resid 4 through 52) selection = (chain 'W' and resid 4 through 52) selection = (chain 'a' and resid 4 through 52) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 19.390 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 : 0.021 0.881 24099 Z= 1.718 Angle : 1.279 11.583 33025 Z= 0.597 Chirality : 0.241 5.212 3168 Planarity : 0.028 0.330 4033 Dihedral : 20.449 178.930 8676 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.16), residues: 2229 helix: -0.76 (0.11), residues: 1533 sheet: 0.78 (1.05), residues: 30 loop : -1.51 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 14 TYR 0.021 0.001 TYR b 43 PHE 0.057 0.002 PHE M 216 TRP 0.043 0.002 TRP L 273 HIS 0.010 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.01428 (24085) covalent geometry : angle 1.27881 (33025) hydrogen bonds : bond 0.12738 ( 1294) hydrogen bonds : angle 5.06783 ( 3732) Misc. bond : bond 0.65991 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.594 Fit side-chains REVERT: 1 30 MET cc_start: 0.5672 (tmm) cc_final: 0.5434 (tmm) REVERT: F 41 TYR cc_start: 0.8542 (m-80) cc_final: 0.8187 (m-80) REVERT: L 8 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8049 (ttp-170) REVERT: M 27 LEU cc_start: 0.8486 (mm) cc_final: 0.8274 (mt) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.5847 time to fit residues: 155.5993 Evaluate side-chains 186 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 20 GLN 2 16 GLN 3 20 GLN 7 20 GLN 9 42 ASN C 23 GLN D 9 GLN ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 ASN ** L 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 ASN S 20 GLN T 21 HIS Z 16 GLN b 21 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114316 restraints weight = 26076.142| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.29 r_work: 0.3191 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24099 Z= 0.156 Angle : 0.799 15.651 33025 Z= 0.310 Chirality : 0.040 0.252 3168 Planarity : 0.004 0.048 4033 Dihedral : 20.130 179.960 4602 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.03 % Allowed : 7.12 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.17), residues: 2229 helix: 1.28 (0.12), residues: 1554 sheet: 2.17 (1.21), residues: 20 loop : -0.68 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 53 TYR 0.014 0.001 TYR M 193 PHE 0.020 0.001 PHE S 11 TRP 0.019 0.001 TRP M 157 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00369 (24085) covalent geometry : angle 0.79897 (33025) hydrogen bonds : bond 0.05212 ( 1294) hydrogen bonds : angle 3.81463 ( 3732) Misc. bond : bond 0.00182 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.5706 (tmm) cc_final: 0.5325 (tmm) REVERT: 7 3 LYS cc_start: 0.8103 (mtpt) cc_final: 0.7886 (mtpp) REVERT: 7 15 ARG cc_start: 0.7545 (mmt180) cc_final: 0.7336 (mmt180) REVERT: C 30 MET cc_start: 0.7549 (mmm) cc_final: 0.7277 (mmm) REVERT: F 41 TYR cc_start: 0.8992 (m-80) cc_final: 0.8536 (m-80) REVERT: H 46 ASP cc_start: 0.7984 (p0) cc_final: 0.7663 (p0) REVERT: H 178 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: H 184 GLU cc_start: 0.8535 (tt0) cc_final: 0.8269 (tt0) REVERT: H 228 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8189 (pt0) REVERT: H 235 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7488 (t0) REVERT: M 26 ASP cc_start: 0.7994 (t0) cc_final: 0.7631 (t70) REVERT: M 36 ASN cc_start: 0.8097 (m-40) cc_final: 0.7756 (t0) REVERT: M 69 MET cc_start: 0.9248 (mmp) cc_final: 0.9021 (mmp) REVERT: Q 6 LYS cc_start: 0.8097 (mttt) cc_final: 0.7821 (mttp) REVERT: Q 9 GLN cc_start: 0.8224 (mt0) cc_final: 0.7861 (mm110) REVERT: S 51 TYR cc_start: 0.8525 (m-80) cc_final: 0.7918 (m-80) REVERT: W 11 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6214 (m-10) outliers start: 20 outliers final: 10 residues processed: 213 average time/residue: 0.5157 time to fit residues: 127.4895 Evaluate side-chains 200 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 26 SER Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 147 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 69 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** L 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 ASN W 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113662 restraints weight = 26348.236| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.29 r_work: 0.3201 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24099 Z= 0.124 Angle : 0.708 15.299 33025 Z= 0.274 Chirality : 0.037 0.139 3168 Planarity : 0.003 0.043 4033 Dihedral : 18.882 179.951 4602 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.24 % Allowed : 9.14 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.17), residues: 2229 helix: 2.00 (0.13), residues: 1556 sheet: 2.49 (1.16), residues: 20 loop : -0.51 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 46 TYR 0.013 0.001 TYR M 303 PHE 0.016 0.001 PHE S 11 TRP 0.016 0.001 TRP M 74 HIS 0.006 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00274 (24085) covalent geometry : angle 0.70755 (33025) hydrogen bonds : bond 0.04683 ( 1294) hydrogen bonds : angle 3.54099 ( 3732) Misc. bond : bond 0.00199 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6085 (tmm) cc_final: 0.5696 (tmm) REVERT: 1 41 TYR cc_start: 0.7431 (m-80) cc_final: 0.6730 (m-80) REVERT: H 46 ASP cc_start: 0.8092 (p0) cc_final: 0.7733 (p0) REVERT: H 178 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8251 (mt0) REVERT: H 184 GLU cc_start: 0.8461 (tt0) cc_final: 0.8222 (tt0) REVERT: H 228 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8136 (pt0) REVERT: H 235 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7531 (t0) REVERT: I 7 ILE cc_start: 0.8892 (tt) cc_final: 0.8686 (tp) REVERT: M 26 ASP cc_start: 0.7895 (t0) cc_final: 0.7546 (t70) REVERT: M 36 ASN cc_start: 0.7943 (m-40) cc_final: 0.7676 (t0) REVERT: M 69 MET cc_start: 0.9233 (mmp) cc_final: 0.9019 (mmp) REVERT: O 5 TYR cc_start: 0.8344 (p90) cc_final: 0.7951 (p90) REVERT: Q 9 GLN cc_start: 0.8114 (mt0) cc_final: 0.7774 (mm110) REVERT: W 11 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6368 (m-10) REVERT: X 40 CYS cc_start: 0.8224 (m) cc_final: 0.8009 (m) outliers start: 24 outliers final: 8 residues processed: 227 average time/residue: 0.5182 time to fit residues: 137.5612 Evaluate side-chains 204 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain b residue 40 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 105 optimal weight: 0.6980 chunk 200 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 197 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 9 GLN 7 42 ASN D 20 GLN ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 171 ASN L 200 ASN L 205 GLN L 262 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.147959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109238 restraints weight = 26459.643| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.29 r_work: 0.3135 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24099 Z= 0.151 Angle : 0.740 19.683 33025 Z= 0.291 Chirality : 0.038 0.137 3168 Planarity : 0.003 0.043 4033 Dihedral : 18.930 179.912 4602 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.70 % Allowed : 9.76 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.17), residues: 2229 helix: 2.05 (0.12), residues: 1554 sheet: 1.33 (1.02), residues: 27 loop : -0.40 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 46 TYR 0.016 0.001 TYR M 193 PHE 0.019 0.001 PHE S 11 TRP 0.016 0.001 TRP M 74 HIS 0.008 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00359 (24085) covalent geometry : angle 0.74008 (33025) hydrogen bonds : bond 0.05027 ( 1294) hydrogen bonds : angle 3.58046 ( 3732) Misc. bond : bond 0.00251 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6027 (tmm) cc_final: 0.5617 (tmm) REVERT: 1 41 TYR cc_start: 0.7366 (m-80) cc_final: 0.6608 (m-80) REVERT: A 40 ASP cc_start: 0.8565 (t0) cc_final: 0.8345 (t0) REVERT: H 46 ASP cc_start: 0.8266 (p0) cc_final: 0.7859 (p0) REVERT: H 178 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8308 (mt0) REVERT: H 184 GLU cc_start: 0.8511 (tt0) cc_final: 0.8296 (tt0) REVERT: H 228 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8172 (pt0) REVERT: H 235 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7637 (t0) REVERT: I 7 ILE cc_start: 0.8842 (tt) cc_final: 0.8630 (tp) REVERT: M 26 ASP cc_start: 0.7936 (t0) cc_final: 0.7545 (t70) REVERT: M 36 ASN cc_start: 0.7992 (m-40) cc_final: 0.7693 (t0) REVERT: M 69 MET cc_start: 0.9243 (mmp) cc_final: 0.9024 (mmp) REVERT: O 5 TYR cc_start: 0.8362 (p90) cc_final: 0.7983 (p90) REVERT: O 26 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8155 (mp) REVERT: Q 6 LYS cc_start: 0.7989 (mttt) cc_final: 0.7710 (mttp) REVERT: Q 9 GLN cc_start: 0.8153 (mt0) cc_final: 0.7913 (mm-40) REVERT: S 51 TYR cc_start: 0.8475 (m-80) cc_final: 0.7967 (m-80) REVERT: U 53 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7589 (ptt180) REVERT: W 11 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.6301 (m-10) REVERT: X 39 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7491 (mp) outliers start: 33 outliers final: 9 residues processed: 222 average time/residue: 0.5374 time to fit residues: 138.6582 Evaluate side-chains 211 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 30 MET Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 39 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 150 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 GLN F 32 HIS L 200 ASN M 5 GLN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 9 GLN b 39 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.145415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107063 restraints weight = 26625.367| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.27 r_work: 0.3106 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24099 Z= 0.188 Angle : 0.787 19.994 33025 Z= 0.311 Chirality : 0.040 0.159 3168 Planarity : 0.004 0.045 4033 Dihedral : 18.984 179.831 4602 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.17 % Allowed : 10.17 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.17), residues: 2229 helix: 1.96 (0.12), residues: 1539 sheet: 1.27 (1.00), residues: 27 loop : -0.32 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 46 TYR 0.019 0.002 TYR M 193 PHE 0.023 0.002 PHE S 11 TRP 0.017 0.002 TRP M 74 HIS 0.008 0.001 HIS M 266 Details of bonding type rmsd covalent geometry : bond 0.00458 (24085) covalent geometry : angle 0.78662 (33025) hydrogen bonds : bond 0.05427 ( 1294) hydrogen bonds : angle 3.67078 ( 3732) Misc. bond : bond 0.00292 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.667 Fit side-chains REVERT: 1 30 MET cc_start: 0.5989 (tmm) cc_final: 0.5557 (tmm) REVERT: 3 51 TYR cc_start: 0.7340 (m-80) cc_final: 0.6804 (m-80) REVERT: H 55 LEU cc_start: 0.7815 (mt) cc_final: 0.6988 (tt) REVERT: H 178 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8334 (mt0) REVERT: H 184 GLU cc_start: 0.8520 (tt0) cc_final: 0.8243 (tt0) REVERT: H 228 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8175 (pt0) REVERT: H 235 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7718 (t0) REVERT: M 26 ASP cc_start: 0.7806 (t0) cc_final: 0.7345 (t70) REVERT: M 36 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7710 (t0) REVERT: M 69 MET cc_start: 0.9270 (mmp) cc_final: 0.9002 (mmp) REVERT: O 5 TYR cc_start: 0.8400 (p90) cc_final: 0.7980 (p90) REVERT: O 26 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8222 (mp) REVERT: Q 9 GLN cc_start: 0.8255 (mt0) cc_final: 0.7986 (mm-40) REVERT: U 15 ARG cc_start: 0.5641 (ttp80) cc_final: 0.5034 (mtp180) REVERT: U 45 ASP cc_start: 0.8350 (m-30) cc_final: 0.7941 (m-30) REVERT: U 53 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7623 (ptt-90) REVERT: W 11 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.6309 (m-10) REVERT: X 39 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7533 (mp) outliers start: 42 outliers final: 13 residues processed: 226 average time/residue: 0.5517 time to fit residues: 144.5093 Evaluate side-chains 217 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 36 ASN Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 30 MET Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 39 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 42 ASN S 9 GLN b 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.108392 restraints weight = 26646.783| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.28 r_work: 0.3114 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24099 Z= 0.151 Angle : 0.742 20.724 33025 Z= 0.290 Chirality : 0.038 0.140 3168 Planarity : 0.003 0.041 4033 Dihedral : 18.553 179.891 4602 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.70 % Allowed : 11.62 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.17), residues: 2229 helix: 2.10 (0.12), residues: 1539 sheet: 1.34 (0.97), residues: 27 loop : -0.28 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 46 TYR 0.018 0.001 TYR M 193 PHE 0.019 0.001 PHE S 11 TRP 0.017 0.001 TRP M 74 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00358 (24085) covalent geometry : angle 0.74239 (33025) hydrogen bonds : bond 0.05081 ( 1294) hydrogen bonds : angle 3.56464 ( 3732) Misc. bond : bond 0.00251 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.5986 (tmm) cc_final: 0.5535 (tmm) REVERT: H 55 LEU cc_start: 0.7835 (mt) cc_final: 0.6978 (tt) REVERT: H 178 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8304 (mt0) REVERT: H 184 GLU cc_start: 0.8552 (tt0) cc_final: 0.8275 (tt0) REVERT: H 228 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8152 (pt0) REVERT: H 235 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7702 (t0) REVERT: M 10 GLN cc_start: 0.9177 (mt0) cc_final: 0.8968 (mt0) REVERT: M 26 ASP cc_start: 0.7812 (t0) cc_final: 0.7350 (t70) REVERT: M 36 ASN cc_start: 0.8033 (m-40) cc_final: 0.7710 (t0) REVERT: M 69 MET cc_start: 0.9257 (mmp) cc_final: 0.8941 (mmp) REVERT: O 5 TYR cc_start: 0.8406 (p90) cc_final: 0.7930 (p90) REVERT: O 26 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8168 (mp) REVERT: Q 9 GLN cc_start: 0.8159 (mt0) cc_final: 0.7891 (mm-40) REVERT: U 15 ARG cc_start: 0.5657 (ttp80) cc_final: 0.5139 (mtp180) REVERT: U 45 ASP cc_start: 0.8276 (m-30) cc_final: 0.7828 (m-30) REVERT: U 53 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7543 (ptt-90) REVERT: W 11 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.6286 (m-10) REVERT: X 39 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7490 (mp) REVERT: b 43 TYR cc_start: 0.5086 (OUTLIER) cc_final: 0.4730 (t80) outliers start: 33 outliers final: 12 residues processed: 231 average time/residue: 0.5419 time to fit residues: 145.5163 Evaluate side-chains 219 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 99 ASP Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 30 MET Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain b residue 43 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 98 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 109 optimal weight: 0.5980 chunk 192 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 179 optimal weight: 0.9980 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 200 ASN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107392 restraints weight = 26630.520| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.28 r_work: 0.3112 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24099 Z= 0.160 Angle : 0.750 20.934 33025 Z= 0.294 Chirality : 0.039 0.145 3168 Planarity : 0.003 0.040 4033 Dihedral : 18.387 179.877 4602 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.86 % Allowed : 11.93 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.17), residues: 2229 helix: 2.12 (0.12), residues: 1538 sheet: 1.39 (0.97), residues: 27 loop : -0.27 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 46 TYR 0.018 0.001 TYR M 193 PHE 0.021 0.001 PHE S 11 TRP 0.017 0.001 TRP M 74 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00383 (24085) covalent geometry : angle 0.75011 (33025) hydrogen bonds : bond 0.05119 ( 1294) hydrogen bonds : angle 3.58338 ( 3732) Misc. bond : bond 0.00247 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6023 (tmm) cc_final: 0.5501 (tmm) REVERT: H 178 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8312 (mt0) REVERT: H 184 GLU cc_start: 0.8557 (tt0) cc_final: 0.8283 (tt0) REVERT: H 228 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8114 (pt0) REVERT: H 235 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7695 (t0) REVERT: H 250 ASP cc_start: 0.8015 (m-30) cc_final: 0.7237 (p0) REVERT: M 10 GLN cc_start: 0.9182 (mt0) cc_final: 0.8953 (mt0) REVERT: M 26 ASP cc_start: 0.7842 (t0) cc_final: 0.7265 (t0) REVERT: M 36 ASN cc_start: 0.8075 (m-40) cc_final: 0.7736 (t0) REVERT: M 69 MET cc_start: 0.9236 (mmp) cc_final: 0.8994 (mmp) REVERT: O 5 TYR cc_start: 0.8424 (p90) cc_final: 0.7970 (p90) REVERT: O 26 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8151 (mp) REVERT: Q 9 GLN cc_start: 0.8183 (mt0) cc_final: 0.7896 (mm-40) REVERT: U 15 ARG cc_start: 0.5577 (ttp80) cc_final: 0.5003 (mtp180) REVERT: U 53 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7502 (ptt-90) REVERT: W 11 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.6250 (m-10) REVERT: X 39 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7459 (mp) REVERT: b 43 TYR cc_start: 0.5084 (OUTLIER) cc_final: 0.4741 (t80) outliers start: 36 outliers final: 14 residues processed: 235 average time/residue: 0.5295 time to fit residues: 144.8037 Evaluate side-chains 228 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 99 ASP Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 30 MET Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain b residue 43 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 137 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 77 optimal weight: 0.0270 chunk 110 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 42 ASN L 200 ASN b 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.111239 restraints weight = 26363.911| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.28 r_work: 0.3159 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24099 Z= 0.114 Angle : 0.689 20.140 33025 Z= 0.267 Chirality : 0.036 0.133 3168 Planarity : 0.003 0.037 4033 Dihedral : 17.785 179.958 4602 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.24 % Allowed : 12.65 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.17), residues: 2229 helix: 2.37 (0.12), residues: 1543 sheet: 1.45 (0.97), residues: 27 loop : -0.22 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 15 TYR 0.014 0.001 TYR M 193 PHE 0.015 0.001 PHE S 11 TRP 0.017 0.001 TRP M 74 HIS 0.005 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00257 (24085) covalent geometry : angle 0.68867 (33025) hydrogen bonds : bond 0.04591 ( 1294) hydrogen bonds : angle 3.42925 ( 3732) Misc. bond : bond 0.00176 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6021 (tmm) cc_final: 0.5482 (tmm) REVERT: A 1 MET cc_start: 0.8060 (tpp) cc_final: 0.7806 (tpt) REVERT: H 184 GLU cc_start: 0.8500 (tt0) cc_final: 0.8235 (tt0) REVERT: H 228 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8085 (pt0) REVERT: H 250 ASP cc_start: 0.8023 (m-30) cc_final: 0.7226 (p0) REVERT: M 26 ASP cc_start: 0.7813 (t0) cc_final: 0.7344 (t70) REVERT: M 36 ASN cc_start: 0.7916 (m-40) cc_final: 0.7682 (t0) REVERT: M 69 MET cc_start: 0.9198 (mmp) cc_final: 0.8909 (mmp) REVERT: O 5 TYR cc_start: 0.8418 (p90) cc_final: 0.7961 (p90) REVERT: O 26 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8127 (mp) REVERT: Q 6 LYS cc_start: 0.8008 (mttt) cc_final: 0.7724 (mttp) REVERT: Q 9 GLN cc_start: 0.8143 (mt0) cc_final: 0.7882 (mm-40) REVERT: U 53 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7398 (ptt180) REVERT: W 11 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6234 (m-10) REVERT: X 39 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7437 (mp) REVERT: X 40 CYS cc_start: 0.8320 (m) cc_final: 0.8071 (m) REVERT: b 43 TYR cc_start: 0.5140 (OUTLIER) cc_final: 0.4780 (t80) outliers start: 24 outliers final: 13 residues processed: 233 average time/residue: 0.5400 time to fit residues: 146.5928 Evaluate side-chains 224 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain M residue 99 ASP Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain U residue 30 MET Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain b residue 43 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 3 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 10 GLN O 9 GLN b 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.146745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.108551 restraints weight = 26568.328| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.28 r_work: 0.3119 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24099 Z= 0.161 Angle : 0.741 20.775 33025 Z= 0.291 Chirality : 0.039 0.141 3168 Planarity : 0.003 0.038 4033 Dihedral : 17.993 179.864 4602 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.39 % Allowed : 12.85 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.17), residues: 2229 helix: 2.24 (0.12), residues: 1538 sheet: 1.34 (0.97), residues: 27 loop : -0.21 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 46 TYR 0.018 0.002 TYR M 193 PHE 0.021 0.001 PHE S 11 TRP 0.016 0.001 TRP M 74 HIS 0.008 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00386 (24085) covalent geometry : angle 0.74087 (33025) hydrogen bonds : bond 0.05049 ( 1294) hydrogen bonds : angle 3.53807 ( 3732) Misc. bond : bond 0.00259 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6074 (tmm) cc_final: 0.5591 (tmm) REVERT: A 1 MET cc_start: 0.8038 (tpp) cc_final: 0.7805 (tpt) REVERT: H 161 ASP cc_start: 0.7900 (m-30) cc_final: 0.7696 (m-30) REVERT: H 184 GLU cc_start: 0.8508 (tt0) cc_final: 0.8226 (tt0) REVERT: H 228 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8052 (pt0) REVERT: H 250 ASP cc_start: 0.7974 (m-30) cc_final: 0.7226 (p0) REVERT: M 26 ASP cc_start: 0.7839 (t0) cc_final: 0.7252 (t0) REVERT: M 36 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7734 (t0) REVERT: M 69 MET cc_start: 0.9228 (mmp) cc_final: 0.8984 (mmp) REVERT: O 5 TYR cc_start: 0.8400 (p90) cc_final: 0.7953 (p90) REVERT: O 26 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8141 (mp) REVERT: Q 9 GLN cc_start: 0.8157 (mt0) cc_final: 0.7791 (mm110) REVERT: U 15 ARG cc_start: 0.5495 (ttp80) cc_final: 0.5001 (mtp180) REVERT: U 53 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7461 (ptt180) REVERT: W 11 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6340 (m-10) REVERT: X 39 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7433 (mp) REVERT: b 43 TYR cc_start: 0.5168 (OUTLIER) cc_final: 0.4818 (t80) outliers start: 27 outliers final: 13 residues processed: 221 average time/residue: 0.5426 time to fit residues: 138.9636 Evaluate side-chains 221 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain M residue 36 ASN Chi-restraints excluded: chain M residue 99 ASP Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain U residue 30 MET Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain b residue 43 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 120 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 20 GLN 7 42 ASN O 9 GLN b 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.149573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111636 restraints weight = 26640.307| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.27 r_work: 0.3167 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24099 Z= 0.119 Angle : 0.694 20.019 33025 Z= 0.270 Chirality : 0.037 0.134 3168 Planarity : 0.003 0.037 4033 Dihedral : 17.589 179.936 4602 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.24 % Allowed : 13.06 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.17), residues: 2229 helix: 2.38 (0.12), residues: 1543 sheet: 1.46 (0.98), residues: 27 loop : -0.23 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 46 TYR 0.017 0.001 TYR Q 5 PHE 0.016 0.001 PHE S 11 TRP 0.016 0.001 TRP M 74 HIS 0.006 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00274 (24085) covalent geometry : angle 0.69384 (33025) hydrogen bonds : bond 0.04640 ( 1294) hydrogen bonds : angle 3.43588 ( 3732) Misc. bond : bond 0.00187 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6133 (tmm) cc_final: 0.5636 (tmm) REVERT: A 1 MET cc_start: 0.7983 (tpp) cc_final: 0.7716 (tpt) REVERT: D 42 ASN cc_start: 0.8969 (t0) cc_final: 0.8395 (t0) REVERT: H 184 GLU cc_start: 0.8464 (tt0) cc_final: 0.8230 (tt0) REVERT: H 228 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8098 (pt0) REVERT: H 250 ASP cc_start: 0.7974 (m-30) cc_final: 0.7190 (p0) REVERT: M 26 ASP cc_start: 0.7761 (t0) cc_final: 0.7269 (t70) REVERT: M 36 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7652 (t0) REVERT: M 69 MET cc_start: 0.9180 (mmp) cc_final: 0.8882 (mmp) REVERT: O 5 TYR cc_start: 0.8392 (p90) cc_final: 0.7943 (p90) REVERT: O 26 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8099 (mp) REVERT: Q 6 LYS cc_start: 0.7913 (mttt) cc_final: 0.7636 (mttp) REVERT: Q 9 GLN cc_start: 0.8085 (mt0) cc_final: 0.7740 (mm110) REVERT: U 53 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7354 (ptt180) REVERT: W 11 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6256 (m-10) REVERT: X 39 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7430 (mp) REVERT: X 40 CYS cc_start: 0.8322 (m) cc_final: 0.8077 (m) REVERT: b 43 TYR cc_start: 0.5163 (OUTLIER) cc_final: 0.4820 (t80) outliers start: 24 outliers final: 14 residues processed: 223 average time/residue: 0.5210 time to fit residues: 135.4220 Evaluate side-chains 225 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 36 ASN Chi-restraints excluded: chain M residue 99 ASP Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain U residue 30 MET Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain b residue 43 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 67 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 20 GLN O 9 GLN b 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.148602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110354 restraints weight = 26531.162| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.27 r_work: 0.3150 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24099 Z= 0.131 Angle : 0.707 20.420 33025 Z= 0.277 Chirality : 0.037 0.133 3168 Planarity : 0.003 0.037 4033 Dihedral : 17.605 179.926 4602 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.29 % Allowed : 13.11 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.17), residues: 2229 helix: 2.37 (0.12), residues: 1553 sheet: 1.71 (1.15), residues: 17 loop : -0.18 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 46 TYR 0.016 0.001 TYR Q 5 PHE 0.018 0.001 PHE S 11 TRP 0.016 0.001 TRP M 74 HIS 0.006 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00305 (24085) covalent geometry : angle 0.70676 (33025) hydrogen bonds : bond 0.04781 ( 1294) hydrogen bonds : angle 3.46378 ( 3732) Misc. bond : bond 0.00216 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7624.41 seconds wall clock time: 130 minutes 27.46 seconds (7827.46 seconds total)