Starting phenix.real_space_refine on Thu May 22 12:36:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygl_39255/05_2025/8ygl_39255.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygl_39255/05_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_39255/05_2025/8ygl_39255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygl_39255/05_2025/8ygl_39255.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygl_39255/05_2025/8ygl_39255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygl_39255/05_2025/8ygl_39255.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 2, 'U10:plan-10': 4, 'U10:plan-11': 4} 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: 13.77, per 1000 atoms: 0.59 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: 7.96 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.87 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: 6.25 Time building geometry restraints manager: 8.67 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.990 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 49.280 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.870 ------------------------------------------------------------------------------- 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 : 16.00 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.043 0.002 TRP L 273 HIS 0.010 0.001 HIS M 182 PHE 0.057 0.002 PHE M 216 TYR 0.021 0.001 TYR b 43 ARG 0.011 0.001 ARG A 14 Details of bonding type rmsd hydrogen bonds : bond 0.12738 ( 1294) hydrogen bonds : angle 5.06783 ( 3732) covalent geometry : bond 0.01428 (24085) covalent geometry : angle 1.27881 (33025) 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 : 1.981 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: 1.3256 time to fit residues: 352.7886 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 : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 197 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 9 GLN 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** ** G 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 ASN ** L 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 ASN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN T 21 HIS Z 16 GLN b 21 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.151855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113640 restraints weight = 26228.560| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.27 r_work: 0.3196 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24099 Z= 0.169 Angle : 0.821 17.250 33025 Z= 0.317 Chirality : 0.040 0.213 3168 Planarity : 0.004 0.049 4033 Dihedral : 20.097 179.952 4602 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.98 % Allowed : 7.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2229 helix: 1.25 (0.12), residues: 1554 sheet: 2.22 (1.22), residues: 20 loop : -0.69 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 157 HIS 0.008 0.001 HIS M 182 PHE 0.019 0.001 PHE S 11 TYR 0.014 0.001 TYR M 193 ARG 0.004 0.001 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.05269 ( 1294) hydrogen bonds : angle 3.82327 ( 3732) covalent geometry : bond 0.00401 (24085) covalent geometry : angle 0.82059 (33025) Misc. bond : bond 0.00412 ( 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 221 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 2.155 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.5696 (tmm) cc_final: 0.5313 (tmm) REVERT: 7 3 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7879 (mtpp) REVERT: 7 15 ARG cc_start: 0.7558 (mmt180) cc_final: 0.7333 (mmt180) REVERT: C 30 MET cc_start: 0.7572 (mmm) cc_final: 0.7327 (mmm) REVERT: F 3 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7876 (mmtp) REVERT: F 41 TYR cc_start: 0.8999 (m-80) cc_final: 0.8484 (m-80) REVERT: H 46 ASP cc_start: 0.7968 (p0) cc_final: 0.7686 (p0) REVERT: H 178 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8280 (mt0) REVERT: H 184 GLU cc_start: 0.8536 (tt0) cc_final: 0.8252 (tt0) REVERT: H 228 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8178 (pt0) REVERT: H 235 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7479 (t0) REVERT: L 258 ASP cc_start: 0.7985 (t0) cc_final: 0.7782 (t0) REVERT: M 26 ASP cc_start: 0.8010 (t0) cc_final: 0.7636 (t70) REVERT: M 36 ASN cc_start: 0.8098 (m-40) cc_final: 0.7753 (t0) REVERT: M 69 MET cc_start: 0.9218 (mmp) cc_final: 0.9001 (mmp) REVERT: Q 6 LYS cc_start: 0.8069 (mttt) cc_final: 0.7794 (mttp) REVERT: Q 9 GLN cc_start: 0.8217 (mt0) cc_final: 0.7835 (mm110) REVERT: S 51 TYR cc_start: 0.8522 (m-80) cc_final: 0.7916 (m-80) REVERT: W 11 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.6183 (m-10) outliers start: 19 outliers final: 9 residues processed: 209 average time/residue: 1.2090 time to fit residues: 294.6102 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 : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 LYS 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 31 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 101 optimal weight: 0.0010 chunk 196 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- 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 L 200 ASN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110680 restraints weight = 26306.114| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.28 r_work: 0.3152 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24099 Z= 0.148 Angle : 0.744 15.585 33025 Z= 0.291 Chirality : 0.038 0.140 3168 Planarity : 0.004 0.045 4033 Dihedral : 19.204 179.893 4602 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.39 % Allowed : 9.19 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.17), residues: 2229 helix: 1.85 (0.13), residues: 1544 sheet: 1.23 (1.04), residues: 27 loop : -0.56 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 74 HIS 0.007 0.001 HIS M 182 PHE 0.018 0.001 PHE S 11 TYR 0.013 0.001 TYR M 193 ARG 0.006 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.05023 ( 1294) hydrogen bonds : angle 3.62376 ( 3732) covalent geometry : bond 0.00348 (24085) covalent geometry : angle 0.74421 (33025) Misc. bond : bond 0.00226 ( 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 237 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 2.328 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6094 (tmm) cc_final: 0.5704 (tmm) REVERT: 1 41 TYR cc_start: 0.7424 (m-80) cc_final: 0.6687 (m-80) REVERT: 7 3 LYS cc_start: 0.8318 (mtpt) cc_final: 0.8104 (mtpp) REVERT: 7 15 ARG cc_start: 0.7667 (mmt180) cc_final: 0.7426 (mmt180) REVERT: C 30 MET cc_start: 0.7676 (mmm) cc_final: 0.7461 (mmm) REVERT: F 41 TYR cc_start: 0.8967 (m-80) cc_final: 0.8622 (m-80) REVERT: H 46 ASP cc_start: 0.8086 (p0) cc_final: 0.7694 (p0) REVERT: H 178 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8296 (mt0) REVERT: H 184 GLU cc_start: 0.8492 (tt0) cc_final: 0.8238 (tt0) REVERT: H 228 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8159 (pt0) REVERT: H 235 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7622 (t0) REVERT: I 7 ILE cc_start: 0.8915 (tt) cc_final: 0.8698 (tp) REVERT: I 45 ASP cc_start: 0.8048 (m-30) cc_final: 0.7661 (m-30) REVERT: L 56 MET cc_start: 0.8721 (mtp) cc_final: 0.8505 (mtp) REVERT: M 26 ASP cc_start: 0.7970 (t0) cc_final: 0.7596 (t70) REVERT: M 36 ASN cc_start: 0.7959 (m-40) cc_final: 0.7682 (t0) REVERT: M 69 MET cc_start: 0.9258 (mmp) cc_final: 0.9014 (mmp) REVERT: O 5 TYR cc_start: 0.8361 (p90) cc_final: 0.7974 (p90) REVERT: Q 9 GLN cc_start: 0.8172 (mt0) cc_final: 0.7818 (mm110) REVERT: S 51 TYR cc_start: 0.8513 (m-80) cc_final: 0.8003 (m-80) REVERT: W 11 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6337 (m-10) outliers start: 27 outliers final: 9 residues processed: 224 average time/residue: 1.1989 time to fit residues: 314.8242 Evaluate side-chains 210 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 10 THR Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE 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 41 optimal weight: 8.9990 chunk 167 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 130 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 ASN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112499 restraints weight = 26544.304| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.29 r_work: 0.3177 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24099 Z= 0.118 Angle : 0.697 19.550 33025 Z= 0.270 Chirality : 0.036 0.135 3168 Planarity : 0.003 0.040 4033 Dihedral : 18.654 179.940 4602 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.60 % Allowed : 9.65 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.17), residues: 2229 helix: 2.19 (0.12), residues: 1556 sheet: 1.47 (1.02), residues: 27 loop : -0.42 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 74 HIS 0.006 0.001 HIS M 182 PHE 0.016 0.001 PHE S 11 TYR 0.013 0.001 TYR M 193 ARG 0.003 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.04661 ( 1294) hydrogen bonds : angle 3.48725 ( 3732) covalent geometry : bond 0.00268 (24085) covalent geometry : angle 0.69683 (33025) Misc. bond : bond 0.00189 ( 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 244 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 2.117 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6024 (tmm) cc_final: 0.5611 (tmm) REVERT: 1 41 TYR cc_start: 0.7363 (m-80) cc_final: 0.6590 (m-80) REVERT: 7 3 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7915 (mtpp) REVERT: 7 15 ARG cc_start: 0.7638 (mmt180) cc_final: 0.7396 (mmt180) REVERT: A 40 ASP cc_start: 0.8477 (t0) cc_final: 0.8271 (t0) REVERT: C 30 MET cc_start: 0.7642 (mmm) cc_final: 0.7432 (mmm) REVERT: H 46 ASP cc_start: 0.8180 (p0) cc_final: 0.7789 (p0) REVERT: H 178 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: H 184 GLU cc_start: 0.8492 (tt0) cc_final: 0.8254 (tt0) REVERT: H 228 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8161 (pt0) REVERT: H 235 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7616 (t0) REVERT: I 7 ILE cc_start: 0.8821 (tt) cc_final: 0.8618 (tp) REVERT: M 26 ASP cc_start: 0.7934 (t0) cc_final: 0.7549 (t70) REVERT: M 36 ASN cc_start: 0.7965 (m-40) cc_final: 0.7713 (t0) REVERT: M 69 MET cc_start: 0.9199 (mmp) cc_final: 0.8941 (mmp) REVERT: O 5 TYR cc_start: 0.8379 (p90) cc_final: 0.7943 (p90) REVERT: O 26 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8162 (mp) REVERT: Q 9 GLN cc_start: 0.8196 (mt0) cc_final: 0.7827 (mm110) REVERT: S 51 TYR cc_start: 0.8430 (m-80) cc_final: 0.7956 (m-80) REVERT: U 53 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7606 (ptt180) REVERT: W 11 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6391 (m-10) REVERT: X 40 CYS cc_start: 0.8265 (m) cc_final: 0.8012 (m) outliers start: 31 outliers final: 12 residues processed: 229 average time/residue: 1.2093 time to fit residues: 322.5961 Evaluate side-chains 213 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU 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 M residue 99 ASP Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain U residue 30 MET Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 182 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 42 ASN ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 ASN M 5 GLN M 10 GLN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.149548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111054 restraints weight = 26568.138| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.29 r_work: 0.3160 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24099 Z= 0.129 Angle : 0.702 18.700 33025 Z= 0.274 Chirality : 0.037 0.133 3168 Planarity : 0.003 0.039 4033 Dihedral : 18.382 179.918 4602 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.65 % Allowed : 10.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.17), residues: 2229 helix: 2.27 (0.12), residues: 1556 sheet: 1.45 (1.00), residues: 27 loop : -0.31 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 74 HIS 0.007 0.001 HIS M 182 PHE 0.018 0.001 PHE S 11 TYR 0.015 0.001 TYR M 193 ARG 0.004 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.04760 ( 1294) hydrogen bonds : angle 3.47696 ( 3732) covalent geometry : bond 0.00300 (24085) covalent geometry : angle 0.70173 (33025) Misc. bond : bond 0.00212 ( 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 236 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 2.182 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.5962 (tmm) cc_final: 0.5537 (tmm) REVERT: 1 41 TYR cc_start: 0.7386 (m-80) cc_final: 0.6589 (m-80) REVERT: 7 3 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7935 (mtpp) REVERT: 7 15 ARG cc_start: 0.7680 (mmt180) cc_final: 0.7423 (mmt180) REVERT: A 40 ASP cc_start: 0.8585 (t0) cc_final: 0.8357 (t0) REVERT: C 30 MET cc_start: 0.7712 (mmm) cc_final: 0.7497 (mmm) REVERT: H 46 ASP cc_start: 0.8251 (p0) cc_final: 0.7838 (p0) REVERT: H 178 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8268 (mt0) REVERT: H 184 GLU cc_start: 0.8470 (tt0) cc_final: 0.8213 (tt0) REVERT: H 228 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8147 (pt0) REVERT: H 235 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7618 (t0) REVERT: I 7 ILE cc_start: 0.8835 (tt) cc_final: 0.8630 (tp) REVERT: M 26 ASP cc_start: 0.7949 (t0) cc_final: 0.7543 (t70) REVERT: M 36 ASN cc_start: 0.7965 (m-40) cc_final: 0.7683 (t0) REVERT: M 69 MET cc_start: 0.9221 (mmp) cc_final: 0.8962 (mmp) REVERT: O 5 TYR cc_start: 0.8424 (p90) cc_final: 0.8005 (p90) REVERT: O 26 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8191 (mp) REVERT: Q 9 GLN cc_start: 0.8189 (mt0) cc_final: 0.7946 (mm-40) REVERT: S 51 TYR cc_start: 0.8485 (m-80) cc_final: 0.7982 (m-80) REVERT: U 45 ASP cc_start: 0.8288 (m-30) cc_final: 0.7866 (m-30) REVERT: U 53 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7567 (ptt180) REVERT: W 11 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6434 (m-10) REVERT: X 39 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7501 (mp) REVERT: X 40 CYS cc_start: 0.8352 (m) cc_final: 0.8092 (m) outliers start: 32 outliers final: 12 residues processed: 217 average time/residue: 1.1745 time to fit residues: 298.0252 Evaluate side-chains 221 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU 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 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 99 ASP Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain R residue 44 ILE 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 39 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 23 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 165 optimal weight: 0.5980 chunk 185 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 ASN ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 ASN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.150626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112312 restraints weight = 26386.461| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.29 r_work: 0.3170 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24099 Z= 0.114 Angle : 0.672 19.654 33025 Z= 0.260 Chirality : 0.036 0.133 3168 Planarity : 0.003 0.037 4033 Dihedral : 17.850 179.951 4602 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.70 % Allowed : 11.41 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.17), residues: 2229 helix: 2.45 (0.12), residues: 1551 sheet: 1.23 (0.89), residues: 33 loop : -0.18 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 74 HIS 0.006 0.001 HIS M 182 PHE 0.016 0.001 PHE S 11 TYR 0.013 0.001 TYR Q 5 ARG 0.003 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.04501 ( 1294) hydrogen bonds : angle 3.38880 ( 3732) covalent geometry : bond 0.00258 (24085) covalent geometry : angle 0.67185 (33025) Misc. bond : bond 0.00179 ( 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 252 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 219 time to evaluate : 2.473 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.5992 (tmm) cc_final: 0.5493 (tmm) REVERT: 7 3 LYS cc_start: 0.8199 (mtpt) cc_final: 0.7935 (mtpp) REVERT: 7 15 ARG cc_start: 0.7641 (mmt180) cc_final: 0.7396 (mmt180) REVERT: A 40 ASP cc_start: 0.8517 (t0) cc_final: 0.8267 (t0) REVERT: C 30 MET cc_start: 0.7664 (mmm) cc_final: 0.7413 (mmm) REVERT: H 46 ASP cc_start: 0.8307 (p0) cc_final: 0.7954 (p0) REVERT: H 178 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8266 (mt0) REVERT: H 184 GLU cc_start: 0.8449 (tt0) cc_final: 0.8219 (tt0) REVERT: M 26 ASP cc_start: 0.7954 (t0) cc_final: 0.7527 (t70) REVERT: M 36 ASN cc_start: 0.7930 (m-40) cc_final: 0.7695 (t0) REVERT: M 69 MET cc_start: 0.9188 (mmp) cc_final: 0.8891 (mmp) REVERT: O 5 TYR cc_start: 0.8365 (p90) cc_final: 0.7960 (p90) REVERT: O 26 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8118 (mp) REVERT: Q 9 GLN cc_start: 0.8168 (mt0) cc_final: 0.7923 (mm-40) REVERT: U 45 ASP cc_start: 0.8196 (m-30) cc_final: 0.7757 (m-30) REVERT: U 53 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7467 (ptt180) REVERT: W 11 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6238 (m-10) REVERT: X 39 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7439 (mp) REVERT: X 40 CYS cc_start: 0.8307 (m) cc_final: 0.8053 (m) outliers start: 33 outliers final: 15 residues processed: 238 average time/residue: 1.1787 time to fit residues: 330.3516 Evaluate side-chains 223 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER 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 99 ASP Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain S residue 9 GLN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 7 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 169 optimal weight: 5.9990 chunk 81 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 193 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 42 ASN ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 ASN L 262 ASN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.111310 restraints weight = 26529.457| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.29 r_work: 0.3150 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2980 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= 0.128 Angle : 0.690 19.786 33025 Z= 0.269 Chirality : 0.037 0.132 3168 Planarity : 0.003 0.038 4033 Dihedral : 17.815 179.930 4602 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.50 % Allowed : 12.34 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.17), residues: 2229 helix: 2.40 (0.12), residues: 1555 sheet: 1.45 (0.98), residues: 27 loop : -0.19 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 74 HIS 0.007 0.001 HIS M 182 PHE 0.017 0.001 PHE S 11 TYR 0.015 0.001 TYR M 193 ARG 0.003 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.04683 ( 1294) hydrogen bonds : angle 3.41755 ( 3732) covalent geometry : bond 0.00297 (24085) covalent geometry : angle 0.69032 (33025) Misc. bond : bond 0.00211 ( 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 238 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 2.192 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.5983 (tmm) cc_final: 0.5467 (tmm) REVERT: 7 3 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7947 (mtpp) REVERT: 7 15 ARG cc_start: 0.7673 (mmt180) cc_final: 0.7409 (mmt180) REVERT: A 40 ASP cc_start: 0.8531 (t0) cc_final: 0.8278 (t0) REVERT: C 30 MET cc_start: 0.7677 (mmm) cc_final: 0.7426 (mmm) REVERT: H 178 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: H 184 GLU cc_start: 0.8457 (tt0) cc_final: 0.8164 (tt0) REVERT: H 235 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7725 (t0) REVERT: M 26 ASP cc_start: 0.7811 (t0) cc_final: 0.7372 (t70) REVERT: M 36 ASN cc_start: 0.7939 (OUTLIER) cc_final: 0.7680 (t0) REVERT: M 69 MET cc_start: 0.9213 (mmp) cc_final: 0.8979 (mmp) REVERT: O 5 TYR cc_start: 0.8386 (p90) cc_final: 0.7985 (p90) REVERT: O 26 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8128 (mp) REVERT: Q 9 GLN cc_start: 0.8176 (mt0) cc_final: 0.7836 (mm110) REVERT: U 45 ASP cc_start: 0.8272 (m-30) cc_final: 0.7841 (m-30) REVERT: U 53 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7457 (ptt180) REVERT: W 11 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6258 (m-10) REVERT: X 39 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7434 (mp) REVERT: X 40 CYS cc_start: 0.8308 (m) cc_final: 0.8040 (m) outliers start: 29 outliers final: 14 residues processed: 224 average time/residue: 1.1991 time to fit residues: 314.2212 Evaluate side-chains 224 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 1 MET 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 178 GLN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 235 ASP 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 0.2980 chunk 216 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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** ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 GLN b 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.108329 restraints weight = 26566.641| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.27 r_work: 0.3120 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3008 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= 0.167 Angle : 0.751 20.871 33025 Z= 0.296 Chirality : 0.039 0.134 3168 Planarity : 0.003 0.040 4033 Dihedral : 18.163 179.892 4602 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.91 % Allowed : 12.03 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.17), residues: 2229 helix: 2.22 (0.12), residues: 1538 sheet: 1.83 (1.19), residues: 17 loop : -0.24 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 74 HIS 0.008 0.001 HIS M 182 PHE 0.022 0.001 PHE S 11 TYR 0.018 0.002 TYR M 193 ARG 0.005 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.05167 ( 1294) hydrogen bonds : angle 3.54873 ( 3732) covalent geometry : bond 0.00402 (24085) covalent geometry : angle 0.75112 (33025) Misc. bond : bond 0.00263 ( 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 245 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 2.099 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6060 (tmm) cc_final: 0.5533 (tmm) REVERT: 7 3 LYS cc_start: 0.8308 (mtpt) cc_final: 0.8021 (mtpp) REVERT: 7 15 ARG cc_start: 0.7773 (mmt180) cc_final: 0.7441 (mmt180) REVERT: A 40 ASP cc_start: 0.8612 (t0) cc_final: 0.8334 (t0) REVERT: C 30 MET cc_start: 0.7725 (mmm) cc_final: 0.7461 (mmm) REVERT: H 178 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8256 (mt0) REVERT: M 26 ASP cc_start: 0.7842 (t0) cc_final: 0.7371 (t70) REVERT: M 36 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7700 (t0) REVERT: M 69 MET cc_start: 0.9272 (mmp) cc_final: 0.9017 (mmp) REVERT: O 5 TYR cc_start: 0.8431 (p90) cc_final: 0.8022 (p90) REVERT: O 26 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8148 (mp) REVERT: Q 9 GLN cc_start: 0.8213 (mt0) cc_final: 0.7833 (mm110) REVERT: U 15 ARG cc_start: 0.5522 (ttp80) cc_final: 0.5006 (mtp180) REVERT: U 53 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7500 (ptt180) REVERT: W 11 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.6350 (m-10) REVERT: X 39 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7487 (mp) outliers start: 37 outliers final: 16 residues processed: 228 average time/residue: 1.2451 time to fit residues: 330.6249 Evaluate side-chains 225 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER 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 205 GLN Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 36 ASN Chi-restraints excluded: chain M residue 293 ASN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 13 optimal weight: 6.9990 chunk 167 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 190 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 42 ASN ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3721 r_free = 0.3721 target = 0.147520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109277 restraints weight = 26530.346| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.28 r_work: 0.3125 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24099 Z= 0.141 Angle : 0.725 20.653 33025 Z= 0.283 Chirality : 0.038 0.133 3168 Planarity : 0.003 0.039 4033 Dihedral : 17.903 179.921 4602 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.39 % Allowed : 12.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.17), residues: 2229 helix: 2.29 (0.12), residues: 1538 sheet: 1.83 (1.17), residues: 17 loop : -0.22 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 74 HIS 0.007 0.001 HIS M 182 PHE 0.019 0.001 PHE S 11 TYR 0.017 0.001 TYR M 193 ARG 0.003 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.04916 ( 1294) hydrogen bonds : angle 3.49550 ( 3732) covalent geometry : bond 0.00333 (24085) covalent geometry : angle 0.72488 (33025) Misc. bond : bond 0.00235 ( 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 233 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 2.113 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6008 (tmm) cc_final: 0.5473 (tmm) REVERT: 7 3 LYS cc_start: 0.8274 (mtpt) cc_final: 0.8000 (mtpp) REVERT: 7 15 ARG cc_start: 0.7767 (mmt180) cc_final: 0.7445 (mmt180) REVERT: A 40 ASP cc_start: 0.8525 (t0) cc_final: 0.8271 (t0) REVERT: C 30 MET cc_start: 0.7579 (mmm) cc_final: 0.7293 (mmm) REVERT: H 178 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8201 (mt0) REVERT: K 3 LYS cc_start: 0.7885 (mttm) cc_final: 0.7669 (tttm) REVERT: M 26 ASP cc_start: 0.7814 (t0) cc_final: 0.7228 (t0) REVERT: M 36 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7712 (t0) REVERT: M 69 MET cc_start: 0.9241 (mmp) cc_final: 0.8924 (mmp) REVERT: O 5 TYR cc_start: 0.8416 (p90) cc_final: 0.7935 (p90) REVERT: O 26 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8140 (mp) REVERT: Q 9 GLN cc_start: 0.8154 (mt0) cc_final: 0.7799 (mm110) REVERT: U 15 ARG cc_start: 0.5560 (ttp80) cc_final: 0.5145 (mtp180) REVERT: U 53 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7500 (ptt-90) REVERT: W 11 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6336 (m-10) REVERT: X 39 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7442 (mp) outliers start: 27 outliers final: 17 residues processed: 221 average time/residue: 1.2281 time to fit residues: 317.9745 Evaluate side-chains 224 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER 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 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 S residue 9 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 21 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 193 optimal weight: 0.0470 chunk 36 optimal weight: 7.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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** ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.150999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112702 restraints weight = 26533.837| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.31 r_work: 0.3176 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24099 Z= 0.110 Angle : 0.677 19.931 33025 Z= 0.262 Chirality : 0.036 0.134 3168 Planarity : 0.003 0.038 4033 Dihedral : 17.439 179.981 4602 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.29 % Allowed : 12.65 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.17), residues: 2229 helix: 2.49 (0.12), residues: 1555 sheet: 1.23 (0.89), residues: 33 loop : -0.23 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 74 HIS 0.006 0.001 HIS M 266 PHE 0.014 0.001 PHE S 11 TYR 0.017 0.001 TYR Q 5 ARG 0.002 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 1294) hydrogen bonds : angle 3.39573 ( 3732) covalent geometry : bond 0.00246 (24085) covalent geometry : angle 0.67689 (33025) Misc. bond : bond 0.00171 ( 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 233 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 2.042 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6053 (tmm) cc_final: 0.5470 (tmm) REVERT: 7 3 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7869 (mtpp) REVERT: 7 15 ARG cc_start: 0.7782 (mmt180) cc_final: 0.7491 (mmt180) REVERT: C 30 MET cc_start: 0.7665 (mmm) cc_final: 0.7359 (mmm) REVERT: H 178 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8225 (mt0) REVERT: M 26 ASP cc_start: 0.7802 (t0) cc_final: 0.7331 (t70) REVERT: M 36 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7679 (t0) REVERT: M 69 MET cc_start: 0.9180 (mmp) cc_final: 0.8894 (mmp) REVERT: O 5 TYR cc_start: 0.8432 (p90) cc_final: 0.8043 (p90) REVERT: O 26 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8141 (mp) REVERT: Q 6 LYS cc_start: 0.7963 (mttt) cc_final: 0.7668 (mttp) REVERT: Q 9 GLN cc_start: 0.8168 (mt0) cc_final: 0.7907 (mm-40) REVERT: U 53 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7400 (ptt180) REVERT: W 11 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6264 (m-10) REVERT: X 39 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7464 (mp) REVERT: X 40 CYS cc_start: 0.8330 (m) cc_final: 0.8102 (m) outliers start: 25 outliers final: 17 residues processed: 224 average time/residue: 1.1600 time to fit residues: 304.2058 Evaluate side-chains 224 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER 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 205 GLN Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 36 ASN Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain O residue 26 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 20.0000 chunk 160 optimal weight: 0.7980 chunk 217 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.148319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.109933 restraints weight = 26414.767| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.29 r_work: 0.3135 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24099 Z= 0.150 Angle : 0.724 20.361 33025 Z= 0.285 Chirality : 0.038 0.133 3168 Planarity : 0.003 0.038 4033 Dihedral : 17.724 179.897 4602 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.39 % Allowed : 12.80 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.17), residues: 2229 helix: 2.34 (0.12), residues: 1539 sheet: 1.73 (1.16), residues: 17 loop : -0.21 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 74 HIS 0.008 0.001 HIS M 182 PHE 0.020 0.001 PHE S 11 TYR 0.017 0.001 TYR M 193 ARG 0.004 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.04940 ( 1294) hydrogen bonds : angle 3.49195 ( 3732) covalent geometry : bond 0.00356 (24085) covalent geometry : angle 0.72436 (33025) Misc. bond : bond 0.00248 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15269.54 seconds wall clock time: 263 minutes 49.44 seconds (15829.44 seconds total)