Starting phenix.real_space_refine on Thu Jun 19 19:42:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygl_39255/06_2025/8ygl_39255.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygl_39255/06_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_39255/06_2025/8ygl_39255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygl_39255/06_2025/8ygl_39255.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygl_39255/06_2025/8ygl_39255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygl_39255/06_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-5710/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: 13.71, 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: 7.11 Conformation dependent library (CDL) restraints added in 2.3 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: 1.82 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: 6.06 Time building geometry restraints manager: 8.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 8734 1.38 - 1.56: 15019 1.56 - 1.74: 68 1.74 - 1.92: 128 1.92 - 2.10: 136 Bond restraints: 24085 Sorted by residual: bond pdb=" C23 U10 M 407 " pdb=" C24 U10 M 407 " ideal model delta sigma weight residual 1.470 1.324 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" C23 U10 M 403 " pdb=" C24 U10 M 403 " ideal model delta sigma weight residual 1.470 1.324 0.146 2.00e-02 2.50e+03 5.31e+01 bond pdb=" C33 U10 M 407 " pdb=" C34 U10 M 407 " ideal model delta sigma weight residual 1.470 1.325 0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" C8 U10 M 407 " pdb=" C9 U10 M 407 " ideal model delta sigma weight residual 1.470 1.325 0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" C13 U10 M 407 " pdb=" C14 U10 M 407 " ideal model delta sigma weight residual 1.470 1.325 0.145 2.00e-02 2.50e+03 5.23e+01 ... (remaining 24080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 30672 2.32 - 4.63: 1832 4.63 - 6.95: 409 6.95 - 9.27: 78 9.27 - 11.58: 34 Bond angle restraints: 33025 Sorted by residual: angle pdb=" ND BCL V 102 " pdb="MG BCL V 102 " pdb=" NC BCL V 102 " ideal model delta sigma weight residual 85.24 80.08 5.15 9.98e-01 1.00e+00 2.67e+01 angle pdb=" ND BCL T 101 " pdb="MG BCL T 101 " pdb=" NC BCL T 101 " ideal model delta sigma weight residual 85.24 80.12 5.12 9.98e-01 1.00e+00 2.63e+01 angle pdb=" ND BCL E 101 " pdb="MG BCL E 101 " pdb=" NC BCL E 101 " ideal model delta sigma weight residual 85.24 80.19 5.05 9.98e-01 1.00e+00 2.56e+01 angle pdb=" ND BCL M 405 " pdb="MG BCL M 405 " pdb=" NC BCL M 405 " ideal model delta sigma weight residual 85.24 80.19 5.04 9.98e-01 1.00e+00 2.56e+01 angle pdb=" ND BCL 8 101 " pdb="MG BCL 8 101 " pdb=" NC BCL 8 101 " ideal model delta sigma weight residual 85.24 80.21 5.03 9.98e-01 1.00e+00 2.54e+01 ... (remaining 33020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 12203 35.79 - 71.57: 656 71.57 - 107.36: 49 107.36 - 143.14: 12 143.14 - 178.93: 14 Dihedral angle restraints: 12934 sinusoidal: 6308 harmonic: 6626 Sorted by residual: dihedral pdb=" CBD BCL 1 101 " pdb=" CGD BCL 1 101 " pdb=" O2D BCL 1 101 " pdb=" CED BCL 1 101 " ideal model delta sinusoidal sigma weight residual -180.00 -14.79 -165.21 1 5.00e+00 4.00e-02 7.55e+02 dihedral pdb=" C1 BCL N 102 " pdb=" CGA BCL N 102 " pdb=" O2A BCL N 102 " pdb=" CBA BCL N 102 " ideal model delta sinusoidal sigma weight residual -180.00 -4.70 -175.30 1 6.00e+00 2.78e-02 5.32e+02 dihedral pdb=" CBD BCL U 101 " pdb=" CGD BCL U 101 " pdb=" O2D BCL U 101 " pdb=" CED BCL U 101 " ideal model delta sinusoidal sigma weight residual -180.00 -70.60 -109.40 1 5.00e+00 4.00e-02 5.12e+02 ... (remaining 12931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.042: 3162 1.042 - 2.085: 0 2.085 - 3.127: 0 3.127 - 4.169: 0 4.169 - 5.212: 6 Chirality restraints: 3168 Sorted by residual: chirality pdb=" C18 BCL E 101 " pdb=" C17 BCL E 101 " pdb=" C19 BCL E 101 " pdb=" C20 BCL E 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.50 5.21 2.00e-01 2.50e+01 6.79e+02 chirality pdb=" C18 BCL J 101 " pdb=" C17 BCL J 101 " pdb=" C19 BCL J 101 " pdb=" C20 BCL J 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.50 5.21 2.00e-01 2.50e+01 6.78e+02 chirality pdb=" C18 BCL C 101 " pdb=" C17 BCL C 101 " pdb=" C19 BCL C 101 " pdb=" C20 BCL C 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.49 5.20 2.00e-01 2.50e+01 6.75e+02 ... (remaining 3165 not shown) Planarity restraints: 4033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL 1 101 " -0.361 1.50e-02 4.44e+03 3.04e-01 2.05e+03 pdb=" C2 BCL 1 101 " 0.524 1.50e-02 4.44e+03 pdb=" C3 BCL 1 101 " 0.114 1.50e-02 4.44e+03 pdb=" C4 BCL 1 101 " -0.093 1.50e-02 4.44e+03 pdb=" C5 BCL 1 101 " -0.185 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL 2 101 " 0.359 1.50e-02 4.44e+03 3.02e-01 2.03e+03 pdb=" C2 BCL 2 101 " -0.525 1.50e-02 4.44e+03 pdb=" C3 BCL 2 101 " -0.111 1.50e-02 4.44e+03 pdb=" C4 BCL 2 101 " 0.104 1.50e-02 4.44e+03 pdb=" C5 BCL 2 101 " 0.173 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL E 101 " 0.355 1.50e-02 4.44e+03 2.98e-01 1.97e+03 pdb=" C2 BCL E 101 " -0.514 1.50e-02 4.44e+03 pdb=" C3 BCL E 101 " -0.109 1.50e-02 4.44e+03 pdb=" C4 BCL E 101 " 0.187 1.50e-02 4.44e+03 pdb=" C5 BCL E 101 " 0.081 1.50e-02 4.44e+03 ... (remaining 4030 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 111 2.50 - 3.10: 15754 3.10 - 3.70: 35340 3.70 - 4.30: 56331 4.30 - 4.90: 91740 Nonbonded interactions: 199276 Sorted by model distance: nonbonded pdb=" OE1 GLN O 20 " pdb=" OH TYR P 24 " model vdw 1.900 3.040 nonbonded pdb=" OG SER M 152 " pdb=" OG1 THR M 277 " model vdw 1.965 3.040 nonbonded pdb=" O CYS L 248 " pdb=" OG1 THR L 252 " model vdw 2.005 3.040 nonbonded pdb=" OH TYR 0 24 " pdb=" OE1 GLN 9 20 " model vdw 2.008 3.040 nonbonded pdb=" OE1 GLN K 20 " pdb=" OH TYR N 24 " model vdw 2.011 3.040 ... (remaining 199271 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 10 through 48) selection = (chain '2' and resid 10 through 48) selection = (chain '8' and resid 10 through 48) selection = (chain 'B' and resid 10 through 48) selection = (chain 'C' and resid 15 through 53) selection = (chain 'E' and resid 10 through 48) selection = (chain 'G' and resid 10 through 48) selection = (chain 'J' and resid 10 through 48) selection = (chain 'N' and resid 10 through 48) selection = (chain 'P' and resid 10 through 48) selection = (chain 'R' and resid 10 through 48) selection = (chain 'T' and resid 10 through 48) selection = (chain 'V' and resid 10 through 48) selection = (chain 'Z' and resid 10 through 48) } ncs_group { reference = (chain '1' and resid 4 through 52) selection = (chain '3' and resid 4 through 52) selection = (chain '9' and resid 4 through 52) selection = (chain 'A' and resid 4 through 52) selection = (chain 'D' and resid 4 through 52) selection = (chain 'F' and resid 4 through 52) selection = (chain 'I' and resid 4 through 52) selection = (chain 'K' and resid 4 through 52) selection = (chain 'O' and resid 4 through 52) selection = (chain 'Q' and resid 4 through 52) selection = (chain 'S' and resid 4 through 52) selection = (chain 'U' and resid 4 through 52) selection = (chain 'W' and resid 4 through 52) selection = (chain 'a' and resid 4 through 52) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 48.690 Find NCS groups from input model: 1.150 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: 0.010 Load rotamer database and sin/cos tables:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.190 ------------------------------------------------------------------------------- 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 : 1.973 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: 1.3672 time to fit residues: 364.4686 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 : 2.078 ------------------------------------------------------------------------------- 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 = 53)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113639 restraints weight = 26228.551| |-----------------------------------------------------------------------------| 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 3.82326 ( 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 : 2.087 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.5695 (tmm) cc_final: 0.5312 (tmm) REVERT: 7 3 LYS cc_start: 0.8103 (mtpt) cc_final: 0.7880 (mtpp) REVERT: 7 15 ARG cc_start: 0.7559 (mmt180) cc_final: 0.7334 (mmt180) REVERT: C 30 MET cc_start: 0.7577 (mmm) cc_final: 0.7333 (mmm) REVERT: F 3 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7877 (mmtp) REVERT: F 41 TYR cc_start: 0.8998 (m-80) cc_final: 0.8484 (m-80) REVERT: H 46 ASP cc_start: 0.7967 (p0) cc_final: 0.7685 (p0) REVERT: H 178 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8281 (mt0) REVERT: H 184 GLU cc_start: 0.8537 (tt0) cc_final: 0.8253 (tt0) REVERT: H 228 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8177 (pt0) REVERT: H 235 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7480 (t0) REVERT: L 258 ASP cc_start: 0.7986 (t0) cc_final: 0.7783 (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: 0.9219 (mmp) cc_final: 0.9001 (mmp) REVERT: Q 6 LYS cc_start: 0.8074 (mttt) cc_final: 0.7799 (mttp) REVERT: Q 9 GLN cc_start: 0.8221 (mt0) cc_final: 0.7839 (mm110) REVERT: S 51 TYR cc_start: 0.8522 (m-80) cc_final: 0.7917 (m-80) REVERT: W 11 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6187 (m-10) outliers start: 19 outliers final: 9 residues processed: 209 average time/residue: 1.2444 time to fit residues: 303.9798 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 : 2.149 ------------------------------------------------------------------------------- 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: 0.2980 chunk 159 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 196 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.149483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.111131 restraints weight = 26291.626| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.28 r_work: 0.3160 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24099 Z= 0.143 Angle : 0.737 15.457 33025 Z= 0.288 Chirality : 0.038 0.139 3168 Planarity : 0.003 0.044 4033 Dihedral : 19.152 179.937 4602 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.39 % Allowed : 9.09 % Favored : 89.52 % 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: 1.75 (0.17), residues: 2229 helix: 1.88 (0.13), residues: 1544 sheet: 1.27 (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 0.017 0.001 PHE S 11 TYR 0.013 0.001 TYR M 303 ARG 0.004 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.04971 ( 1294) hydrogen bonds : angle 3.61154 ( 3732) covalent geometry : bond 0.00335 (24085) covalent geometry : angle 0.73676 (33025) Misc. bond : bond 0.00222 ( 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 : 2.679 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6108 (tmm) cc_final: 0.5712 (tmm) REVERT: 1 41 TYR cc_start: 0.7466 (m-80) cc_final: 0.6735 (m-80) REVERT: 7 3 LYS cc_start: 0.8311 (mtpt) cc_final: 0.8097 (mtpp) REVERT: 7 15 ARG cc_start: 0.7641 (mmt180) cc_final: 0.7413 (mmt180) REVERT: C 30 MET cc_start: 0.7713 (mmm) cc_final: 0.7504 (mmm) REVERT: H 46 ASP cc_start: 0.8078 (p0) cc_final: 0.7697 (p0) REVERT: H 178 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8264 (mt0) REVERT: H 184 GLU cc_start: 0.8481 (tt0) cc_final: 0.8224 (tt0) REVERT: H 228 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8159 (pt0) REVERT: H 235 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7615 (t0) REVERT: I 7 ILE cc_start: 0.8910 (tt) cc_final: 0.8693 (tp) REVERT: I 45 ASP cc_start: 0.8034 (m-30) cc_final: 0.7624 (m-30) REVERT: L 56 MET cc_start: 0.8718 (mtp) cc_final: 0.8502 (mtp) REVERT: M 26 ASP cc_start: 0.7963 (t0) cc_final: 0.7592 (t70) REVERT: M 36 ASN cc_start: 0.7951 (m-40) cc_final: 0.7679 (t0) REVERT: M 69 MET cc_start: 0.9254 (mmp) cc_final: 0.9007 (mmp) REVERT: M 158 MET cc_start: 0.8885 (mmm) cc_final: 0.8640 (mmm) REVERT: O 5 TYR cc_start: 0.8365 (p90) cc_final: 0.7983 (p90) REVERT: Q 9 GLN cc_start: 0.8158 (mt0) cc_final: 0.7808 (mm110) REVERT: S 51 TYR cc_start: 0.8516 (m-80) cc_final: 0.8029 (m-80) REVERT: W 11 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.6373 (m-10) outliers start: 27 outliers final: 8 residues processed: 224 average time/residue: 1.6406 time to fit residues: 429.6717 Evaluate side-chains 208 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 2.118 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 167 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 130 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 L 205 GLN W 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.112924 restraints weight = 26525.268| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.29 r_work: 0.3182 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24099 Z= 0.116 Angle : 0.693 19.948 33025 Z= 0.268 Chirality : 0.036 0.135 3168 Planarity : 0.003 0.039 4033 Dihedral : 18.611 179.936 4602 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.65 % Allowed : 9.55 % Favored : 88.80 % 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: 2.22 (0.17), residues: 2229 helix: 2.22 (0.12), residues: 1556 sheet: 1.51 (1.02), residues: 27 loop : -0.39 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 74 HIS 0.005 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 0.04618 ( 1294) hydrogen bonds : angle 3.47063 ( 3732) covalent geometry : bond 0.00263 (24085) covalent geometry : angle 0.69296 (33025) Misc. bond : bond 0.00170 ( 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 242 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 2.167 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6029 (tmm) cc_final: 0.5614 (tmm) REVERT: 1 41 TYR cc_start: 0.7436 (m-80) cc_final: 0.6684 (m-80) REVERT: 7 3 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7908 (mtpp) REVERT: 7 15 ARG cc_start: 0.7622 (mmt180) cc_final: 0.7385 (mmt180) REVERT: A 40 ASP cc_start: 0.8486 (t0) cc_final: 0.8231 (t0) REVERT: C 30 MET cc_start: 0.7648 (mmm) cc_final: 0.7439 (mmm) REVERT: H 46 ASP cc_start: 0.8173 (p0) cc_final: 0.7783 (p0) REVERT: H 178 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: H 184 GLU cc_start: 0.8469 (tt0) cc_final: 0.8252 (tt0) REVERT: H 228 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8157 (pt0) REVERT: L 202 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7897 (mt-10) REVERT: L 258 ASP cc_start: 0.7996 (t0) cc_final: 0.7742 (t0) REVERT: M 26 ASP cc_start: 0.7933 (t0) cc_final: 0.7543 (t70) REVERT: M 36 ASN cc_start: 0.7955 (m-40) cc_final: 0.7707 (t0) REVERT: M 69 MET cc_start: 0.9198 (mmp) cc_final: 0.8941 (mmp) REVERT: O 5 TYR cc_start: 0.8367 (p90) cc_final: 0.7931 (p90) REVERT: O 26 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8165 (mp) REVERT: Q 9 GLN cc_start: 0.8133 (mt0) cc_final: 0.7763 (mm110) REVERT: U 53 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7605 (ptt180) REVERT: W 11 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6384 (m-10) REVERT: X 40 CYS cc_start: 0.8257 (m) cc_final: 0.8016 (m) outliers start: 32 outliers final: 8 residues processed: 225 average time/residue: 1.2312 time to fit residues: 324.0426 Evaluate side-chains 207 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 2.243 ------------------------------------------------------------------------------- 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 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 U residue 53 ARG Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain W residue 11 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 10.0000 chunk 163 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 82 optimal weight: 0.0670 chunk 182 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 173 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 42 ASN D 20 GLN ** 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** b 39 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.151778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113441 restraints weight = 26463.478| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.30 r_work: 0.3199 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24099 Z= 0.109 Angle : 0.664 18.278 33025 Z= 0.257 Chirality : 0.036 0.133 3168 Planarity : 0.003 0.037 4033 Dihedral : 17.976 179.950 4602 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.55 % Allowed : 10.58 % Favored : 87.87 % 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: 2.51 (0.17), residues: 2229 helix: 2.43 (0.12), residues: 1556 sheet: 1.22 (0.89), residues: 33 loop : -0.25 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 74 HIS 0.005 0.001 HIS M 182 PHE 0.015 0.001 PHE S 11 TYR 0.013 0.001 TYR M 193 ARG 0.002 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 1294) hydrogen bonds : angle 3.38051 ( 3732) covalent geometry : bond 0.00242 (24085) covalent geometry : angle 0.66430 (33025) Misc. bond : bond 0.00170 ( 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 249 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 2.041 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.5948 (tmm) cc_final: 0.5454 (tmm) REVERT: 1 41 TYR cc_start: 0.7378 (m-80) cc_final: 0.6552 (m-80) REVERT: 7 3 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7888 (mtpp) REVERT: 7 15 ARG cc_start: 0.7605 (mmt180) cc_final: 0.7386 (mmt180) REVERT: A 1 MET cc_start: 0.8050 (tpp) cc_final: 0.7842 (tpt) REVERT: C 30 MET cc_start: 0.7683 (mmm) cc_final: 0.7458 (mmm) REVERT: D 42 ASN cc_start: 0.8920 (t0) cc_final: 0.8325 (t0) REVERT: E 37 ILE cc_start: 0.8738 (mt) cc_final: 0.8486 (mm) REVERT: H 46 ASP cc_start: 0.8239 (p0) cc_final: 0.7814 (p0) REVERT: H 184 GLU cc_start: 0.8414 (tt0) cc_final: 0.8145 (tt0) REVERT: L 258 ASP cc_start: 0.8028 (t0) cc_final: 0.7812 (t0) REVERT: M 26 ASP cc_start: 0.7936 (t0) cc_final: 0.7540 (t70) REVERT: M 36 ASN cc_start: 0.7906 (m-40) cc_final: 0.7695 (t0) REVERT: M 69 MET cc_start: 0.9173 (mmp) cc_final: 0.8953 (mmp) REVERT: O 5 TYR cc_start: 0.8412 (p90) cc_final: 0.8007 (p90) REVERT: O 26 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8173 (mp) REVERT: Q 6 LYS cc_start: 0.8045 (mttt) cc_final: 0.7776 (mttp) REVERT: Q 9 GLN cc_start: 0.8165 (mt0) cc_final: 0.7739 (mm-40) REVERT: U 53 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7519 (ptt180) REVERT: W 11 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.6362 (m-10) REVERT: X 39 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7461 (mp) REVERT: X 40 CYS cc_start: 0.8350 (m) cc_final: 0.8081 (m) outliers start: 30 outliers final: 11 residues processed: 236 average time/residue: 1.2089 time to fit residues: 332.5650 Evaluate side-chains 216 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 214 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 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=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: 0.9990 chunk 152 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 119 optimal weight: 0.0050 chunk 118 optimal weight: 3.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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** L 200 ASN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113217 restraints weight = 26126.917| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.29 r_work: 0.3186 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24099 Z= 0.120 Angle : 0.676 19.735 33025 Z= 0.263 Chirality : 0.036 0.133 3168 Planarity : 0.003 0.036 4033 Dihedral : 17.829 179.948 4602 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.34 % Allowed : 11.87 % Favored : 86.78 % 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: 2.53 (0.17), residues: 2229 helix: 2.43 (0.12), residues: 1556 sheet: 1.29 (0.87), residues: 33 loop : -0.20 (0.25), residues: 640 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 0.017 0.001 PHE S 11 TYR 0.014 0.001 TYR M 193 ARG 0.003 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 1294) hydrogen bonds : angle 3.39601 ( 3732) covalent geometry : bond 0.00275 (24085) covalent geometry : angle 0.67595 (33025) Misc. bond : bond 0.00194 ( 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 234 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 2.353 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.5983 (tmm) cc_final: 0.5529 (tmm) REVERT: 7 3 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7940 (mtpp) REVERT: 7 15 ARG cc_start: 0.7702 (mmt180) cc_final: 0.7478 (mmt180) REVERT: C 30 MET cc_start: 0.7679 (mmm) cc_final: 0.7417 (mmm) REVERT: D 42 ASN cc_start: 0.8931 (t0) cc_final: 0.8729 (t0) REVERT: H 46 ASP cc_start: 0.8317 (p0) cc_final: 0.7907 (p0) REVERT: H 55 LEU cc_start: 0.7825 (mt) cc_final: 0.6982 (tt) REVERT: H 150 ARG cc_start: 0.7743 (mtt180) cc_final: 0.6046 (pmt170) REVERT: H 178 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8246 (mt0) REVERT: H 184 GLU cc_start: 0.8448 (tt0) cc_final: 0.8217 (tt0) REVERT: I 3 LYS cc_start: 0.8449 (mtpp) cc_final: 0.8176 (mtpt) REVERT: L 258 ASP cc_start: 0.8064 (t0) cc_final: 0.7850 (t0) REVERT: M 26 ASP cc_start: 0.7916 (t0) cc_final: 0.7518 (t70) REVERT: M 36 ASN cc_start: 0.7943 (m-40) cc_final: 0.7712 (t0) REVERT: M 69 MET cc_start: 0.9204 (mmp) cc_final: 0.8983 (mmp) REVERT: O 5 TYR cc_start: 0.8386 (p90) cc_final: 0.7983 (p90) REVERT: O 26 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8142 (mp) REVERT: Q 9 GLN cc_start: 0.8235 (mt0) cc_final: 0.7981 (mm-40) REVERT: U 53 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7498 (ptt180) REVERT: W 11 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6380 (m-10) REVERT: X 39 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7471 (mp) REVERT: X 40 CYS cc_start: 0.8362 (m) cc_final: 0.8114 (m) outliers start: 26 outliers final: 10 residues processed: 224 average time/residue: 1.2467 time to fit residues: 328.3260 Evaluate side-chains 216 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 2.130 ------------------------------------------------------------------------------- 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 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 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: 10.0000 chunk 106 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.145555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107294 restraints weight = 26546.883| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.26 r_work: 0.3112 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 24099 Z= 0.211 Angle : 0.795 21.039 33025 Z= 0.316 Chirality : 0.041 0.149 3168 Planarity : 0.004 0.042 4033 Dihedral : 18.535 179.804 4602 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.01 % Allowed : 11.67 % Favored : 86.32 % 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: 2.10 (0.17), residues: 2229 helix: 2.09 (0.12), residues: 1538 sheet: 1.55 (0.95), residues: 27 loop : -0.24 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 74 HIS 0.009 0.001 HIS M 182 PHE 0.026 0.002 PHE S 11 TYR 0.021 0.002 TYR M 193 ARG 0.005 0.000 ARG E 46 Details of bonding type rmsd hydrogen bonds : bond 0.05447 ( 1294) hydrogen bonds : angle 3.62329 ( 3732) covalent geometry : bond 0.00519 (24085) covalent geometry : angle 0.79497 (33025) Misc. bond : bond 0.00327 ( 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 245 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 2.259 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6077 (tmm) cc_final: 0.5617 (tmm) REVERT: 7 3 LYS cc_start: 0.8316 (mtpt) cc_final: 0.8022 (mtpp) REVERT: 7 15 ARG cc_start: 0.7825 (mmt180) cc_final: 0.7445 (mmt180) REVERT: C 30 MET cc_start: 0.7686 (mmm) cc_final: 0.7423 (mmm) REVERT: H 55 LEU cc_start: 0.7854 (mt) cc_final: 0.7030 (tt) REVERT: H 178 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8323 (mt0) REVERT: H 184 GLU cc_start: 0.8502 (tt0) cc_final: 0.8220 (tt0) REVERT: H 228 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8132 (pt0) REVERT: L 258 ASP cc_start: 0.8001 (t0) cc_final: 0.7695 (t0) REVERT: M 26 ASP cc_start: 0.7784 (t0) cc_final: 0.7322 (t70) REVERT: M 36 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7744 (t0) REVERT: M 69 MET cc_start: 0.9263 (mmp) cc_final: 0.8998 (mmp) REVERT: O 5 TYR cc_start: 0.8409 (p90) cc_final: 0.7999 (p90) REVERT: O 26 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8169 (mp) REVERT: Q 9 GLN cc_start: 0.8294 (mt0) cc_final: 0.7982 (mm-40) REVERT: U 15 ARG cc_start: 0.5591 (ttp80) cc_final: 0.5032 (mtp180) REVERT: U 53 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7516 (ptt180) REVERT: W 11 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6368 (m-10) REVERT: X 39 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7456 (mp) outliers start: 39 outliers final: 13 residues processed: 224 average time/residue: 1.3524 time to fit residues: 351.9194 Evaluate side-chains 214 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 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 S residue 9 GLN 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: 0.5980 chunk 216 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.149459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111560 restraints weight = 26345.770| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.26 r_work: 0.3174 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3058 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= 0.118 Angle : 0.693 20.325 33025 Z= 0.269 Chirality : 0.036 0.134 3168 Planarity : 0.003 0.037 4033 Dihedral : 17.810 179.952 4602 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.14 % Allowed : 12.91 % Favored : 85.96 % 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: 2.46 (0.17), residues: 2229 helix: 2.39 (0.12), residues: 1538 sheet: 1.39 (0.86), residues: 33 loop : -0.20 (0.24), residues: 658 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 0.015 0.001 TYR M 193 ARG 0.002 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.04653 ( 1294) hydrogen bonds : angle 3.42426 ( 3732) covalent geometry : bond 0.00269 (24085) covalent geometry : angle 0.69308 (33025) Misc. bond : bond 0.00184 ( 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 229 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 2.753 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6009 (tmm) cc_final: 0.5475 (tmm) REVERT: 7 3 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7940 (mtpp) REVERT: 7 15 ARG cc_start: 0.7745 (mmt180) cc_final: 0.7372 (mmt180) REVERT: A 1 MET cc_start: 0.8080 (tpp) cc_final: 0.7829 (tpt) REVERT: C 30 MET cc_start: 0.7607 (mmm) cc_final: 0.7338 (mmm) REVERT: H 184 GLU cc_start: 0.8489 (tt0) cc_final: 0.8251 (tt0) REVERT: K 3 LYS cc_start: 0.7804 (mttm) cc_final: 0.7581 (tttm) REVERT: L 258 ASP cc_start: 0.8025 (t0) cc_final: 0.7779 (t0) REVERT: M 26 ASP cc_start: 0.7751 (t0) cc_final: 0.7276 (t70) REVERT: M 36 ASN cc_start: 0.7916 (m-40) cc_final: 0.7673 (t0) REVERT: M 69 MET cc_start: 0.9203 (mmp) cc_final: 0.8922 (mmp) REVERT: O 5 TYR cc_start: 0.8357 (p90) cc_final: 0.7858 (p90) REVERT: O 26 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8158 (mp) REVERT: Q 9 GLN cc_start: 0.8146 (mt0) cc_final: 0.7883 (mm-40) REVERT: U 53 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7480 (ptt180) REVERT: W 11 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6288 (m-10) REVERT: X 39 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7439 (mp) REVERT: X 40 CYS cc_start: 0.8302 (m) cc_final: 0.8031 (m) outliers start: 22 outliers final: 10 residues processed: 221 average time/residue: 1.2380 time to fit residues: 319.8907 Evaluate side-chains 214 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain 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 261 THR Chi-restraints excluded: chain O residue 26 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 13 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 157 optimal weight: 0.0670 chunk 76 optimal weight: 5.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 42 ASN D 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110005 restraints weight = 26253.536| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.29 r_work: 0.3141 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24099 Z= 0.143 Angle : 0.720 20.514 33025 Z= 0.282 Chirality : 0.038 0.134 3168 Planarity : 0.003 0.038 4033 Dihedral : 17.873 179.896 4602 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.14 % Allowed : 13.01 % Favored : 85.85 % 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: 2.38 (0.17), residues: 2229 helix: 2.33 (0.12), residues: 1538 sheet: 1.59 (0.94), residues: 27 loop : -0.21 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 74 HIS 0.007 0.001 HIS M 266 PHE 0.020 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 0.04912 ( 1294) hydrogen bonds : angle 3.48700 ( 3732) covalent geometry : bond 0.00341 (24085) covalent geometry : angle 0.72043 (33025) Misc. bond : bond 0.00237 ( 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 229 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 2.060 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6071 (tmm) cc_final: 0.5531 (tmm) REVERT: 7 3 LYS cc_start: 0.8286 (mtpt) cc_final: 0.8014 (mtpp) REVERT: 7 15 ARG cc_start: 0.7819 (mmt180) cc_final: 0.7511 (mmt180) REVERT: A 1 MET cc_start: 0.8065 (tpp) cc_final: 0.7833 (tpt) REVERT: C 30 MET cc_start: 0.7603 (mmm) cc_final: 0.7333 (mmm) REVERT: H 184 GLU cc_start: 0.8488 (tt0) cc_final: 0.8246 (tt0) REVERT: I 3 LYS cc_start: 0.8547 (mtpp) cc_final: 0.8195 (mtmm) REVERT: L 258 ASP cc_start: 0.8086 (t0) cc_final: 0.7832 (t0) REVERT: M 26 ASP cc_start: 0.7809 (t0) cc_final: 0.7333 (t70) REVERT: M 36 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7717 (t0) REVERT: M 69 MET cc_start: 0.9232 (mmp) cc_final: 0.8985 (mmp) REVERT: O 5 TYR cc_start: 0.8427 (p90) cc_final: 0.7946 (p90) REVERT: O 26 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8160 (mp) REVERT: Q 9 GLN cc_start: 0.8215 (mt0) cc_final: 0.7847 (mm110) REVERT: U 53 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7504 (ptt-90) REVERT: W 11 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.6328 (m-10) REVERT: X 39 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7423 (mp) outliers start: 22 outliers final: 12 residues processed: 223 average time/residue: 1.2590 time to fit residues: 331.1054 Evaluate side-chains 221 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 36 ASN Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain U residue 30 MET Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 39 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 21 optimal weight: 0.0570 chunk 165 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 193 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 9 GLN ** 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 = 0.3760 r_free = 0.3760 target = 0.151110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112996 restraints weight = 26484.939| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.30 r_work: 0.3181 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3192 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= 0.107 Angle : 0.672 19.793 33025 Z= 0.260 Chirality : 0.036 0.134 3168 Planarity : 0.003 0.037 4033 Dihedral : 17.397 179.986 4602 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.77 % Allowed : 13.42 % 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: 2.65 (0.17), residues: 2229 helix: 2.53 (0.12), residues: 1555 sheet: 1.42 (0.87), residues: 33 loop : -0.18 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 74 HIS 0.005 0.001 HIS M 266 PHE 0.014 0.001 PHE S 11 TYR 0.013 0.001 TYR C 29 ARG 0.002 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 1294) hydrogen bonds : angle 3.37515 ( 3732) covalent geometry : bond 0.00237 (24085) covalent geometry : angle 0.67226 (33025) Misc. bond : bond 0.00159 ( 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 227 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 2.205 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6076 (tmm) cc_final: 0.5520 (tmm) REVERT: 7 3 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7827 (mtpp) REVERT: 7 15 ARG cc_start: 0.7723 (mmt180) cc_final: 0.7443 (mmt180) REVERT: A 1 MET cc_start: 0.7947 (tpp) cc_final: 0.7688 (tpt) REVERT: C 30 MET cc_start: 0.7607 (mmm) cc_final: 0.7338 (mmm) REVERT: H 184 GLU cc_start: 0.8447 (tt0) cc_final: 0.8218 (tt0) REVERT: I 3 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8132 (mtmm) REVERT: L 258 ASP cc_start: 0.8093 (t0) cc_final: 0.7874 (t0) REVERT: M 26 ASP cc_start: 0.7777 (t0) cc_final: 0.7301 (t70) REVERT: M 36 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7675 (t0) REVERT: M 69 MET cc_start: 0.9158 (mmp) cc_final: 0.8816 (mmp) REVERT: O 5 TYR cc_start: 0.8390 (p90) cc_final: 0.7928 (p90) REVERT: O 26 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8113 (mp) REVERT: Q 6 LYS cc_start: 0.7971 (mttt) cc_final: 0.7689 (mttp) REVERT: Q 9 GLN cc_start: 0.8130 (mt0) cc_final: 0.7860 (mm-40) REVERT: U 53 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7406 (ptt180) REVERT: W 11 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6207 (m-10) REVERT: X 39 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7410 (mp) outliers start: 15 outliers final: 9 residues processed: 223 average time/residue: 1.1983 time to fit residues: 312.4969 Evaluate side-chains 212 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain M residue 36 ASN Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain O residue 26 LEU 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: 0.9980 chunk 217 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 21 optimal weight: 0.0770 chunk 86 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 20 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.109752 restraints weight = 26311.792| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.29 r_work: 0.3134 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24099 Z= 0.142 Angle : 0.713 20.234 33025 Z= 0.280 Chirality : 0.038 0.133 3168 Planarity : 0.003 0.037 4033 Dihedral : 17.627 179.913 4602 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.98 % Allowed : 13.37 % Favored : 85.65 % 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: 1553 sheet: 1.78 (1.14), residues: 17 loop : -0.17 (0.24), residues: 659 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 0.019 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 0.04847 ( 1294) hydrogen bonds : angle 3.46102 ( 3732) covalent geometry : bond 0.00337 (24085) covalent geometry : angle 0.71341 (33025) Misc. bond : bond 0.00234 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16009.13 seconds wall clock time: 276 minutes 44.43 seconds (16604.43 seconds total)