Starting phenix.real_space_refine on Sat Sep 12 16:20:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dg8_7883/09_2026/6dg8_7883_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dg8_7883/09_2026/6dg8_7883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dg8_7883/09_2026/6dg8_7883_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dg8_7883/09_2026/6dg8_7883_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dg8_7883/09_2026/6dg8_7883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dg8_7883/09_2026/6dg8_7883.map" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 10980 2.51 5 N 2690 2.21 5 O 3000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16715 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3235 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3235 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3235 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3235 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3235 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'SRO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.66, per 1000 atoms: 0.22 Number of scatterers: 16715 At special positions: 0 Unit cell: (104.272, 108.528, 172.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 3000 8.00 N 2690 7.00 C 10980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 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=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG I 1 " - " ASN B 164 " " NAG P 1 " - " ASN D 82 " Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 640.1 milliseconds 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3800 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 43.2% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 3.556A pdb=" N SER A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.761A pdb=" N SER A 92 " --> pdb=" O PRO A 89 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 93 " --> pdb=" O THR A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 93' Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.657A pdb=" N SER A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 241 removed outlier: 4.398A pdb=" N VAL A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.122A pdb=" N THR A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 Processing helix chain 'A' and resid 319 through 330 Processing helix chain 'A' and resid 398 through 417 Processing helix chain 'A' and resid 418 through 423 removed outlier: 3.731A pdb=" N GLU A 421 " --> pdb=" O GLU A 418 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 422 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 423 " --> pdb=" O ARG A 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 418 through 423' Processing helix chain 'A' and resid 428 through 462 removed outlier: 4.156A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 20 removed outlier: 3.556A pdb=" N SER B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.760A pdb=" N SER B 92 " --> pdb=" O PRO B 89 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 93 " --> pdb=" O THR B 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 93' Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.658A pdb=" N SER B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 241 removed outlier: 4.399A pdb=" N VAL B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 249 through 273 removed outlier: 4.122A pdb=" N THR B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 308 Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 398 through 417 Processing helix chain 'B' and resid 418 through 423 removed outlier: 3.731A pdb=" N GLU B 421 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL B 422 " --> pdb=" O MET B 419 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B 423 " --> pdb=" O ARG B 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 418 through 423' Processing helix chain 'B' and resid 428 through 462 removed outlier: 4.156A pdb=" N VAL B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 20 removed outlier: 3.556A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.760A pdb=" N SER C 92 " --> pdb=" O PRO C 89 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 93 " --> pdb=" O THR C 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 93' Processing helix chain 'C' and resid 170 through 176 removed outlier: 3.657A pdb=" N SER C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 241 removed outlier: 4.399A pdb=" N VAL C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 249 through 273 removed outlier: 4.122A pdb=" N THR C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 308 Processing helix chain 'C' and resid 319 through 330 Processing helix chain 'C' and resid 398 through 417 Processing helix chain 'C' and resid 418 through 423 removed outlier: 3.731A pdb=" N GLU C 421 " --> pdb=" O GLU C 418 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL C 422 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 423 " --> pdb=" O ARG C 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 418 through 423' Processing helix chain 'C' and resid 428 through 462 removed outlier: 4.158A pdb=" N VAL C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.556A pdb=" N SER D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.760A pdb=" N SER D 92 " --> pdb=" O PRO D 89 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 93 " --> pdb=" O THR D 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 93' Processing helix chain 'D' and resid 170 through 176 removed outlier: 3.657A pdb=" N SER D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 241 removed outlier: 4.400A pdb=" N VAL D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 249 through 273 removed outlier: 4.123A pdb=" N THR D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 308 Processing helix chain 'D' and resid 319 through 330 Processing helix chain 'D' and resid 398 through 417 Processing helix chain 'D' and resid 418 through 423 removed outlier: 3.731A pdb=" N GLU D 421 " --> pdb=" O GLU D 418 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 422 " --> pdb=" O MET D 419 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA D 423 " --> pdb=" O ARG D 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 418 through 423' Processing helix chain 'D' and resid 428 through 462 removed outlier: 4.156A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 20 removed outlier: 3.555A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.760A pdb=" N SER E 92 " --> pdb=" O PRO E 89 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE E 93 " --> pdb=" O THR E 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 93' Processing helix chain 'E' and resid 170 through 176 removed outlier: 3.657A pdb=" N SER E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 241 removed outlier: 4.399A pdb=" N VAL E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 249 through 273 removed outlier: 4.122A pdb=" N THR E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 Processing helix chain 'E' and resid 319 through 330 Processing helix chain 'E' and resid 398 through 417 Processing helix chain 'E' and resid 418 through 423 removed outlier: 3.731A pdb=" N GLU E 421 " --> pdb=" O GLU E 418 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL E 422 " --> pdb=" O MET E 419 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA E 423 " --> pdb=" O ARG E 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 418 through 423' Processing helix chain 'E' and resid 428 through 462 removed outlier: 4.158A pdb=" N VAL E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88 removed outlier: 7.842A pdb=" N GLN A 130 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL A 106 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL A 132 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88 removed outlier: 8.073A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 46 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.584A pdb=" N THR A 154 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N TYR A 207 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLU A 198 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLU A 209 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE A 196 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LYS A 211 " --> pdb=" O PRO A 194 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR A 213 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL A 192 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE A 215 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 88 removed outlier: 7.842A pdb=" N GLN B 130 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 106 " --> pdb=" O GLN B 130 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL B 132 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 88 removed outlier: 8.073A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR B 46 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.585A pdb=" N THR B 154 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N TYR B 207 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLU B 198 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N GLU B 209 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE B 196 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LYS B 211 " --> pdb=" O PRO B 194 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR B 213 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL B 192 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE B 215 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 86 through 88 removed outlier: 7.842A pdb=" N GLN C 130 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 106 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL C 132 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 86 through 88 removed outlier: 8.073A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR C 46 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.584A pdb=" N THR C 154 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N TYR C 207 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLU C 198 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLU C 209 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE C 196 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LYS C 211 " --> pdb=" O PRO C 194 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR C 213 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL C 192 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE C 215 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 88 removed outlier: 7.841A pdb=" N GLN D 130 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL D 106 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL D 132 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 86 through 88 removed outlier: 8.072A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR D 46 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.585A pdb=" N THR D 154 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N TYR D 207 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLU D 198 " --> pdb=" O TYR D 207 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N GLU D 209 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE D 196 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LYS D 211 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR D 213 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL D 192 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE D 215 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 86 through 88 removed outlier: 7.841A pdb=" N GLN E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL E 106 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL E 132 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 86 through 88 removed outlier: 8.073A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR E 46 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.583A pdb=" N THR E 154 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N TYR E 207 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLU E 198 " --> pdb=" O TYR E 207 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N GLU E 209 " --> pdb=" O PHE E 196 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE E 196 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LYS E 211 " --> pdb=" O PRO E 194 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR E 213 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL E 192 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE E 215 " --> pdb=" O LEU E 190 " (cutoff:3.500A) 810 hydrogen bonds defined for protein. 2370 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: 2.71 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5028 1.34 - 1.46: 3473 1.46 - 1.58: 8598 1.58 - 1.69: 1 1.69 - 1.81: 70 Bond restraints: 17170 Sorted by residual: bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.589 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.65e+00 bond pdb=" CD1 SRO E 501 " pdb=" NE1 SRO E 501 " ideal model delta sigma weight residual 1.377 1.319 0.058 2.00e-02 2.50e+03 8.45e+00 bond pdb=" CD1 SRO D 501 " pdb=" NE1 SRO D 501 " ideal model delta sigma weight residual 1.377 1.319 0.058 2.00e-02 2.50e+03 8.41e+00 ... (remaining 17165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 22620 2.61 - 5.21: 635 5.21 - 7.82: 145 7.82 - 10.42: 45 10.42 - 13.03: 5 Bond angle restraints: 23450 Sorted by residual: angle pdb=" C GLU C 78 " pdb=" N ASP C 79 " pdb=" CA ASP C 79 " ideal model delta sigma weight residual 122.61 132.07 -9.46 1.56e+00 4.11e-01 3.68e+01 angle pdb=" C GLU A 78 " pdb=" N ASP A 79 " pdb=" CA ASP A 79 " ideal model delta sigma weight residual 122.61 132.05 -9.44 1.56e+00 4.11e-01 3.66e+01 angle pdb=" C GLU E 78 " pdb=" N ASP E 79 " pdb=" CA ASP E 79 " ideal model delta sigma weight residual 122.61 132.05 -9.44 1.56e+00 4.11e-01 3.66e+01 angle pdb=" C GLU D 78 " pdb=" N ASP D 79 " pdb=" CA ASP D 79 " ideal model delta sigma weight residual 122.61 132.05 -9.44 1.56e+00 4.11e-01 3.66e+01 angle pdb=" C GLU B 78 " pdb=" N ASP B 79 " pdb=" CA ASP B 79 " ideal model delta sigma weight residual 122.61 132.02 -9.41 1.56e+00 4.11e-01 3.64e+01 ... (remaining 23445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.58: 9982 23.58 - 47.16: 461 47.16 - 70.74: 29 70.74 - 94.32: 50 94.32 - 117.89: 23 Dihedral angle restraints: 10545 sinusoidal: 4710 harmonic: 5835 Sorted by residual: dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual 93.00 133.15 -40.15 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 149 " pdb=" CB CYS D 149 " ideal model delta sinusoidal sigma weight residual 93.00 133.14 -40.14 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 133.10 -40.10 1 1.00e+01 1.00e-02 2.26e+01 ... (remaining 10542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2390 0.085 - 0.171: 348 0.171 - 0.256: 36 0.256 - 0.341: 7 0.341 - 0.426: 1 Chirality restraints: 2782 Sorted by residual: chirality pdb=" C2 NAG I 1 " pdb=" C1 NAG I 1 " pdb=" C3 NAG I 1 " pdb=" N2 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.07 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 2779 not shown) Planarity restraints: 2832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 229 " -0.041 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO D 230 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 230 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 230 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 229 " 0.041 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO A 230 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 229 " 0.041 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO B 230 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 230 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 230 " 0.035 5.00e-02 4.00e+02 ... (remaining 2829 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 71 2.51 - 3.11: 11130 3.11 - 3.71: 26122 3.71 - 4.30: 33535 4.30 - 4.90: 52936 Nonbonded interactions: 123794 Sorted by model distance: nonbonded pdb=" NH1 ARG C 306 " pdb=" OD2 ASP C 312 " model vdw 1.916 3.120 nonbonded pdb=" NH1 ARG A 306 " pdb=" OD2 ASP A 312 " model vdw 1.916 3.120 nonbonded pdb=" NH1 ARG E 306 " pdb=" OD2 ASP E 312 " model vdw 1.917 3.120 nonbonded pdb=" NH1 ARG B 306 " pdb=" OD2 ASP B 312 " model vdw 1.917 3.120 nonbonded pdb=" NH1 ARG D 306 " pdb=" OD2 ASP D 312 " model vdw 1.917 3.120 ... (remaining 123789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 462) selection = (chain 'B' and resid 8 through 462) selection = chain 'C' selection = (chain 'D' and resid 8 through 462) selection = (chain 'E' and resid 8 through 462) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' } 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.170 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.005 0.101 17197 Z= 0.282 Angle : 1.150 13.026 23526 Z= 0.576 Chirality : 0.059 0.426 2782 Planarity : 0.007 0.061 2830 Dihedral : 15.092 117.894 6730 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.55 % Allowed : 11.33 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.14), residues: 1935 helix: -1.52 (0.13), residues: 740 sheet: -1.36 (0.26), residues: 330 loop : -3.41 (0.13), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 306 TYR 0.016 0.002 TYR B 67 PHE 0.014 0.002 PHE A 199 TRP 0.015 0.001 TRP C 75 HIS 0.007 0.001 HIS D 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.28 (17170) covalent geometry : angle 1.14079 / 0.57 (23450) SS BOND : bond 0.00042 / 0.02 ( 5) SS BOND : angle 0.67003 / 0.40 ( 10) hydrogen bonds : bond 0.14353 / 9.05 ( 780) hydrogen bonds : angle 6.54137 / 4.42 ( 2370) link_BETA1-4 : bond 0.00899 / 0.59 ( 20) link_BETA1-4 : angle 1.79236 / 1.16 ( 60) link_NAG-ASN : bond 0.05118 / 2.56 ( 2) link_NAG-ASN : angle 8.27189 / 4.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8735 (mm110) cc_final: 0.8019 (mt0) REVERT: B 147 GLN cc_start: 0.8542 (mm110) cc_final: 0.8005 (mt0) REVERT: D 111 ASN cc_start: 0.8489 (m-40) cc_final: 0.8195 (p0) outliers start: 10 outliers final: 0 residues processed: 109 average time/residue: 0.1134 time to fit residues: 20.0826 Evaluate side-chains 49 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0010 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 overall best weight: 1.8170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN A 164 ASN A 309 HIS B 82 ASN B 309 HIS C 82 ASN C 164 ASN C 309 HIS D 164 ASN D 309 HIS E 82 ASN E 164 ASN E 309 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.060517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.042882 restraints weight = 149192.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.043803 restraints weight = 92165.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.044312 restraints weight = 68499.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.044696 restraints weight = 58274.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.044889 restraints weight = 52061.083| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17197 Z= 0.150 Angle : 0.696 9.933 23526 Z= 0.340 Chirality : 0.044 0.290 2782 Planarity : 0.005 0.055 2830 Dihedral : 11.422 93.093 2895 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.44 % Allowed : 14.14 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.16), residues: 1935 helix: 0.63 (0.18), residues: 720 sheet: -1.35 (0.23), residues: 395 loop : -2.82 (0.15), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 306 TYR 0.012 0.001 TYR A 262 PHE 0.012 0.001 PHE E 254 TRP 0.030 0.001 TRP A 459 HIS 0.002 0.001 HIS A 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (17170) covalent geometry : angle 0.68325 / 0.34 (23450) SS BOND : bond 0.00112 / 0.06 ( 5) SS BOND : angle 0.50865 / 0.27 ( 10) hydrogen bonds : bond 0.04048 / 2.58 ( 780) hydrogen bonds : angle 5.15799 / 3.48 ( 2370) link_BETA1-4 : bond 0.00409 / 0.27 ( 20) link_BETA1-4 : angle 2.00256 / 1.22 ( 60) link_NAG-ASN : bond 0.01348 / 0.69 ( 2) link_NAG-ASN : angle 5.66524 / 3.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.9322 (tpp) cc_final: 0.8944 (tpp) REVERT: A 221 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8366 (pt) REVERT: B 147 GLN cc_start: 0.8435 (mm110) cc_final: 0.7941 (mt0) REVERT: B 213 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.5664 (m-80) REVERT: B 221 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8264 (pt) REVERT: B 256 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7426 (tp) REVERT: C 221 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8559 (pt) REVERT: C 397 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6676 (tm) REVERT: D 221 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8715 (pt) REVERT: E 221 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8618 (pt) outliers start: 26 outliers final: 0 residues processed: 75 average time/residue: 0.1017 time to fit residues: 12.8284 Evaluate side-chains 48 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 40 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 163 optimal weight: 0.0010 chunk 149 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 105 optimal weight: 0.0370 chunk 114 optimal weight: 8.9990 overall best weight: 1.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 411 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.059340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.041756 restraints weight = 151264.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.042658 restraints weight = 93405.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.043099 restraints weight = 69118.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.043520 restraints weight = 59354.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.043740 restraints weight = 52678.041| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17197 Z= 0.120 Angle : 0.670 9.969 23526 Z= 0.314 Chirality : 0.044 0.279 2782 Planarity : 0.004 0.056 2830 Dihedral : 8.869 86.726 2895 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.65 % Allowed : 14.86 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.17), residues: 1935 helix: 1.44 (0.18), residues: 720 sheet: -1.24 (0.23), residues: 395 loop : -2.61 (0.16), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 400 TYR 0.011 0.001 TYR C 262 PHE 0.010 0.001 PHE A 254 TRP 0.014 0.001 TRP A 459 HIS 0.004 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (17170) covalent geometry : angle 0.65792 / 0.31 (23450) SS BOND : bond 0.00077 / 0.04 ( 5) SS BOND : angle 0.32374 / 0.18 ( 10) hydrogen bonds : bond 0.03596 / 2.32 ( 780) hydrogen bonds : angle 4.64264 / 3.13 ( 2370) link_BETA1-4 : bond 0.00539 / 0.31 ( 20) link_BETA1-4 : angle 1.95944 / 1.16 ( 60) link_NAG-ASN : bond 0.01478 / 0.73 ( 2) link_NAG-ASN : angle 5.37034 / 2.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 47 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.9380 (tpp) cc_final: 0.9134 (tpp) REVERT: B 147 GLN cc_start: 0.8485 (mm110) cc_final: 0.7950 (mt0) REVERT: B 213 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.5819 (m-80) REVERT: B 459 TRP cc_start: 0.6099 (t-100) cc_final: 0.5770 (t-100) REVERT: C 256 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7740 (tp) REVERT: C 459 TRP cc_start: 0.6163 (t-100) cc_final: 0.5767 (t-100) REVERT: E 167 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8661 (tm) REVERT: E 210 MET cc_start: 0.9419 (tpp) cc_final: 0.9198 (tpp) outliers start: 48 outliers final: 3 residues processed: 95 average time/residue: 0.1069 time to fit residues: 17.1105 Evaluate side-chains 45 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain E residue 167 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 120 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 147 GLN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 HIS C 125 ASN C 147 GLN D 125 ASN D 147 GLN E 125 ASN E 147 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.052609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.034891 restraints weight = 156684.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.035679 restraints weight = 99805.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.036022 restraints weight = 76005.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.036378 restraints weight = 66697.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.036564 restraints weight = 60047.458| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 17197 Z= 0.303 Angle : 0.857 12.349 23526 Z= 0.413 Chirality : 0.048 0.316 2782 Planarity : 0.007 0.066 2830 Dihedral : 8.263 80.809 2895 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.09 % Allowed : 14.48 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.17), residues: 1935 helix: 1.32 (0.18), residues: 715 sheet: -1.55 (0.23), residues: 395 loop : -2.47 (0.17), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 439 TYR 0.016 0.002 TYR D 23 PHE 0.025 0.003 PHE B 438 TRP 0.021 0.003 TRP A 75 HIS 0.012 0.002 HIS D 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.30 (17170) covalent geometry : angle 0.84364 / 0.41 (23450) SS BOND : bond 0.00650 / 0.33 ( 5) SS BOND : angle 1.71849 / 1.04 ( 10) hydrogen bonds : bond 0.04365 / 2.78 ( 780) hydrogen bonds : angle 4.88512 / 3.32 ( 2370) link_BETA1-4 : bond 0.00462 / 0.28 ( 20) link_BETA1-4 : angle 2.51254 / 1.46 ( 60) link_NAG-ASN : bond 0.00364 / 0.18 ( 2) link_NAG-ASN : angle 5.29393 / 3.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 42 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 167 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8932 (tm) REVERT: B 213 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.7192 (m-80) REVERT: C 183 ASN cc_start: 0.8454 (t0) cc_final: 0.8082 (p0) REVERT: E 167 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9015 (tm) REVERT: E 235 MET cc_start: 0.9154 (tpt) cc_final: 0.8924 (tmm) outliers start: 56 outliers final: 14 residues processed: 97 average time/residue: 0.1078 time to fit residues: 17.3472 Evaluate side-chains 56 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 39 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 324 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 132 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 GLN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN D 184 GLN E 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.052026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.034906 restraints weight = 155348.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.035674 restraints weight = 98104.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.036138 restraints weight = 74150.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.036318 restraints weight = 62654.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.036571 restraints weight = 57218.441| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17197 Z= 0.197 Angle : 0.709 11.145 23526 Z= 0.340 Chirality : 0.044 0.260 2782 Planarity : 0.005 0.055 2830 Dihedral : 7.677 71.378 2895 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.43 % Allowed : 15.69 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.18), residues: 1935 helix: 1.71 (0.19), residues: 720 sheet: -1.45 (0.23), residues: 395 loop : -2.34 (0.18), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 416 TYR 0.014 0.001 TYR A 223 PHE 0.019 0.001 PHE B 438 TRP 0.017 0.002 TRP E 75 HIS 0.004 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (17170) covalent geometry : angle 0.69853 / 0.34 (23450) SS BOND : bond 0.00274 / 0.14 ( 5) SS BOND : angle 1.13830 / 0.68 ( 10) hydrogen bonds : bond 0.03734 / 2.37 ( 780) hydrogen bonds : angle 4.67258 / 3.17 ( 2370) link_BETA1-4 : bond 0.00381 / 0.22 ( 20) link_BETA1-4 : angle 2.04410 / 1.24 ( 60) link_NAG-ASN : bond 0.01161 / 0.58 ( 2) link_NAG-ASN : angle 4.76025 / 2.71 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 33 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8774 (pt) REVERT: B 167 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8840 (tm) REVERT: B 213 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7104 (m-80) REVERT: B 221 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8709 (pt) REVERT: C 167 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8911 (tm) REVERT: C 221 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8916 (pt) REVERT: D 221 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8944 (pt) REVERT: E 167 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8925 (tm) REVERT: E 221 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8963 (pt) REVERT: E 235 MET cc_start: 0.9162 (tpt) cc_final: 0.8962 (tmm) outliers start: 44 outliers final: 17 residues processed: 77 average time/residue: 0.0974 time to fit residues: 13.0177 Evaluate side-chains 59 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 33 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 189 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 ASN C 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.051831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.034741 restraints weight = 155534.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.035524 restraints weight = 98006.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.035995 restraints weight = 73811.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.036248 restraints weight = 62354.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.036456 restraints weight = 56571.011| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17197 Z= 0.160 Angle : 0.683 10.747 23526 Z= 0.323 Chirality : 0.043 0.274 2782 Planarity : 0.004 0.054 2830 Dihedral : 6.730 59.017 2895 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.88 % Allowed : 16.13 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.18), residues: 1935 helix: 1.83 (0.19), residues: 745 sheet: -1.25 (0.24), residues: 395 loop : -2.52 (0.18), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 424 TYR 0.011 0.001 TYR C 448 PHE 0.012 0.001 PHE B 438 TRP 0.014 0.002 TRP B 320 HIS 0.005 0.001 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (17170) covalent geometry : angle 0.67034 / 0.32 (23450) SS BOND : bond 0.00291 / 0.15 ( 5) SS BOND : angle 0.94115 / 0.55 ( 10) hydrogen bonds : bond 0.03472 / 2.22 ( 780) hydrogen bonds : angle 4.48054 / 3.03 ( 2370) link_BETA1-4 : bond 0.00292 / 0.17 ( 20) link_BETA1-4 : angle 2.19730 / 1.30 ( 60) link_NAG-ASN : bond 0.00920 / 0.45 ( 2) link_NAG-ASN : angle 4.91645 / 2.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 34 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.9170 (tpp) cc_final: 0.8921 (tpp) REVERT: A 221 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8805 (pt) REVERT: B 167 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8857 (tm) REVERT: B 213 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7057 (m-80) REVERT: B 221 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8716 (pt) REVERT: C 167 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8904 (tm) REVERT: C 210 MET cc_start: 0.9122 (tpp) cc_final: 0.8783 (tpp) REVERT: C 221 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8928 (pt) REVERT: D 221 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8945 (pt) REVERT: E 167 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8937 (tm) REVERT: E 221 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8969 (pt) outliers start: 34 outliers final: 17 residues processed: 68 average time/residue: 0.1026 time to fit residues: 12.0062 Evaluate side-chains 60 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 34 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 45 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 191 optimal weight: 0.3980 chunk 99 optimal weight: 6.9990 chunk 189 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 125 ASN A 309 HIS B 101 ASN C 411 HIS D 101 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.050248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.033093 restraints weight = 155821.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.033857 restraints weight = 99334.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.034301 restraints weight = 75419.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.034452 restraints weight = 64079.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.034705 restraints weight = 59279.496| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.6254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17197 Z= 0.247 Angle : 0.755 14.110 23526 Z= 0.362 Chirality : 0.044 0.321 2782 Planarity : 0.005 0.050 2830 Dihedral : 6.629 57.916 2895 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.32 % Allowed : 16.02 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.18), residues: 1935 helix: 1.62 (0.19), residues: 750 sheet: -1.34 (0.25), residues: 385 loop : -2.41 (0.18), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 424 TYR 0.013 0.002 TYR D 23 PHE 0.022 0.002 PHE B 233 TRP 0.018 0.002 TRP A 456 HIS 0.004 0.002 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.25 (17170) covalent geometry : angle 0.74371 / 0.36 (23450) SS BOND : bond 0.00373 / 0.19 ( 5) SS BOND : angle 1.28875 / 0.77 ( 10) hydrogen bonds : bond 0.03824 / 2.45 ( 780) hydrogen bonds : angle 4.66843 / 3.16 ( 2370) link_BETA1-4 : bond 0.00337 / 0.21 ( 20) link_BETA1-4 : angle 2.14597 / 1.27 ( 60) link_NAG-ASN : bond 0.00660 / 0.32 ( 2) link_NAG-ASN : angle 5.11960 / 2.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 32 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8916 (pt) REVERT: B 167 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8974 (tm) REVERT: B 213 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7123 (m-80) REVERT: B 221 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8822 (pt) REVERT: C 167 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8959 (tm) REVERT: C 221 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8975 (pt) REVERT: D 221 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9030 (pt) REVERT: E 167 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9064 (tm) REVERT: E 221 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9034 (pt) outliers start: 42 outliers final: 28 residues processed: 73 average time/residue: 0.1057 time to fit residues: 12.9510 Evaluate side-chains 69 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 32 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 448 TYR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 324 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 11 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 118 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 54.7648 > 50:) chunk 32 optimal weight: 0.0570 chunk 72 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 35 optimal weight: 0.0870 overall best weight: 2.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 309 HIS ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.050790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.033914 restraints weight = 156113.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.034703 restraints weight = 97942.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.035163 restraints weight = 73450.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.035324 restraints weight = 61795.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.035594 restraints weight = 56995.032| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17197 Z= 0.158 Angle : 0.695 10.400 23526 Z= 0.328 Chirality : 0.043 0.276 2782 Planarity : 0.004 0.052 2830 Dihedral : 6.140 59.731 2895 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.04 % Allowed : 16.85 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.18), residues: 1935 helix: 1.88 (0.19), residues: 750 sheet: -1.18 (0.25), residues: 385 loop : -2.50 (0.18), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 424 TYR 0.010 0.001 TYR C 448 PHE 0.012 0.001 PHE B 303 TRP 0.015 0.002 TRP A 456 HIS 0.004 0.001 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (17170) covalent geometry : angle 0.68511 / 0.33 (23450) SS BOND : bond 0.00209 / 0.11 ( 5) SS BOND : angle 1.00506 / 0.60 ( 10) hydrogen bonds : bond 0.03484 / 2.22 ( 780) hydrogen bonds : angle 4.47570 / 3.03 ( 2370) link_BETA1-4 : bond 0.00325 / 0.19 ( 20) link_BETA1-4 : angle 1.86260 / 1.12 ( 60) link_NAG-ASN : bond 0.01010 / 0.49 ( 2) link_NAG-ASN : angle 4.91482 / 2.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 32 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8909 (pt) REVERT: B 167 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8898 (tm) REVERT: B 213 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.6837 (m-80) REVERT: B 217 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8329 (ttt90) REVERT: B 221 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8769 (pt) REVERT: C 12 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8446 (mm) REVERT: C 167 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8950 (tm) REVERT: C 221 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8974 (pt) REVERT: D 221 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8998 (pt) REVERT: E 167 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9007 (tm) REVERT: E 221 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9011 (pt) outliers start: 37 outliers final: 25 residues processed: 69 average time/residue: 0.1248 time to fit residues: 13.8545 Evaluate side-chains 68 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 32 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 128 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.050772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.033952 restraints weight = 155743.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.034729 restraints weight = 97153.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.035199 restraints weight = 72891.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.035370 restraints weight = 61304.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.035659 restraints weight = 55544.537| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17197 Z= 0.151 Angle : 0.687 11.210 23526 Z= 0.324 Chirality : 0.043 0.276 2782 Planarity : 0.004 0.053 2830 Dihedral : 5.782 59.287 2895 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.27 % Allowed : 17.07 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.19), residues: 1935 helix: 1.98 (0.19), residues: 750 sheet: -1.07 (0.25), residues: 385 loop : -2.50 (0.18), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 217 TYR 0.010 0.001 TYR D 61 PHE 0.008 0.001 PHE D 438 TRP 0.016 0.002 TRP A 456 HIS 0.004 0.001 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (17170) covalent geometry : angle 0.67791 / 0.32 (23450) SS BOND : bond 0.00214 / 0.11 ( 5) SS BOND : angle 0.91309 / 0.55 ( 10) hydrogen bonds : bond 0.03404 / 2.18 ( 780) hydrogen bonds : angle 4.37292 / 2.95 ( 2370) link_BETA1-4 : bond 0.00298 / 0.17 ( 20) link_BETA1-4 : angle 1.74294 / 1.05 ( 60) link_NAG-ASN : bond 0.00970 / 0.47 ( 2) link_NAG-ASN : angle 4.94409 / 2.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 32 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8905 (pt) REVERT: B 167 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8923 (tm) REVERT: B 213 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7024 (m-80) REVERT: B 217 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8413 (ttt90) REVERT: B 221 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8768 (pt) REVERT: C 12 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8496 (mm) REVERT: C 167 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8943 (tm) REVERT: C 221 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8962 (pt) REVERT: D 12 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8444 (mm) REVERT: D 221 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8970 (pt) REVERT: E 167 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8994 (tm) REVERT: E 221 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8996 (pt) outliers start: 41 outliers final: 23 residues processed: 73 average time/residue: 0.1198 time to fit residues: 14.1267 Evaluate side-chains 67 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 32 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 169 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 0.2980 chunk 191 optimal weight: 30.0000 chunk 83 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.051329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.034623 restraints weight = 154317.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.035400 restraints weight = 95615.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.035882 restraints weight = 71411.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.036040 restraints weight = 59793.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.036308 restraints weight = 55098.330| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.6433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17197 Z= 0.122 Angle : 0.684 12.374 23526 Z= 0.321 Chirality : 0.043 0.272 2782 Planarity : 0.004 0.054 2830 Dihedral : 5.522 59.663 2895 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.93 % Allowed : 17.40 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.19), residues: 1935 helix: 2.10 (0.19), residues: 750 sheet: -0.88 (0.26), residues: 385 loop : -2.56 (0.17), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 219 TYR 0.009 0.001 TYR E 64 PHE 0.009 0.001 PHE B 303 TRP 0.013 0.002 TRP A 456 HIS 0.003 0.001 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (17170) covalent geometry : angle 0.67552 / 0.32 (23450) SS BOND : bond 0.00130 / 0.07 ( 5) SS BOND : angle 0.67277 / 0.41 ( 10) hydrogen bonds : bond 0.03265 / 2.08 ( 780) hydrogen bonds : angle 4.27725 / 2.88 ( 2370) link_BETA1-4 : bond 0.00343 / 0.20 ( 20) link_BETA1-4 : angle 1.63432 / 0.99 ( 60) link_NAG-ASN : bond 0.01147 / 0.56 ( 2) link_NAG-ASN : angle 4.85511 / 2.77 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 32 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8920 (pt) REVERT: B 167 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8911 (tm) REVERT: B 210 MET cc_start: 0.9260 (tpp) cc_final: 0.9025 (tpt) REVERT: B 213 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7014 (m-80) REVERT: B 221 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8751 (pt) REVERT: C 167 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8899 (tm) REVERT: C 221 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8949 (pt) REVERT: D 221 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8937 (pt) REVERT: E 167 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8973 (tm) REVERT: E 221 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8969 (pt) outliers start: 35 outliers final: 22 residues processed: 67 average time/residue: 0.1088 time to fit residues: 12.1225 Evaluate side-chains 63 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 32 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 111 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.049655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.032748 restraints weight = 155041.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.033489 restraints weight = 97868.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.033933 restraints weight = 74105.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.034094 restraints weight = 62683.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.034378 restraints weight = 57142.806| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.6999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17197 Z= 0.218 Angle : 0.738 12.185 23526 Z= 0.352 Chirality : 0.043 0.293 2782 Planarity : 0.005 0.052 2830 Dihedral : 5.782 58.036 2895 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.32 % Allowed : 17.18 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 1935 helix: 1.88 (0.19), residues: 750 sheet: -1.10 (0.26), residues: 385 loop : -2.48 (0.18), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 424 TYR 0.013 0.001 TYR B 23 PHE 0.014 0.002 PHE B 212 TRP 0.018 0.002 TRP A 456 HIS 0.004 0.001 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (17170) covalent geometry : angle 0.72820 / 0.35 (23450) SS BOND : bond 0.00321 / 0.16 ( 5) SS BOND : angle 1.20490 / 0.72 ( 10) hydrogen bonds : bond 0.03605 / 2.30 ( 780) hydrogen bonds : angle 4.50190 / 3.03 ( 2370) link_BETA1-4 : bond 0.00353 / 0.23 ( 20) link_BETA1-4 : angle 1.81150 / 1.08 ( 60) link_NAG-ASN : bond 0.00711 / 0.34 ( 2) link_NAG-ASN : angle 5.11295 / 2.94 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2778.94 seconds wall clock time: 48 minutes 55.41 seconds (2935.41 seconds total)