Starting phenix.real_space_refine on Thu Jul 2 22:01:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7puy_13662/07_2026/7puy_13662.cif Found real_map, /net/cci-nas-00/data/ceres_data/7puy_13662/07_2026/7puy_13662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7puy_13662/07_2026/7puy_13662.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7puy_13662/07_2026/7puy_13662.cif" model { file = "/net/cci-nas-00/data/ceres_data/7puy_13662/07_2026/7puy_13662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7puy_13662/07_2026/7puy_13662.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7puy_13662/07_2026/7puy_13662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7puy_13662/07_2026/7puy_13662.map" } resolution = 3.3 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= 0.017 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 90 5.16 5 C 6576 2.51 5 N 1686 2.21 5 O 2043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10395 Number of models: 1 Model: "" Number of chains: 24 Chain: "a" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1535 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "b" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1535 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "c" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1535 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1745 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 3 Chain: "B" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1745 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 3 Chain: "C" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1745 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 3 Chain: "D" 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 chiralities: 2 Chain: "E" 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 chiralities: 2 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 chiralities: 2 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {'BDP': 1, 'XYS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 2 Chain: "I" 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 chiralities: 2 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 chiralities: 2 Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {'BDP': 1, 'XYS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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 chiralities: 2 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 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 chiralities: 2 Chain: "O" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {'BDP': 1, 'XYS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" 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 chiralities: 2 Chain: "B" 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 chiralities: 2 Chain: "C" 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 chiralities: 2 Time building chain proxies: 2.38, per 1000 atoms: 0.23 Number of scatterers: 10395 At special positions: 0 Unit cell: (86.154, 92.382, 123.522, 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 90 16.00 O 2043 8.00 N 1686 7.00 C 6576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.03 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.03 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " 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 ALPHA1-3 " BDP G 2 " - " XYS G 3 " " BDP K 2 " - " XYS K 3 " " BDP O 2 " - " XYS O 3 " BETA1-3 " XYS G 1 " - " BDP G 2 " " XYS K 1 " - " BDP K 2 " " XYS O 1 " - " BDP O 2 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 301 " - " ASN A 99 " " NAG A 302 " - " ASN A 109 " " NAG B 301 " - " ASN B 99 " " NAG B 302 " - " ASN B 109 " " NAG C 301 " - " ASN C 99 " " NAG C 302 " - " ASN C 109 " " NAG D 1 " - " ASN A 119 " " NAG E 1 " - " ASN A 167 " " NAG F 1 " - " ASN A 79 " " NAG H 1 " - " ASN B 119 " " NAG I 1 " - " ASN B 167 " " NAG J 1 " - " ASN B 79 " " NAG L 1 " - " ASN C 119 " " NAG M 1 " - " ASN C 167 " " NAG N 1 " - " ASN C 79 " " NAG a 601 " - " ASN a 365 " " NAG a 602 " - " ASN a 373 " " NAG a 603 " - " ASN a 395 " " NAG b 601 " - " ASN b 365 " " NAG b 602 " - " ASN b 373 " " NAG b 603 " - " ASN b 395 " " NAG c 601 " - " ASN c 365 " " NAG c 602 " - " ASN c 373 " " NAG c 603 " - " ASN c 395 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 336.7 milliseconds 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 9 sheets defined 47.3% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'a' and resid 294 through 300 removed outlier: 3.595A pdb=" N VAL a 298 " --> pdb=" O GLY a 294 " (cutoff:3.500A) Processing helix chain 'a' and resid 301 through 303 No H-bonds generated for 'chain 'a' and resid 301 through 303' Processing helix chain 'a' and resid 308 through 325 Processing helix chain 'a' and resid 333 through 345 removed outlier: 4.390A pdb=" N ILE a 337 " --> pdb=" O SER a 333 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 348 through 360 Processing helix chain 'a' and resid 399 through 426 removed outlier: 3.591A pdb=" N GLU a 418 " --> pdb=" O MET a 414 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR a 419 " --> pdb=" O LEU a 415 " (cutoff:3.500A) Processing helix chain 'a' and resid 427 through 448 removed outlier: 3.858A pdb=" N VAL a 431 " --> pdb=" O PRO a 427 " (cutoff:3.500A) Processing helix chain 'b' and resid 294 through 300 removed outlier: 3.596A pdb=" N VAL b 298 " --> pdb=" O GLY b 294 " (cutoff:3.500A) Processing helix chain 'b' and resid 301 through 303 No H-bonds generated for 'chain 'b' and resid 301 through 303' Processing helix chain 'b' and resid 308 through 325 Processing helix chain 'b' and resid 333 through 345 removed outlier: 4.390A pdb=" N ILE b 337 " --> pdb=" O SER b 333 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 348 through 360 Processing helix chain 'b' and resid 399 through 426 removed outlier: 3.591A pdb=" N GLU b 418 " --> pdb=" O MET b 414 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR b 419 " --> pdb=" O LEU b 415 " (cutoff:3.500A) Processing helix chain 'b' and resid 427 through 448 removed outlier: 3.858A pdb=" N VAL b 431 " --> pdb=" O PRO b 427 " (cutoff:3.500A) Processing helix chain 'c' and resid 294 through 300 removed outlier: 3.596A pdb=" N VAL c 298 " --> pdb=" O GLY c 294 " (cutoff:3.500A) Processing helix chain 'c' and resid 301 through 303 No H-bonds generated for 'chain 'c' and resid 301 through 303' Processing helix chain 'c' and resid 308 through 325 Processing helix chain 'c' and resid 333 through 345 removed outlier: 4.390A pdb=" N ILE c 337 " --> pdb=" O SER c 333 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 348 through 360 Processing helix chain 'c' and resid 399 through 426 removed outlier: 3.591A pdb=" N GLU c 418 " --> pdb=" O MET c 414 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR c 419 " --> pdb=" O LEU c 415 " (cutoff:3.500A) Processing helix chain 'c' and resid 427 through 448 removed outlier: 3.859A pdb=" N VAL c 431 " --> pdb=" O PRO c 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.996A pdb=" N PHE A 7 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 10 " --> pdb=" O THR A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 35 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.584A pdb=" N GLY A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 removed outlier: 3.624A pdb=" N SER A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 removed outlier: 3.996A pdb=" N PHE B 7 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN B 9 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU B 10 " --> pdb=" O THR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 35 Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.583A pdb=" N GLY B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 248 removed outlier: 3.624A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 removed outlier: 3.996A pdb=" N PHE C 7 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN C 9 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 35 Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.583A pdb=" N GLY C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 248 removed outlier: 3.624A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 279 through 280 Processing sheet with id=AA2, first strand: chain 'a' and resid 392 through 393 removed outlier: 9.535A pdb=" N LYS a 384 " --> pdb=" O SER a 367 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N SER a 367 " --> pdb=" O LYS a 384 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TRP a 386 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN a 365 " --> pdb=" O TRP a 386 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 67 " --> pdb=" O ASN a 373 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'b' and resid 279 through 280 Processing sheet with id=AA4, first strand: chain 'b' and resid 392 through 393 removed outlier: 9.535A pdb=" N LYS b 384 " --> pdb=" O SER b 367 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N SER b 367 " --> pdb=" O LYS b 384 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TRP b 386 " --> pdb=" O ASN b 365 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN b 365 " --> pdb=" O TRP b 386 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 67 " --> pdb=" O ASN b 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 279 through 280 Processing sheet with id=AA6, first strand: chain 'c' and resid 392 through 393 removed outlier: 9.535A pdb=" N LYS c 384 " --> pdb=" O SER c 367 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N SER c 367 " --> pdb=" O LYS c 384 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TRP c 386 " --> pdb=" O ASN c 365 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN c 365 " --> pdb=" O TRP c 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 84 through 87 removed outlier: 3.622A pdb=" N THR A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.622A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 84 through 87 removed outlier: 3.622A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1326 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: 1.59 Time building geometry restraints manager: 1.38 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: 3234 1.34 - 1.46: 2640 1.46 - 1.58: 4584 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 10602 Sorted by residual: bond pdb=" C3 BDP O 2 " pdb=" O3 BDP O 2 " ideal model delta sigma weight residual 1.411 1.516 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C3 BDP K 2 " pdb=" O3 BDP K 2 " ideal model delta sigma weight residual 1.411 1.516 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C3 BDP G 2 " pdb=" O3 BDP G 2 " ideal model delta sigma weight residual 1.411 1.515 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C1 XYS G 3 " pdb=" O5 XYS G 3 " ideal model delta sigma weight residual 1.412 1.499 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C1 XYS O 3 " pdb=" O5 XYS O 3 " ideal model delta sigma weight residual 1.412 1.499 -0.087 2.00e-02 2.50e+03 1.89e+01 ... (remaining 10597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 13460 1.39 - 2.78: 730 2.78 - 4.17: 90 4.17 - 5.56: 42 5.56 - 6.95: 18 Bond angle restraints: 14340 Sorted by residual: angle pdb=" C LEU C 103 " pdb=" N GLU C 104 " pdb=" CA GLU C 104 " ideal model delta sigma weight residual 121.42 126.59 -5.17 1.43e+00 4.89e-01 1.30e+01 angle pdb=" C LEU A 103 " pdb=" N GLU A 104 " pdb=" CA GLU A 104 " ideal model delta sigma weight residual 121.42 126.57 -5.15 1.43e+00 4.89e-01 1.30e+01 angle pdb=" C LEU B 103 " pdb=" N GLU B 104 " pdb=" CA GLU B 104 " ideal model delta sigma weight residual 121.42 126.57 -5.15 1.43e+00 4.89e-01 1.30e+01 angle pdb=" CA GLU A 104 " pdb=" CB GLU A 104 " pdb=" CG GLU A 104 " ideal model delta sigma weight residual 114.10 120.25 -6.15 2.00e+00 2.50e-01 9.45e+00 angle pdb=" CA GLU C 104 " pdb=" CB GLU C 104 " pdb=" CG GLU C 104 " ideal model delta sigma weight residual 114.10 120.23 -6.13 2.00e+00 2.50e-01 9.39e+00 ... (remaining 14335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.47: 5727 26.47 - 52.93: 249 52.93 - 79.40: 15 79.40 - 105.87: 9 105.87 - 132.34: 6 Dihedral angle restraints: 6006 sinusoidal: 2439 harmonic: 3567 Sorted by residual: dihedral pdb=" CB CYS a 301 " pdb=" SG CYS a 301 " pdb=" SG CYS a 310 " pdb=" CB CYS a 310 " ideal model delta sinusoidal sigma weight residual 93.00 144.74 -51.74 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CB CYS b 301 " pdb=" SG CYS b 301 " pdb=" SG CYS b 310 " pdb=" CB CYS b 310 " ideal model delta sinusoidal sigma weight residual 93.00 144.71 -51.71 1 1.00e+01 1.00e-02 3.65e+01 dihedral pdb=" CB CYS c 301 " pdb=" SG CYS c 301 " pdb=" SG CYS c 310 " pdb=" CB CYS c 310 " ideal model delta sinusoidal sigma weight residual 93.00 144.70 -51.70 1 1.00e+01 1.00e-02 3.65e+01 ... (remaining 6003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1536 0.071 - 0.141: 177 0.141 - 0.212: 12 0.212 - 0.282: 0 0.282 - 0.353: 3 Chirality restraints: 1728 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 79 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 79 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN C 79 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 1725 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY a 429 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C GLY a 429 " 0.051 2.00e-02 2.50e+03 pdb=" O GLY a 429 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU a 430 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY c 429 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C GLY c 429 " 0.051 2.00e-02 2.50e+03 pdb=" O GLY c 429 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU c 430 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY b 429 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C GLY b 429 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY b 429 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU b 430 " 0.017 2.00e-02 2.50e+03 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 147 2.63 - 3.20: 9718 3.20 - 3.77: 16343 3.77 - 4.33: 22345 4.33 - 4.90: 36253 Nonbonded interactions: 84806 Sorted by model distance: nonbonded pdb=" O PHE C 233 " pdb=" O4 NAG c 601 " model vdw 2.067 3.040 nonbonded pdb=" OE1 GLU A 100 " pdb=" OG1 THR A 101 " model vdw 2.181 3.040 nonbonded pdb=" OE1 GLU C 100 " pdb=" OG1 THR C 101 " model vdw 2.181 3.040 nonbonded pdb=" OE1 GLU B 100 " pdb=" OG1 THR B 101 " model vdw 2.181 3.040 nonbonded pdb=" O PHE B 233 " pdb=" O4 NAG b 601 " model vdw 2.233 3.040 ... (remaining 84801 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.620 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 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 : 0.006 0.105 10659 Z= 0.282 Angle : 0.752 6.952 14493 Z= 0.361 Chirality : 0.046 0.353 1728 Planarity : 0.005 0.039 1746 Dihedral : 15.072 132.335 3648 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.90 % Allowed : 2.72 % Favored : 95.38 % 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: -0.75 (0.22), residues: 1194 helix: 0.26 (0.23), residues: 489 sheet: -0.31 (0.43), residues: 141 loop : -1.18 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 250 TYR 0.017 0.002 TYR C 253 PHE 0.018 0.001 PHE C 191 TRP 0.014 0.002 TRP c 283 HIS 0.006 0.001 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.28 (10602) covalent geometry : angle 0.73808 / 0.36 (14340) SS BOND : bond 0.00244 / 0.16 ( 18) SS BOND : angle 1.48276 / 0.90 ( 36) hydrogen bonds : bond 0.13415 / 8.53 ( 481) hydrogen bonds : angle 6.39787 / 4.56 ( 1326) link_ALPHA1-3 : bond 0.00069 / 0.04 ( 3) link_ALPHA1-3 : angle 0.31177 / 0.17 ( 9) link_BETA1-3 : bond 0.00920 / 0.52 ( 3) link_BETA1-3 : angle 1.63830 / 0.83 ( 9) link_BETA1-4 : bond 0.00396 / 0.27 ( 9) link_BETA1-4 : angle 1.77812 / 0.96 ( 27) link_NAG-ASN : bond 0.00477 / 0.28 ( 24) link_NAG-ASN : angle 1.65661 / 1.18 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 279 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 284 MET cc_start: 0.6545 (mtt) cc_final: 0.6335 (mtp) REVERT: b 323 ILE cc_start: 0.7560 (mm) cc_final: 0.7348 (mt) outliers start: 21 outliers final: 6 residues processed: 294 average time/residue: 0.1027 time to fit residues: 42.0299 Evaluate side-chains 194 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 188 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 18 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.0770 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.177624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.153837 restraints weight = 15811.620| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.35 r_work: 0.3916 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10659 Z= 0.150 Angle : 0.693 7.521 14493 Z= 0.352 Chirality : 0.044 0.185 1728 Planarity : 0.004 0.052 1746 Dihedral : 9.795 123.428 1317 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.54 % Allowed : 11.41 % Favored : 87.05 % 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: -0.19 (0.23), residues: 1194 helix: 0.95 (0.23), residues: 474 sheet: -0.37 (0.44), residues: 138 loop : -0.94 (0.22), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 256 TYR 0.015 0.001 TYR B 253 PHE 0.014 0.002 PHE C 233 TRP 0.013 0.001 TRP B 210 HIS 0.007 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (10602) covalent geometry : angle 0.67866 / 0.35 (14340) SS BOND : bond 0.00482 / 0.32 ( 18) SS BOND : angle 1.34240 / 0.82 ( 36) hydrogen bonds : bond 0.04429 / 2.92 ( 481) hydrogen bonds : angle 5.46227 / 3.90 ( 1326) link_ALPHA1-3 : bond 0.00293 / 0.17 ( 3) link_ALPHA1-3 : angle 1.00595 / 0.54 ( 9) link_BETA1-3 : bond 0.00889 / 0.50 ( 3) link_BETA1-3 : angle 2.28861 / 1.17 ( 9) link_BETA1-4 : bond 0.00266 / 0.18 ( 9) link_BETA1-4 : angle 1.17832 / 0.67 ( 27) link_NAG-ASN : bond 0.00320 / 0.20 ( 24) link_NAG-ASN : angle 1.61519 / 1.16 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 410 MET cc_start: 0.6358 (mtp) cc_final: 0.6049 (mtp) REVERT: b 312 MET cc_start: 0.8002 (mmt) cc_final: 0.7782 (mmp) REVERT: b 323 ILE cc_start: 0.7663 (mm) cc_final: 0.7459 (mt) REVERT: c 312 MET cc_start: 0.7690 (mmm) cc_final: 0.6965 (mmp) REVERT: A 191 PHE cc_start: 0.6853 (m-80) cc_final: 0.6073 (t80) REVERT: B 191 PHE cc_start: 0.6656 (m-80) cc_final: 0.6143 (t80) REVERT: C 80 MET cc_start: 0.5435 (mmp) cc_final: 0.5126 (mmp) outliers start: 17 outliers final: 9 residues processed: 220 average time/residue: 0.0871 time to fit residues: 27.7575 Evaluate side-chains 197 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain C residue 4 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.176236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.152098 restraints weight = 15932.549| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.37 r_work: 0.3884 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10659 Z= 0.145 Angle : 0.645 7.330 14493 Z= 0.329 Chirality : 0.043 0.183 1728 Planarity : 0.004 0.059 1746 Dihedral : 9.565 119.662 1314 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.72 % Allowed : 13.22 % Favored : 85.05 % 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: 0.06 (0.24), residues: 1194 helix: 1.25 (0.24), residues: 474 sheet: -0.72 (0.44), residues: 144 loop : -0.75 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 282 TYR 0.018 0.002 TYR A 166 PHE 0.018 0.002 PHE C 191 TRP 0.013 0.001 TRP B 210 HIS 0.008 0.001 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (10602) covalent geometry : angle 0.62901 / 0.33 (14340) SS BOND : bond 0.00568 / 0.39 ( 18) SS BOND : angle 1.47367 / 0.91 ( 36) hydrogen bonds : bond 0.03945 / 2.60 ( 481) hydrogen bonds : angle 5.22146 / 3.72 ( 1326) link_ALPHA1-3 : bond 0.00380 / 0.21 ( 3) link_ALPHA1-3 : angle 1.05642 / 0.56 ( 9) link_BETA1-3 : bond 0.01142 / 0.64 ( 3) link_BETA1-3 : angle 2.34398 / 1.20 ( 9) link_BETA1-4 : bond 0.00330 / 0.22 ( 9) link_BETA1-4 : angle 1.23897 / 0.72 ( 27) link_NAG-ASN : bond 0.00266 / 0.17 ( 24) link_NAG-ASN : angle 1.53420 / 1.10 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 410 MET cc_start: 0.6653 (mtp) cc_final: 0.6374 (mtp) REVERT: b 312 MET cc_start: 0.8043 (mmt) cc_final: 0.7725 (mmp) REVERT: b 332 MET cc_start: 0.7371 (mmp) cc_final: 0.6955 (mmm) REVERT: c 312 MET cc_start: 0.7560 (mmm) cc_final: 0.6941 (mmp) REVERT: c 428 LEU cc_start: 0.7253 (mp) cc_final: 0.6995 (mp) REVERT: A 191 PHE cc_start: 0.6770 (m-80) cc_final: 0.6439 (t80) REVERT: B 80 MET cc_start: 0.6063 (mmp) cc_final: 0.5841 (mmp) REVERT: B 191 PHE cc_start: 0.7074 (m-80) cc_final: 0.6814 (t80) REVERT: C 146 ASN cc_start: 0.7940 (m-40) cc_final: 0.7620 (m110) REVERT: C 253 TYR cc_start: 0.7862 (m-80) cc_final: 0.7495 (m-10) outliers start: 19 outliers final: 13 residues processed: 220 average time/residue: 0.0700 time to fit residues: 22.5858 Evaluate side-chains 193 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 431 VAL Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 95 optimal weight: 0.0980 chunk 60 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 305 HIS A 131 HIS A 149 GLN B 3 GLN B 131 HIS ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN C 131 HIS C 209 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.167941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.143669 restraints weight = 16196.693| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.34 r_work: 0.3773 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10659 Z= 0.203 Angle : 0.734 8.406 14493 Z= 0.374 Chirality : 0.045 0.217 1728 Planarity : 0.005 0.063 1746 Dihedral : 9.768 120.927 1314 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.08 % Allowed : 13.86 % Favored : 83.06 % 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: -0.13 (0.23), residues: 1194 helix: 1.21 (0.23), residues: 453 sheet: -0.61 (0.44), residues: 138 loop : -0.96 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 248 TYR 0.025 0.002 TYR C 253 PHE 0.018 0.002 PHE A 191 TRP 0.014 0.002 TRP B 210 HIS 0.009 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (10602) covalent geometry : angle 0.70661 / 0.37 (14340) SS BOND : bond 0.00873 / 0.60 ( 18) SS BOND : angle 3.01393 / 1.89 ( 36) hydrogen bonds : bond 0.04352 / 2.87 ( 481) hydrogen bonds : angle 5.34645 / 3.81 ( 1326) link_ALPHA1-3 : bond 0.00315 / 0.17 ( 3) link_ALPHA1-3 : angle 1.12232 / 0.61 ( 9) link_BETA1-3 : bond 0.01065 / 0.60 ( 3) link_BETA1-3 : angle 2.20919 / 1.12 ( 9) link_BETA1-4 : bond 0.00300 / 0.20 ( 9) link_BETA1-4 : angle 1.47348 / 0.85 ( 27) link_NAG-ASN : bond 0.00251 / 0.17 ( 24) link_NAG-ASN : angle 1.72624 / 1.24 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 359 MET cc_start: 0.7888 (mtt) cc_final: 0.7675 (mtm) REVERT: a 410 MET cc_start: 0.6822 (mtp) cc_final: 0.6560 (mtp) REVERT: b 312 MET cc_start: 0.8161 (mmt) cc_final: 0.7780 (mmt) REVERT: b 332 MET cc_start: 0.7817 (mmp) cc_final: 0.7305 (mmt) REVERT: b 390 ASN cc_start: 0.7949 (t0) cc_final: 0.7562 (t0) REVERT: A 16 GLU cc_start: 0.6231 (pm20) cc_final: 0.5861 (pm20) REVERT: B 207 ARG cc_start: 0.5295 (mmm160) cc_final: 0.4972 (mmm160) REVERT: C 191 PHE cc_start: 0.7111 (OUTLIER) cc_final: 0.6823 (t80) outliers start: 34 outliers final: 21 residues processed: 224 average time/residue: 0.0790 time to fit residues: 26.0886 Evaluate side-chains 204 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 263 THR Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 191 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 305 HIS c 305 HIS ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.164268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139851 restraints weight = 16312.912| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.35 r_work: 0.3727 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 10659 Z= 0.236 Angle : 0.772 12.244 14493 Z= 0.392 Chirality : 0.047 0.244 1728 Planarity : 0.005 0.066 1746 Dihedral : 9.845 121.058 1314 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.71 % Allowed : 15.76 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.30 (0.23), residues: 1194 helix: 1.12 (0.23), residues: 453 sheet: -0.94 (0.44), residues: 138 loop : -1.04 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 282 TYR 0.019 0.002 TYR a 278 PHE 0.054 0.002 PHE B 191 TRP 0.015 0.002 TRP B 210 HIS 0.009 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.24 (10602) covalent geometry : angle 0.74191 / 0.38 (14340) SS BOND : bond 0.00991 / 0.67 ( 18) SS BOND : angle 3.28386 / 1.98 ( 36) hydrogen bonds : bond 0.04612 / 3.07 ( 481) hydrogen bonds : angle 5.43265 / 3.86 ( 1326) link_ALPHA1-3 : bond 0.00163 / 0.09 ( 3) link_ALPHA1-3 : angle 1.23987 / 0.68 ( 9) link_BETA1-3 : bond 0.01005 / 0.57 ( 3) link_BETA1-3 : angle 2.21097 / 1.13 ( 9) link_BETA1-4 : bond 0.00244 / 0.16 ( 9) link_BETA1-4 : angle 1.44394 / 0.83 ( 27) link_NAG-ASN : bond 0.00315 / 0.21 ( 24) link_NAG-ASN : angle 1.79490 / 1.28 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 278 TYR cc_start: 0.7370 (t80) cc_final: 0.7158 (t80) REVERT: a 351 MET cc_start: 0.8609 (tpp) cc_final: 0.8397 (tpp) REVERT: a 410 MET cc_start: 0.6848 (mtp) cc_final: 0.6478 (mtp) REVERT: b 312 MET cc_start: 0.8261 (mmt) cc_final: 0.7874 (mmp) REVERT: b 332 MET cc_start: 0.7860 (mmp) cc_final: 0.7321 (mmt) REVERT: b 390 ASN cc_start: 0.8015 (t0) cc_final: 0.7545 (t0) REVERT: b 410 MET cc_start: 0.7014 (mtp) cc_final: 0.6717 (mtp) REVERT: B 66 TYR cc_start: 0.7487 (m-80) cc_final: 0.7278 (m-80) REVERT: B 104 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7220 (mm-30) REVERT: C 15 ILE cc_start: 0.8475 (tp) cc_final: 0.8243 (tp) REVERT: C 75 MET cc_start: 0.7591 (mtt) cc_final: 0.7390 (mtp) REVERT: C 191 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.6586 (t80) REVERT: C 207 ARG cc_start: 0.4875 (mmm160) cc_final: 0.4556 (mmm160) outliers start: 41 outliers final: 27 residues processed: 223 average time/residue: 0.0705 time to fit residues: 23.3869 Evaluate side-chains 205 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain c residue 428 LEU Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 223 GLN Chi-restraints excluded: chain C residue 252 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 91 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.167599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143570 restraints weight = 16341.092| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.33 r_work: 0.3773 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10659 Z= 0.150 Angle : 0.696 11.717 14493 Z= 0.352 Chirality : 0.043 0.210 1728 Planarity : 0.005 0.069 1746 Dihedral : 9.704 119.525 1314 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.72 % Allowed : 18.21 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.19 (0.24), residues: 1194 helix: 1.27 (0.23), residues: 471 sheet: -1.10 (0.43), residues: 138 loop : -1.03 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 282 TYR 0.013 0.002 TYR B 219 PHE 0.051 0.002 PHE A 191 TRP 0.012 0.001 TRP B 210 HIS 0.008 0.001 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (10602) covalent geometry : angle 0.66778 / 0.34 (14340) SS BOND : bond 0.00690 / 0.46 ( 18) SS BOND : angle 3.21112 / 1.95 ( 36) hydrogen bonds : bond 0.03847 / 2.59 ( 481) hydrogen bonds : angle 5.34871 / 3.78 ( 1326) link_ALPHA1-3 : bond 0.00389 / 0.22 ( 3) link_ALPHA1-3 : angle 1.20869 / 0.67 ( 9) link_BETA1-3 : bond 0.00955 / 0.54 ( 3) link_BETA1-3 : angle 1.90880 / 0.98 ( 9) link_BETA1-4 : bond 0.00275 / 0.19 ( 9) link_BETA1-4 : angle 1.23140 / 0.71 ( 27) link_NAG-ASN : bond 0.00346 / 0.22 ( 24) link_NAG-ASN : angle 1.51529 / 1.10 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: a 278 TYR cc_start: 0.7207 (t80) cc_final: 0.7002 (t80) REVERT: a 410 MET cc_start: 0.6868 (mtp) cc_final: 0.6595 (mtp) REVERT: b 312 MET cc_start: 0.8042 (mmt) cc_final: 0.7787 (mmp) REVERT: b 332 MET cc_start: 0.7799 (mmp) cc_final: 0.7415 (mmt) REVERT: b 390 ASN cc_start: 0.8029 (t0) cc_final: 0.7574 (t0) REVERT: b 410 MET cc_start: 0.6820 (mtp) cc_final: 0.6508 (mtp) REVERT: c 335 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7900 (mm-40) REVERT: A 16 GLU cc_start: 0.6113 (pm20) cc_final: 0.5709 (pm20) REVERT: A 134 MET cc_start: 0.8513 (mmm) cc_final: 0.8311 (tpp) REVERT: B 66 TYR cc_start: 0.7442 (m-80) cc_final: 0.7232 (m-80) REVERT: C 191 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6608 (t80) outliers start: 30 outliers final: 20 residues processed: 218 average time/residue: 0.0812 time to fit residues: 26.3017 Evaluate side-chains 206 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 430 LEU Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 23 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.163975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.139672 restraints weight = 16140.314| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.33 r_work: 0.3725 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10659 Z= 0.214 Angle : 0.763 11.187 14493 Z= 0.386 Chirality : 0.045 0.229 1728 Planarity : 0.005 0.067 1746 Dihedral : 9.870 121.126 1312 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.81 % Allowed : 19.11 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.41 (0.24), residues: 1194 helix: 1.14 (0.23), residues: 471 sheet: -1.49 (0.41), residues: 144 loop : -1.12 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 248 TYR 0.019 0.002 TYR B 219 PHE 0.045 0.002 PHE A 191 TRP 0.015 0.002 TRP B 210 HIS 0.009 0.001 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (10602) covalent geometry : angle 0.72649 / 0.37 (14340) SS BOND : bond 0.00836 / 0.56 ( 18) SS BOND : angle 3.65138 / 2.17 ( 36) hydrogen bonds : bond 0.04378 / 2.90 ( 481) hydrogen bonds : angle 5.50837 / 3.89 ( 1326) link_ALPHA1-3 : bond 0.00262 / 0.16 ( 3) link_ALPHA1-3 : angle 1.22936 / 0.68 ( 9) link_BETA1-3 : bond 0.00990 / 0.56 ( 3) link_BETA1-3 : angle 2.09311 / 1.07 ( 9) link_BETA1-4 : bond 0.00203 / 0.13 ( 9) link_BETA1-4 : angle 1.58873 / 0.88 ( 27) link_NAG-ASN : bond 0.00316 / 0.20 ( 24) link_NAG-ASN : angle 1.90664 / 1.43 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 278 TYR cc_start: 0.7835 (t80) cc_final: 0.7225 (t80) REVERT: a 332 MET cc_start: 0.7842 (mmt) cc_final: 0.7548 (mmp) REVERT: a 410 MET cc_start: 0.6828 (mtp) cc_final: 0.6440 (mtp) REVERT: b 312 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7671 (mmp) REVERT: b 332 MET cc_start: 0.7992 (mmp) cc_final: 0.7357 (mmt) REVERT: b 390 ASN cc_start: 0.7938 (t0) cc_final: 0.7415 (t0) REVERT: b 410 MET cc_start: 0.6874 (mtp) cc_final: 0.6623 (mtp) REVERT: A 16 GLU cc_start: 0.6322 (pm20) cc_final: 0.5922 (pm20) REVERT: C 191 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6600 (t80) outliers start: 31 outliers final: 23 residues processed: 208 average time/residue: 0.0770 time to fit residues: 23.9611 Evaluate side-chains 201 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 430 LEU Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 312 MET Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 428 LEU Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 223 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.166443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.142663 restraints weight = 16181.162| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.30 r_work: 0.3767 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10659 Z= 0.153 Angle : 0.705 12.065 14493 Z= 0.357 Chirality : 0.043 0.196 1728 Planarity : 0.005 0.069 1746 Dihedral : 9.781 119.446 1312 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.81 % Allowed : 20.11 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.38 (0.24), residues: 1194 helix: 1.24 (0.23), residues: 471 sheet: -1.65 (0.40), residues: 144 loop : -1.13 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 282 TYR 0.019 0.002 TYR A 219 PHE 0.041 0.002 PHE A 191 TRP 0.013 0.001 TRP B 210 HIS 0.009 0.001 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (10602) covalent geometry : angle 0.67333 / 0.35 (14340) SS BOND : bond 0.00573 / 0.38 ( 18) SS BOND : angle 3.42367 / 2.07 ( 36) hydrogen bonds : bond 0.03825 / 2.57 ( 481) hydrogen bonds : angle 5.43959 / 3.85 ( 1326) link_ALPHA1-3 : bond 0.00305 / 0.18 ( 3) link_ALPHA1-3 : angle 1.22902 / 0.68 ( 9) link_BETA1-3 : bond 0.00974 / 0.55 ( 3) link_BETA1-3 : angle 1.85838 / 0.95 ( 9) link_BETA1-4 : bond 0.00276 / 0.19 ( 9) link_BETA1-4 : angle 1.27889 / 0.73 ( 27) link_NAG-ASN : bond 0.00273 / 0.17 ( 24) link_NAG-ASN : angle 1.62304 / 1.23 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: a 278 TYR cc_start: 0.7746 (t80) cc_final: 0.7146 (t80) REVERT: a 332 MET cc_start: 0.7927 (mmt) cc_final: 0.7727 (mmp) REVERT: a 410 MET cc_start: 0.6859 (mtp) cc_final: 0.6576 (mtp) REVERT: b 312 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7752 (mmp) REVERT: b 332 MET cc_start: 0.7944 (mmp) cc_final: 0.7366 (mmt) REVERT: b 390 ASN cc_start: 0.8022 (t0) cc_final: 0.7521 (t0) REVERT: b 410 MET cc_start: 0.6824 (mtp) cc_final: 0.6493 (mtp) REVERT: A 16 GLU cc_start: 0.6297 (pm20) cc_final: 0.5888 (pm20) REVERT: B 16 GLU cc_start: 0.6267 (pm20) cc_final: 0.5993 (pm20) REVERT: B 66 TYR cc_start: 0.7604 (m-80) cc_final: 0.7358 (m-80) REVERT: B 207 ARG cc_start: 0.5838 (mmm160) cc_final: 0.5284 (mmm160) REVERT: C 15 ILE cc_start: 0.8325 (tp) cc_final: 0.8102 (tp) outliers start: 31 outliers final: 25 residues processed: 205 average time/residue: 0.0817 time to fit residues: 24.9023 Evaluate side-chains 201 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 430 LEU Chi-restraints excluded: chain b residue 312 MET Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 223 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 81 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.166735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.141942 restraints weight = 15921.872| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.37 r_work: 0.3749 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10659 Z= 0.182 Angle : 0.751 15.460 14493 Z= 0.377 Chirality : 0.044 0.205 1728 Planarity : 0.005 0.070 1746 Dihedral : 9.822 120.149 1312 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.99 % Allowed : 20.56 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.44 (0.24), residues: 1194 helix: 1.24 (0.23), residues: 471 sheet: -1.76 (0.39), residues: 144 loop : -1.18 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 282 TYR 0.018 0.002 TYR B 219 PHE 0.040 0.002 PHE A 191 TRP 0.014 0.001 TRP B 210 HIS 0.006 0.001 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (10602) covalent geometry : angle 0.71507 / 0.36 (14340) SS BOND : bond 0.00709 / 0.48 ( 18) SS BOND : angle 3.88577 / 2.40 ( 36) hydrogen bonds : bond 0.04076 / 2.72 ( 481) hydrogen bonds : angle 5.45191 / 3.87 ( 1326) link_ALPHA1-3 : bond 0.00178 / 0.11 ( 3) link_ALPHA1-3 : angle 1.19696 / 0.66 ( 9) link_BETA1-3 : bond 0.00927 / 0.52 ( 3) link_BETA1-3 : angle 1.91049 / 0.98 ( 9) link_BETA1-4 : bond 0.00199 / 0.14 ( 9) link_BETA1-4 : angle 1.24968 / 0.74 ( 27) link_NAG-ASN : bond 0.00261 / 0.16 ( 24) link_NAG-ASN : angle 1.74479 / 1.30 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: a 278 TYR cc_start: 0.7675 (t80) cc_final: 0.7158 (t80) REVERT: a 410 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6618 (mtp) REVERT: b 312 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7678 (mmp) REVERT: b 390 ASN cc_start: 0.8002 (t0) cc_final: 0.7474 (t0) REVERT: b 410 MET cc_start: 0.6801 (mtp) cc_final: 0.6468 (mtp) REVERT: c 332 MET cc_start: 0.7990 (mmt) cc_final: 0.7626 (mmt) REVERT: A 16 GLU cc_start: 0.6385 (pm20) cc_final: 0.5994 (pm20) REVERT: B 66 TYR cc_start: 0.7666 (m-80) cc_final: 0.7437 (m-80) REVERT: B 251 ASP cc_start: 0.8027 (m-30) cc_final: 0.7787 (m-30) outliers start: 33 outliers final: 28 residues processed: 199 average time/residue: 0.0772 time to fit residues: 23.0161 Evaluate side-chains 203 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 410 MET Chi-restraints excluded: chain a residue 430 LEU Chi-restraints excluded: chain b residue 312 MET Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 223 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.166514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.141819 restraints weight = 15833.062| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.36 r_work: 0.3752 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10659 Z= 0.172 Angle : 0.748 16.434 14493 Z= 0.375 Chirality : 0.044 0.208 1728 Planarity : 0.005 0.068 1746 Dihedral : 9.816 119.729 1312 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.81 % Allowed : 20.29 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.34 (0.24), residues: 1194 helix: 1.26 (0.23), residues: 474 sheet: -1.25 (0.45), residues: 114 loop : -1.25 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 282 TYR 0.016 0.002 TYR B 94 PHE 0.039 0.002 PHE A 191 TRP 0.014 0.001 TRP B 210 HIS 0.009 0.001 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (10602) covalent geometry : angle 0.71227 / 0.36 (14340) SS BOND : bond 0.00634 / 0.43 ( 18) SS BOND : angle 3.89131 / 2.38 ( 36) hydrogen bonds : bond 0.03964 / 2.66 ( 481) hydrogen bonds : angle 5.43459 / 3.86 ( 1326) link_ALPHA1-3 : bond 0.00114 / 0.07 ( 3) link_ALPHA1-3 : angle 1.16592 / 0.64 ( 9) link_BETA1-3 : bond 0.00976 / 0.55 ( 3) link_BETA1-3 : angle 1.87172 / 0.96 ( 9) link_BETA1-4 : bond 0.00219 / 0.15 ( 9) link_BETA1-4 : angle 1.27433 / 0.74 ( 27) link_NAG-ASN : bond 0.00253 / 0.16 ( 24) link_NAG-ASN : angle 1.69744 / 1.28 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: a 278 TYR cc_start: 0.7664 (t80) cc_final: 0.7206 (t80) REVERT: a 410 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6604 (mtp) REVERT: b 312 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7730 (mmp) REVERT: b 332 MET cc_start: 0.7888 (mmt) cc_final: 0.7525 (mmt) REVERT: b 390 ASN cc_start: 0.7891 (t0) cc_final: 0.7386 (t0) REVERT: b 410 MET cc_start: 0.6785 (mtp) cc_final: 0.6452 (mtp) REVERT: c 332 MET cc_start: 0.7966 (mmt) cc_final: 0.7565 (mmt) REVERT: A 16 GLU cc_start: 0.6398 (pm20) cc_final: 0.6013 (pm20) REVERT: B 66 TYR cc_start: 0.7685 (m-80) cc_final: 0.7465 (m-80) REVERT: B 251 ASP cc_start: 0.8052 (m-30) cc_final: 0.7813 (m-30) outliers start: 31 outliers final: 26 residues processed: 197 average time/residue: 0.0892 time to fit residues: 26.0414 Evaluate side-chains 199 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 410 MET Chi-restraints excluded: chain a residue 430 LEU Chi-restraints excluded: chain b residue 312 MET Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 223 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 10 optimal weight: 0.0670 chunk 23 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.170205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.145906 restraints weight = 15903.416| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.35 r_work: 0.3805 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10659 Z= 0.133 Angle : 0.699 10.638 14493 Z= 0.350 Chirality : 0.043 0.211 1728 Planarity : 0.005 0.067 1746 Dihedral : 9.721 118.351 1312 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.26 % Allowed : 21.47 % Favored : 76.27 % 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: -0.26 (0.24), residues: 1194 helix: 1.38 (0.24), residues: 474 sheet: -1.29 (0.45), residues: 114 loop : -1.24 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 282 TYR 0.011 0.001 TYR B 219 PHE 0.039 0.002 PHE A 191 TRP 0.013 0.001 TRP B 210 HIS 0.009 0.001 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (10602) covalent geometry : angle 0.66951 / 0.34 (14340) SS BOND : bond 0.00476 / 0.32 ( 18) SS BOND : angle 3.42339 / 2.08 ( 36) hydrogen bonds : bond 0.03543 / 2.40 ( 481) hydrogen bonds : angle 5.31543 / 3.78 ( 1326) link_ALPHA1-3 : bond 0.00226 / 0.13 ( 3) link_ALPHA1-3 : angle 1.12262 / 0.62 ( 9) link_BETA1-3 : bond 0.00975 / 0.55 ( 3) link_BETA1-3 : angle 1.69686 / 0.87 ( 9) link_BETA1-4 : bond 0.00283 / 0.19 ( 9) link_BETA1-4 : angle 1.20659 / 0.71 ( 27) link_NAG-ASN : bond 0.00254 / 0.16 ( 24) link_NAG-ASN : angle 1.49186 / 1.14 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2448.37 seconds wall clock time: 42 minutes 54.28 seconds (2574.28 seconds total)