Starting phenix.real_space_refine on Wed Mar 4 03:35:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7puy_13662/03_2026/7puy_13662.cif Found real_map, /net/cci-nas-00/data/ceres_data/7puy_13662/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7puy_13662/03_2026/7puy_13662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7puy_13662/03_2026/7puy_13662.map" model { file = "/net/cci-nas-00/data/ceres_data/7puy_13662/03_2026/7puy_13662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7puy_13662/03_2026/7puy_13662.cif" } 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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.59, per 1000 atoms: 0.25 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: 1.01 Conformation dependent library (CDL) restraints added in 495.7 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: 0.33 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: 1.42 Time building geometry restraints manager: 1.30 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: 6447 26.47 - 52.93: 315 52.93 - 79.40: 27 79.40 - 105.87: 51 105.87 - 132.34: 9 Dihedral angle restraints: 6849 sinusoidal: 3282 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 6846 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: 0.02 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.670 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 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 : 17.932 132.335 4491 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 covalent geometry : bond 0.00569 (10602) covalent geometry : angle 0.73808 (14340) SS BOND : bond 0.00244 ( 18) SS BOND : angle 1.48276 ( 36) hydrogen bonds : bond 0.13415 ( 481) hydrogen bonds : angle 6.39787 ( 1326) link_ALPHA1-3 : bond 0.00069 ( 3) link_ALPHA1-3 : angle 0.31177 ( 9) link_BETA1-3 : bond 0.00920 ( 3) link_BETA1-3 : angle 1.63830 ( 9) link_BETA1-4 : bond 0.00396 ( 9) link_BETA1-4 : angle 1.77812 ( 27) link_NAG-ASN : bond 0.00477 ( 24) link_NAG-ASN : angle 1.65661 ( 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 : 0.404 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: 0.1061 time to fit residues: 42.9710 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 : 0.386 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.177592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.153793 restraints weight = 15810.162| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.34 r_work: 0.3913 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10659 Z= 0.151 Angle : 0.744 8.135 14493 Z= 0.363 Chirality : 0.045 0.211 1728 Planarity : 0.004 0.052 1746 Dihedral : 13.506 102.063 2160 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.54 % Allowed : 11.59 % Favored : 86.87 % 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: -0.21 (0.22), residues: 1194 helix: 0.95 (0.23), residues: 474 sheet: -0.45 (0.45), residues: 135 loop : -0.95 (0.22), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 193 TYR 0.015 0.001 TYR C 253 PHE 0.016 0.002 PHE C 233 TRP 0.013 0.001 TRP B 210 HIS 0.008 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00344 (10602) covalent geometry : angle 0.72720 (14340) SS BOND : bond 0.00654 ( 18) SS BOND : angle 1.39655 ( 36) hydrogen bonds : bond 0.04448 ( 481) hydrogen bonds : angle 5.45962 ( 1326) link_ALPHA1-3 : bond 0.00525 ( 3) link_ALPHA1-3 : angle 1.59736 ( 9) link_BETA1-3 : bond 0.01033 ( 3) link_BETA1-3 : angle 2.95335 ( 9) link_BETA1-4 : bond 0.00389 ( 9) link_BETA1-4 : angle 1.27887 ( 27) link_NAG-ASN : bond 0.00302 ( 24) link_NAG-ASN : angle 1.74024 ( 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 227 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 410 MET cc_start: 0.6383 (mtp) cc_final: 0.6078 (mtp) REVERT: b 312 MET cc_start: 0.8037 (mmt) cc_final: 0.7806 (mmp) REVERT: b 323 ILE cc_start: 0.7669 (mm) cc_final: 0.7468 (mt) REVERT: c 312 MET cc_start: 0.7688 (mmm) cc_final: 0.6954 (mmp) REVERT: A 191 PHE cc_start: 0.6852 (m-80) cc_final: 0.6083 (t80) REVERT: B 191 PHE cc_start: 0.6775 (m-80) cc_final: 0.6206 (t80) REVERT: C 80 MET cc_start: 0.5465 (mmp) cc_final: 0.5165 (mmp) outliers start: 17 outliers final: 9 residues processed: 221 average time/residue: 0.0911 time to fit residues: 29.1812 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 : 0.333 ------------------------------------------------------------------------------- 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: 2.9990 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 43 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 305 HIS A 209 ASN ** A 230 HIS ** 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 = 0.4274 r_free = 0.4274 target = 0.174447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.150175 restraints weight = 15949.395| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.36 r_work: 0.3863 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10659 Z= 0.161 Angle : 0.693 7.315 14493 Z= 0.344 Chirality : 0.045 0.217 1728 Planarity : 0.005 0.061 1746 Dihedral : 9.169 58.940 2157 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.90 % Allowed : 13.32 % Favored : 84.78 % 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: 0.08 (0.23), residues: 1194 helix: 1.38 (0.24), residues: 453 sheet: -0.68 (0.44), residues: 144 loop : -0.78 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 282 TYR 0.020 0.002 TYR C 253 PHE 0.019 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 covalent geometry : bond 0.00373 (10602) covalent geometry : angle 0.67444 (14340) SS BOND : bond 0.00672 ( 18) SS BOND : angle 1.57726 ( 36) hydrogen bonds : bond 0.04078 ( 481) hydrogen bonds : angle 5.23936 ( 1326) link_ALPHA1-3 : bond 0.00331 ( 3) link_ALPHA1-3 : angle 2.10578 ( 9) link_BETA1-3 : bond 0.01211 ( 3) link_BETA1-3 : angle 1.93325 ( 9) link_BETA1-4 : bond 0.00236 ( 9) link_BETA1-4 : angle 1.47739 ( 27) link_NAG-ASN : bond 0.00264 ( 24) link_NAG-ASN : angle 1.76480 ( 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 224 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 312 MET cc_start: 0.8066 (mmt) cc_final: 0.7737 (mmp) REVERT: c 312 MET cc_start: 0.7589 (mmm) cc_final: 0.6958 (mmp) REVERT: c 428 LEU cc_start: 0.7126 (mp) cc_final: 0.6869 (mp) REVERT: B 191 PHE cc_start: 0.6908 (m-80) cc_final: 0.6640 (t80) outliers start: 21 outliers final: 15 residues processed: 217 average time/residue: 0.0888 time to fit residues: 28.4335 Evaluate side-chains 194 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 A residue 164 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR 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: 1.9990 chunk 51 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN B 3 GLN B 131 HIS B 209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.173018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.148903 restraints weight = 16024.684| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.33 r_work: 0.3844 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10659 Z= 0.155 Angle : 0.680 8.129 14493 Z= 0.341 Chirality : 0.044 0.255 1728 Planarity : 0.005 0.065 1746 Dihedral : 7.955 53.177 2157 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.45 % Allowed : 14.58 % Favored : 82.97 % 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: 0.12 (0.24), residues: 1194 helix: 1.45 (0.24), residues: 453 sheet: -0.59 (0.46), residues: 144 loop : -0.81 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 193 TYR 0.009 0.001 TYR B 94 PHE 0.046 0.002 PHE C 191 TRP 0.013 0.001 TRP B 210 HIS 0.009 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00358 (10602) covalent geometry : angle 0.65515 (14340) SS BOND : bond 0.00674 ( 18) SS BOND : angle 2.29998 ( 36) hydrogen bonds : bond 0.03933 ( 481) hydrogen bonds : angle 5.21953 ( 1326) link_ALPHA1-3 : bond 0.00135 ( 3) link_ALPHA1-3 : angle 1.67384 ( 9) link_BETA1-3 : bond 0.01057 ( 3) link_BETA1-3 : angle 2.18373 ( 9) link_BETA1-4 : bond 0.00228 ( 9) link_BETA1-4 : angle 1.44123 ( 27) link_NAG-ASN : bond 0.00247 ( 24) link_NAG-ASN : angle 1.79950 ( 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 219 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 410 MET cc_start: 0.6695 (mtp) cc_final: 0.6403 (mtp) REVERT: b 312 MET cc_start: 0.8061 (mmt) cc_final: 0.7683 (mmt) REVERT: b 390 ASN cc_start: 0.7938 (t0) cc_final: 0.7570 (t0) REVERT: c 428 LEU cc_start: 0.7311 (mp) cc_final: 0.7088 (mp) REVERT: A 16 GLU cc_start: 0.6168 (pm20) cc_final: 0.5796 (pm20) REVERT: C 191 PHE cc_start: 0.6798 (t80) cc_final: 0.6091 (t80) outliers start: 27 outliers final: 18 residues processed: 210 average time/residue: 0.0900 time to fit residues: 27.4810 Evaluate side-chains 197 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 128 LEU Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 128 LEU 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 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.171684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.147513 restraints weight = 15944.826| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.31 r_work: 0.3820 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10659 Z= 0.155 Angle : 0.684 10.496 14493 Z= 0.345 Chirality : 0.043 0.244 1728 Planarity : 0.005 0.068 1746 Dihedral : 7.279 52.809 2157 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.17 % Allowed : 14.67 % Favored : 82.16 % 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: 0.10 (0.24), residues: 1194 helix: 1.43 (0.23), residues: 471 sheet: -0.62 (0.46), residues: 138 loop : -0.88 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 193 TYR 0.020 0.002 TYR C 253 PHE 0.057 0.002 PHE A 191 TRP 0.013 0.001 TRP B 210 HIS 0.006 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00358 (10602) covalent geometry : angle 0.65668 (14340) SS BOND : bond 0.00827 ( 18) SS BOND : angle 2.47603 ( 36) hydrogen bonds : bond 0.03886 ( 481) hydrogen bonds : angle 5.15175 ( 1326) link_ALPHA1-3 : bond 0.00111 ( 3) link_ALPHA1-3 : angle 1.66731 ( 9) link_BETA1-3 : bond 0.01127 ( 3) link_BETA1-3 : angle 2.14811 ( 9) link_BETA1-4 : bond 0.00204 ( 9) link_BETA1-4 : angle 1.48297 ( 27) link_NAG-ASN : bond 0.00229 ( 24) link_NAG-ASN : angle 1.87470 ( 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 240 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 410 MET cc_start: 0.6771 (mtp) cc_final: 0.6463 (mtp) REVERT: b 312 MET cc_start: 0.7997 (mmt) cc_final: 0.7690 (mmp) REVERT: b 332 MET cc_start: 0.7403 (mmt) cc_final: 0.7168 (mmt) REVERT: b 390 ASN cc_start: 0.8040 (t0) cc_final: 0.7677 (t0) REVERT: A 16 GLU cc_start: 0.6213 (pm20) cc_final: 0.5939 (pm20) REVERT: B 104 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7142 (mm-30) REVERT: B 146 ASN cc_start: 0.8037 (m-40) cc_final: 0.7776 (m-40) REVERT: C 15 ILE cc_start: 0.8392 (tp) cc_final: 0.8143 (tp) REVERT: C 16 GLU cc_start: 0.6172 (pm20) cc_final: 0.5927 (pm20) REVERT: C 191 PHE cc_start: 0.6811 (t80) cc_final: 0.6003 (t80) outliers start: 35 outliers final: 24 residues processed: 227 average time/residue: 0.0920 time to fit residues: 30.0782 Evaluate side-chains 206 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 385 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 385 CYS Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 128 LEU 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 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 182 THR Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 223 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 91 optimal weight: 0.1980 chunk 110 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 90 optimal weight: 0.0980 chunk 63 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 335 GLN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.174014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.150122 restraints weight = 16043.677| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.32 r_work: 0.3863 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10659 Z= 0.129 Angle : 0.656 11.012 14493 Z= 0.330 Chirality : 0.042 0.238 1728 Planarity : 0.005 0.070 1746 Dihedral : 6.833 50.867 2157 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.54 % Allowed : 16.94 % Favored : 80.53 % 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: 0.07 (0.24), residues: 1194 helix: 1.43 (0.24), residues: 471 sheet: -0.73 (0.45), residues: 138 loop : -0.91 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 282 TYR 0.015 0.001 TYR a 278 PHE 0.044 0.002 PHE A 191 TRP 0.012 0.001 TRP B 210 HIS 0.005 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00291 (10602) covalent geometry : angle 0.62922 (14340) SS BOND : bond 0.00608 ( 18) SS BOND : angle 2.48564 ( 36) hydrogen bonds : bond 0.03479 ( 481) hydrogen bonds : angle 5.08410 ( 1326) link_ALPHA1-3 : bond 0.00028 ( 3) link_ALPHA1-3 : angle 1.61179 ( 9) link_BETA1-3 : bond 0.01095 ( 3) link_BETA1-3 : angle 1.99402 ( 9) link_BETA1-4 : bond 0.00282 ( 9) link_BETA1-4 : angle 1.38916 ( 27) link_NAG-ASN : bond 0.00321 ( 24) link_NAG-ASN : angle 1.78634 ( 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 233 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 410 MET cc_start: 0.6607 (OUTLIER) cc_final: 0.6336 (mtp) REVERT: b 312 MET cc_start: 0.7989 (mmt) cc_final: 0.7752 (mmp) REVERT: b 332 MET cc_start: 0.7432 (mmt) cc_final: 0.7189 (mmt) REVERT: b 390 ASN cc_start: 0.7979 (t0) cc_final: 0.7564 (t0) REVERT: A 16 GLU cc_start: 0.6268 (pm20) cc_final: 0.6010 (pm20) REVERT: A 104 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6984 (mm-30) REVERT: B 146 ASN cc_start: 0.8046 (m-40) cc_final: 0.7787 (m-40) REVERT: C 129 TYR cc_start: 0.8519 (p90) cc_final: 0.8291 (p90) outliers start: 28 outliers final: 19 residues processed: 221 average time/residue: 0.0870 time to fit residues: 28.0268 Evaluate side-chains 206 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 410 MET 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 385 CYS Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 128 LEU 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 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 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 23 optimal weight: 0.2980 chunk 82 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 31 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.174623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.150921 restraints weight = 15773.167| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.32 r_work: 0.3872 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10659 Z= 0.124 Angle : 0.650 10.446 14493 Z= 0.327 Chirality : 0.041 0.239 1728 Planarity : 0.005 0.071 1746 Dihedral : 6.486 47.479 2155 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.36 % Allowed : 18.12 % Favored : 79.53 % 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: 0.04 (0.24), residues: 1194 helix: 1.42 (0.24), residues: 474 sheet: -0.73 (0.45), residues: 138 loop : -0.95 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 282 TYR 0.012 0.001 TYR a 278 PHE 0.037 0.002 PHE A 191 TRP 0.012 0.001 TRP B 210 HIS 0.005 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00279 (10602) covalent geometry : angle 0.62039 (14340) SS BOND : bond 0.00510 ( 18) SS BOND : angle 2.68170 ( 36) hydrogen bonds : bond 0.03394 ( 481) hydrogen bonds : angle 5.06566 ( 1326) link_ALPHA1-3 : bond 0.00111 ( 3) link_ALPHA1-3 : angle 1.59419 ( 9) link_BETA1-3 : bond 0.01109 ( 3) link_BETA1-3 : angle 1.94620 ( 9) link_BETA1-4 : bond 0.00253 ( 9) link_BETA1-4 : angle 1.44737 ( 27) link_NAG-ASN : bond 0.00279 ( 24) link_NAG-ASN : angle 1.79057 ( 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 224 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 410 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6334 (mtp) REVERT: b 332 MET cc_start: 0.7505 (mmt) cc_final: 0.7290 (mmt) REVERT: b 390 ASN cc_start: 0.8070 (t0) cc_final: 0.7310 (m110) REVERT: c 335 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7596 (mm-40) REVERT: A 16 GLU cc_start: 0.6346 (pm20) cc_final: 0.6083 (pm20) REVERT: B 146 ASN cc_start: 0.8130 (m-40) cc_final: 0.7824 (m-40) REVERT: C 191 PHE cc_start: 0.6679 (t80) cc_final: 0.5842 (t80) outliers start: 26 outliers final: 18 residues processed: 213 average time/residue: 0.0866 time to fit residues: 27.2604 Evaluate side-chains 201 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 410 MET Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 128 LEU 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 128 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 108 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** 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 = 0.4246 r_free = 0.4246 target = 0.172260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.147722 restraints weight = 15853.329| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.37 r_work: 0.3828 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10659 Z= 0.152 Angle : 0.730 14.494 14493 Z= 0.367 Chirality : 0.043 0.296 1728 Planarity : 0.005 0.063 1746 Dihedral : 6.393 43.908 2155 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.90 % Allowed : 17.30 % Favored : 79.80 % 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: -0.10 (0.24), residues: 1194 helix: 1.35 (0.24), residues: 471 sheet: -1.10 (0.43), residues: 144 loop : -0.96 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 282 TYR 0.022 0.002 TYR b 278 PHE 0.035 0.002 PHE A 191 TRP 0.014 0.001 TRP B 210 HIS 0.007 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00351 (10602) covalent geometry : angle 0.68328 (14340) SS BOND : bond 0.00755 ( 18) SS BOND : angle 4.24287 ( 36) hydrogen bonds : bond 0.03642 ( 481) hydrogen bonds : angle 5.13573 ( 1326) link_ALPHA1-3 : bond 0.00155 ( 3) link_ALPHA1-3 : angle 1.66287 ( 9) link_BETA1-3 : bond 0.01067 ( 3) link_BETA1-3 : angle 2.00416 ( 9) link_BETA1-4 : bond 0.00163 ( 9) link_BETA1-4 : angle 1.51502 ( 27) link_NAG-ASN : bond 0.00214 ( 24) link_NAG-ASN : angle 1.89658 ( 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 223 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: b 312 MET cc_start: 0.7594 (mmt) cc_final: 0.7354 (mmt) REVERT: b 390 ASN cc_start: 0.8030 (t0) cc_final: 0.7320 (m110) REVERT: B 104 GLU cc_start: 0.7562 (mm-30) cc_final: 0.6970 (mm-30) REVERT: B 146 ASN cc_start: 0.8128 (m-40) cc_final: 0.7808 (m110) REVERT: C 191 PHE cc_start: 0.6619 (t80) cc_final: 0.5825 (t80) outliers start: 32 outliers final: 24 residues processed: 210 average time/residue: 0.0849 time to fit residues: 26.2613 Evaluate side-chains 209 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 279 CYS Chi-restraints excluded: chain a residue 341 VAL 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 392 SER Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 128 LEU 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 128 LEU Chi-restraints excluded: chain B residue 182 THR 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 223 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 81 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** 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 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 = 0.4227 r_free = 0.4227 target = 0.170178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.145963 restraints weight = 15716.458| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.29 r_work: 0.3813 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10659 Z= 0.169 Angle : 0.751 15.034 14493 Z= 0.377 Chirality : 0.044 0.233 1728 Planarity : 0.005 0.062 1746 Dihedral : 6.306 41.251 2155 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.08 % Allowed : 17.48 % Favored : 79.44 % 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: -0.23 (0.24), residues: 1194 helix: 1.23 (0.23), residues: 471 sheet: -1.03 (0.46), residues: 114 loop : -1.09 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 282 TYR 0.021 0.002 TYR a 278 PHE 0.033 0.002 PHE A 191 TRP 0.014 0.001 TRP B 210 HIS 0.007 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00395 (10602) covalent geometry : angle 0.70507 (14340) SS BOND : bond 0.00562 ( 18) SS BOND : angle 4.25418 ( 36) hydrogen bonds : bond 0.03872 ( 481) hydrogen bonds : angle 5.26337 ( 1326) link_ALPHA1-3 : bond 0.00182 ( 3) link_ALPHA1-3 : angle 1.62556 ( 9) link_BETA1-3 : bond 0.01075 ( 3) link_BETA1-3 : angle 2.00918 ( 9) link_BETA1-4 : bond 0.00189 ( 9) link_BETA1-4 : angle 1.52912 ( 27) link_NAG-ASN : bond 0.00193 ( 24) link_NAG-ASN : angle 1.97179 ( 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 227 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: b 390 ASN cc_start: 0.7928 (t0) cc_final: 0.7249 (m110) REVERT: c 335 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7672 (mm-40) REVERT: B 146 ASN cc_start: 0.8147 (m-40) cc_final: 0.7839 (m-40) REVERT: C 146 ASN cc_start: 0.7787 (m110) cc_final: 0.7565 (m-40) REVERT: C 191 PHE cc_start: 0.6664 (t80) cc_final: 0.5914 (t80) outliers start: 34 outliers final: 24 residues processed: 213 average time/residue: 0.0896 time to fit residues: 28.1719 Evaluate side-chains 203 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 279 CYS Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 430 LEU Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 430 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 128 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 182 THR 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 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 305 HIS ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN ** B 146 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.169397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.145232 restraints weight = 15635.989| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.31 r_work: 0.3803 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10659 Z= 0.172 Angle : 0.769 17.722 14493 Z= 0.386 Chirality : 0.044 0.244 1728 Planarity : 0.005 0.064 1746 Dihedral : 6.309 40.046 2155 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.26 % Allowed : 18.21 % Favored : 79.53 % 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: -0.29 (0.24), residues: 1194 helix: 1.07 (0.23), residues: 486 sheet: -1.10 (0.46), residues: 114 loop : -1.07 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 282 TYR 0.021 0.002 TYR C 94 PHE 0.032 0.002 PHE A 191 TRP 0.014 0.001 TRP B 210 HIS 0.008 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00403 (10602) covalent geometry : angle 0.72238 (14340) SS BOND : bond 0.00589 ( 18) SS BOND : angle 4.39493 ( 36) hydrogen bonds : bond 0.03856 ( 481) hydrogen bonds : angle 5.29940 ( 1326) link_ALPHA1-3 : bond 0.00143 ( 3) link_ALPHA1-3 : angle 1.59967 ( 9) link_BETA1-3 : bond 0.01047 ( 3) link_BETA1-3 : angle 2.01187 ( 9) link_BETA1-4 : bond 0.00217 ( 9) link_BETA1-4 : angle 1.53900 ( 27) link_NAG-ASN : bond 0.00196 ( 24) link_NAG-ASN : angle 1.92750 ( 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 211 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 390 ASN cc_start: 0.7878 (t0) cc_final: 0.7266 (m110) REVERT: B 104 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7247 (mm-30) REVERT: C 146 ASN cc_start: 0.7841 (m110) cc_final: 0.7597 (m-40) REVERT: C 191 PHE cc_start: 0.6717 (t80) cc_final: 0.6196 (t80) outliers start: 25 outliers final: 25 residues processed: 203 average time/residue: 0.0887 time to fit residues: 26.5048 Evaluate side-chains 203 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 279 CYS Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 430 LEU Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 430 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 128 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 182 THR 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 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 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 305 HIS ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** 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 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.171011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.147023 restraints weight = 15778.571| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.31 r_work: 0.3828 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10659 Z= 0.144 Angle : 0.736 11.995 14493 Z= 0.368 Chirality : 0.044 0.367 1728 Planarity : 0.004 0.065 1746 Dihedral : 6.174 40.260 2155 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.54 % Allowed : 18.21 % Favored : 79.26 % 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: -0.26 (0.24), residues: 1194 helix: 1.28 (0.24), residues: 468 sheet: -1.14 (0.46), residues: 114 loop : -1.15 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 282 TYR 0.015 0.002 TYR C 94 PHE 0.032 0.002 PHE A 191 TRP 0.014 0.001 TRP B 210 HIS 0.007 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00331 (10602) covalent geometry : angle 0.69416 (14340) SS BOND : bond 0.00422 ( 18) SS BOND : angle 4.06165 ( 36) hydrogen bonds : bond 0.03619 ( 481) hydrogen bonds : angle 5.26610 ( 1326) link_ALPHA1-3 : bond 0.00093 ( 3) link_ALPHA1-3 : angle 1.60417 ( 9) link_BETA1-3 : bond 0.01068 ( 3) link_BETA1-3 : angle 1.93375 ( 9) link_BETA1-4 : bond 0.00209 ( 9) link_BETA1-4 : angle 1.48817 ( 27) link_NAG-ASN : bond 0.00216 ( 24) link_NAG-ASN : angle 1.81012 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2617.98 seconds wall clock time: 45 minutes 43.93 seconds (2743.93 seconds total)