Starting phenix.real_space_refine on Mon Jul 28 16:59:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7puy_13662/07_2025/7puy_13662.cif Found real_map, /net/cci-nas-00/data/ceres_data/7puy_13662/07_2025/7puy_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_13662/07_2025/7puy_13662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7puy_13662/07_2025/7puy_13662.map" model { file = "/net/cci-nas-00/data/ceres_data/7puy_13662/07_2025/7puy_13662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7puy_13662/07_2025/7puy_13662.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.017 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.71, per 1000 atoms: 0.65 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: 2.81 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.14 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: 2.93 Time building geometry restraints manager: 3.26 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.420 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.440 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.002 TRP c 283 HIS 0.006 0.001 HIS C 93 PHE 0.018 0.001 PHE C 191 TYR 0.017 0.002 TYR C 253 ARG 0.007 0.001 ARG B 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 24) link_NAG-ASN : angle 1.65661 ( 72) link_BETA1-4 : bond 0.00396 ( 9) link_BETA1-4 : angle 1.77812 ( 27) link_ALPHA1-3 : bond 0.00069 ( 3) link_ALPHA1-3 : angle 0.31177 ( 9) hydrogen bonds : bond 0.13415 ( 481) hydrogen bonds : angle 6.39787 ( 1326) SS BOND : bond 0.00244 ( 18) SS BOND : angle 1.48276 ( 36) link_BETA1-3 : bond 0.00920 ( 3) link_BETA1-3 : angle 1.63830 ( 9) covalent geometry : bond 0.00569 (10602) covalent geometry : angle 0.73808 (14340) *********************** 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 : 1.171 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: 0.6338 (mtp) REVERT: b 323 ILE cc_start: 0.7560 (mm) cc_final: 0.7346 (mt) outliers start: 21 outliers final: 6 residues processed: 294 average time/residue: 0.2458 time to fit residues: 99.3060 Evaluate side-chains 192 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 186 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 127 ASN B 131 HIS ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4288 r_free = 0.4288 target = 0.175608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.153234 restraints weight = 15492.940| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.19 r_work: 0.3877 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 10659 Z= 0.186 Angle : 0.771 8.072 14493 Z= 0.378 Chirality : 0.047 0.201 1728 Planarity : 0.005 0.053 1746 Dihedral : 13.049 100.683 2160 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.72 % Allowed : 11.50 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1194 helix: 0.91 (0.23), residues: 471 sheet: -0.51 (0.45), residues: 135 loop : -0.93 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 210 HIS 0.007 0.001 HIS A 93 PHE 0.015 0.002 PHE A 191 TYR 0.019 0.002 TYR C 253 ARG 0.004 0.001 ARG C 256 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 24) link_NAG-ASN : angle 1.85772 ( 72) link_BETA1-4 : bond 0.00202 ( 9) link_BETA1-4 : angle 1.37230 ( 27) link_ALPHA1-3 : bond 0.00255 ( 3) link_ALPHA1-3 : angle 1.40300 ( 9) hydrogen bonds : bond 0.04657 ( 481) hydrogen bonds : angle 5.47296 ( 1326) SS BOND : bond 0.00706 ( 18) SS BOND : angle 1.57095 ( 36) link_BETA1-3 : bond 0.00715 ( 3) link_BETA1-3 : angle 3.18561 ( 9) covalent geometry : bond 0.00432 (10602) covalent geometry : angle 0.75242 (14340) *********************** 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 220 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 351 MET cc_start: 0.8308 (tpp) cc_final: 0.7985 (tpp) REVERT: c 312 MET cc_start: 0.7726 (mmm) cc_final: 0.7055 (mmp) REVERT: B 16 GLU cc_start: 0.6586 (pm20) cc_final: 0.6313 (pm20) REVERT: B 191 PHE cc_start: 0.6915 (m-80) cc_final: 0.6317 (t80) REVERT: C 80 MET cc_start: 0.5591 (mmp) cc_final: 0.5326 (mmp) REVERT: C 253 TYR cc_start: 0.7790 (m-80) cc_final: 0.7549 (m-10) REVERT: C 256 ARG cc_start: 0.8287 (mtp85) cc_final: 0.8075 (mtm180) outliers start: 19 outliers final: 12 residues processed: 216 average time/residue: 0.2822 time to fit residues: 88.0162 Evaluate side-chains 193 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 263 THR Chi-restraints excluded: chain b residue 263 THR 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 A residue 164 VAL 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 4 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 91 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 305 HIS A 92 HIS A 209 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.174283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.149748 restraints weight = 15976.310| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.39 r_work: 0.3855 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2526 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 : 0.686 7.416 14493 Z= 0.343 Chirality : 0.045 0.233 1728 Planarity : 0.004 0.059 1746 Dihedral : 9.163 59.289 2157 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.17 % Allowed : 13.41 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.23), residues: 1194 helix: 1.30 (0.24), residues: 453 sheet: -0.64 (0.45), residues: 144 loop : -0.78 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 210 HIS 0.008 0.001 HIS B 93 PHE 0.013 0.002 PHE A 191 TYR 0.019 0.002 TYR C 253 ARG 0.003 0.000 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 24) link_NAG-ASN : angle 1.76999 ( 72) link_BETA1-4 : bond 0.00252 ( 9) link_BETA1-4 : angle 1.43097 ( 27) link_ALPHA1-3 : bond 0.00310 ( 3) link_ALPHA1-3 : angle 2.09535 ( 9) hydrogen bonds : bond 0.04058 ( 481) hydrogen bonds : angle 5.22042 ( 1326) SS BOND : bond 0.00771 ( 18) SS BOND : angle 1.54479 ( 36) link_BETA1-3 : bond 0.00998 ( 3) link_BETA1-3 : angle 2.22651 ( 9) covalent geometry : bond 0.00356 (10602) covalent geometry : angle 0.66605 (14340) *********************** 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 227 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 410 MET cc_start: 0.6514 (mtp) cc_final: 0.6201 (mtp) REVERT: b 332 MET cc_start: 0.7386 (mmp) cc_final: 0.7017 (mmm) REVERT: c 428 LEU cc_start: 0.7091 (mp) cc_final: 0.6860 (mp) REVERT: B 80 MET cc_start: 0.6003 (mmp) cc_final: 0.5578 (mmp) REVERT: B 191 PHE cc_start: 0.6941 (m-80) cc_final: 0.6702 (t80) REVERT: C 134 MET cc_start: 0.8224 (tpp) cc_final: 0.7629 (tpt) outliers start: 24 outliers final: 18 residues processed: 220 average time/residue: 0.3053 time to fit residues: 96.6633 Evaluate side-chains 200 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 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 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 164 VAL Chi-restraints excluded: chain C residue 182 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 60 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS B 127 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN C 131 HIS C 209 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.168652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.144198 restraints weight = 16018.870| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.34 r_work: 0.3781 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10659 Z= 0.183 Angle : 0.703 6.969 14493 Z= 0.353 Chirality : 0.045 0.219 1728 Planarity : 0.005 0.064 1746 Dihedral : 7.883 52.111 2157 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.90 % Allowed : 13.77 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1194 helix: 1.23 (0.23), residues: 453 sheet: -0.63 (0.46), residues: 144 loop : -0.85 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 210 HIS 0.008 0.001 HIS B 230 PHE 0.017 0.002 PHE A 191 TYR 0.011 0.002 TYR B 94 ARG 0.002 0.000 ARG B 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 24) link_NAG-ASN : angle 1.95232 ( 72) link_BETA1-4 : bond 0.00204 ( 9) link_BETA1-4 : angle 1.59629 ( 27) link_ALPHA1-3 : bond 0.00151 ( 3) link_ALPHA1-3 : angle 1.70588 ( 9) hydrogen bonds : bond 0.04231 ( 481) hydrogen bonds : angle 5.25750 ( 1326) SS BOND : bond 0.00699 ( 18) SS BOND : angle 1.84108 ( 36) link_BETA1-3 : bond 0.01043 ( 3) link_BETA1-3 : angle 2.24641 ( 9) covalent geometry : bond 0.00430 (10602) covalent geometry : angle 0.67971 (14340) *********************** 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 237 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 410 MET cc_start: 0.6627 (mtp) cc_final: 0.6354 (mtp) REVERT: b 332 MET cc_start: 0.7760 (mmp) cc_final: 0.7299 (mmt) REVERT: b 390 ASN cc_start: 0.7961 (t0) cc_final: 0.7554 (t0) REVERT: A 16 GLU cc_start: 0.6226 (pm20) cc_final: 0.5827 (pm20) REVERT: A 164 VAL cc_start: 0.7618 (OUTLIER) cc_final: 0.7357 (p) REVERT: B 80 MET cc_start: 0.6157 (mmp) cc_final: 0.5864 (mmp) REVERT: B 146 ASN cc_start: 0.7991 (m-40) cc_final: 0.7696 (m-40) outliers start: 32 outliers final: 23 residues processed: 224 average time/residue: 0.2065 time to fit residues: 66.9942 Evaluate side-chains 208 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 ASN ** 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 = 0.4237 r_free = 0.4237 target = 0.171132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.147078 restraints weight = 15806.353| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.31 r_work: 0.3826 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3208 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= 0.140 Angle : 0.677 12.988 14493 Z= 0.342 Chirality : 0.043 0.332 1728 Planarity : 0.005 0.068 1746 Dihedral : 7.312 52.765 2157 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.17 % Allowed : 15.58 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1194 helix: 1.29 (0.24), residues: 456 sheet: -0.84 (0.45), residues: 144 loop : -0.90 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 210 HIS 0.007 0.001 HIS A 93 PHE 0.056 0.002 PHE B 191 TYR 0.019 0.002 TYR C 253 ARG 0.006 0.000 ARG B 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 24) link_NAG-ASN : angle 1.81150 ( 72) link_BETA1-4 : bond 0.00304 ( 9) link_BETA1-4 : angle 1.43104 ( 27) link_ALPHA1-3 : bond 0.00175 ( 3) link_ALPHA1-3 : angle 1.63337 ( 9) hydrogen bonds : bond 0.03706 ( 481) hydrogen bonds : angle 5.16959 ( 1326) SS BOND : bond 0.00600 ( 18) SS BOND : angle 2.61101 ( 36) link_BETA1-3 : bond 0.01086 ( 3) link_BETA1-3 : angle 2.06420 ( 9) covalent geometry : bond 0.00321 (10602) covalent geometry : angle 0.64879 (14340) *********************** 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 236 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 410 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6363 (mtp) REVERT: b 332 MET cc_start: 0.7671 (mmp) cc_final: 0.7314 (mmt) REVERT: b 390 ASN cc_start: 0.8028 (t0) cc_final: 0.7635 (t0) REVERT: A 16 GLU cc_start: 0.6201 (pm20) cc_final: 0.5779 (pm20) REVERT: B 80 MET cc_start: 0.6164 (mmp) cc_final: 0.5834 (mmp) REVERT: B 146 ASN cc_start: 0.8081 (m-40) cc_final: 0.7778 (m-40) outliers start: 35 outliers final: 22 residues processed: 224 average time/residue: 0.2547 time to fit residues: 81.8377 Evaluate side-chains 208 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 410 MET 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 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 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 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 164 VAL 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 40 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 112 optimal weight: 7.9990 chunk 59 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 94 optimal weight: 0.0040 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.4268 r_free = 0.4268 target = 0.174276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.151721 restraints weight = 15580.782| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.19 r_work: 0.3856 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10659 Z= 0.131 Angle : 0.690 13.696 14493 Z= 0.347 Chirality : 0.043 0.326 1728 Planarity : 0.005 0.071 1746 Dihedral : 6.947 50.337 2157 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.08 % Allowed : 16.12 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.24), residues: 1194 helix: 1.38 (0.23), residues: 477 sheet: -0.82 (0.45), residues: 132 loop : -1.00 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 210 HIS 0.006 0.001 HIS A 93 PHE 0.041 0.002 PHE B 191 TYR 0.016 0.002 TYR C 253 ARG 0.006 0.000 ARG B 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 24) link_NAG-ASN : angle 1.81045 ( 72) link_BETA1-4 : bond 0.00218 ( 9) link_BETA1-4 : angle 1.45901 ( 27) link_ALPHA1-3 : bond 0.00102 ( 3) link_ALPHA1-3 : angle 1.66120 ( 9) hydrogen bonds : bond 0.03531 ( 481) hydrogen bonds : angle 5.16428 ( 1326) SS BOND : bond 0.00560 ( 18) SS BOND : angle 3.40892 ( 36) link_BETA1-3 : bond 0.01105 ( 3) link_BETA1-3 : angle 2.02657 ( 9) covalent geometry : bond 0.00295 (10602) covalent geometry : angle 0.65398 (14340) *********************** 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 245 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 410 MET cc_start: 0.6682 (OUTLIER) cc_final: 0.6431 (mtp) REVERT: b 332 MET cc_start: 0.7664 (mmp) cc_final: 0.7342 (mmt) REVERT: b 390 ASN cc_start: 0.7943 (t0) cc_final: 0.7522 (t0) REVERT: A 104 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6927 (mm-30) REVERT: B 16 GLU cc_start: 0.6271 (pm20) cc_final: 0.6014 (pm20) REVERT: B 80 MET cc_start: 0.6106 (mmp) cc_final: 0.5567 (mmp) REVERT: B 146 ASN cc_start: 0.8062 (m-40) cc_final: 0.7769 (m-40) REVERT: C 80 MET cc_start: 0.5178 (mmp) cc_final: 0.4795 (mmt) outliers start: 34 outliers final: 22 residues processed: 234 average time/residue: 0.2315 time to fit residues: 77.3830 Evaluate side-chains 209 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 410 MET Chi-restraints excluded: chain a residue 430 LEU Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 385 CYS 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 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 223 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 78 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 ASN ** 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 = 0.4240 r_free = 0.4240 target = 0.171729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.147372 restraints weight = 16033.803| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.34 r_work: 0.3823 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10659 Z= 0.150 Angle : 0.709 12.730 14493 Z= 0.358 Chirality : 0.043 0.264 1728 Planarity : 0.005 0.070 1746 Dihedral : 6.695 46.366 2157 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.99 % Allowed : 17.66 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1194 helix: 1.39 (0.23), residues: 477 sheet: -0.92 (0.45), residues: 132 loop : -1.03 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 210 HIS 0.006 0.001 HIS C 230 PHE 0.038 0.002 PHE B 191 TYR 0.024 0.002 TYR C 94 ARG 0.006 0.001 ARG B 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 24) link_NAG-ASN : angle 2.00004 ( 72) link_BETA1-4 : bond 0.00273 ( 9) link_BETA1-4 : angle 1.55099 ( 27) link_ALPHA1-3 : bond 0.00099 ( 3) link_ALPHA1-3 : angle 1.65151 ( 9) hydrogen bonds : bond 0.03676 ( 481) hydrogen bonds : angle 5.23951 ( 1326) SS BOND : bond 0.00614 ( 18) SS BOND : angle 3.59676 ( 36) link_BETA1-3 : bond 0.01072 ( 3) link_BETA1-3 : angle 2.01404 ( 9) covalent geometry : bond 0.00348 (10602) covalent geometry : angle 0.66833 (14340) *********************** 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 230 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 2.551 Fit side-chains revert: symmetry clash REVERT: a 410 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.6429 (mtp) REVERT: b 332 MET cc_start: 0.7644 (mmp) cc_final: 0.7288 (mmt) REVERT: b 390 ASN cc_start: 0.8001 (t0) cc_final: 0.7559 (t0) REVERT: A 16 GLU cc_start: 0.6177 (pm20) cc_final: 0.5802 (pm20) REVERT: B 80 MET cc_start: 0.5802 (mmp) cc_final: 0.5508 (mmp) REVERT: B 146 ASN cc_start: 0.8104 (m-40) cc_final: 0.7798 (m-40) REVERT: C 80 MET cc_start: 0.5235 (mmp) cc_final: 0.4834 (mmt) outliers start: 33 outliers final: 23 residues processed: 214 average time/residue: 0.2303 time to fit residues: 74.6233 Evaluate side-chains 204 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 410 MET Chi-restraints excluded: chain a residue 430 LEU Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 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 223 GLN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 223 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 13 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 116 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.172069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.147436 restraints weight = 15850.578| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.38 r_work: 0.3829 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3670 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= 0.141 Angle : 0.686 11.453 14493 Z= 0.347 Chirality : 0.043 0.261 1728 Planarity : 0.005 0.065 1746 Dihedral : 6.477 44.226 2157 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.90 % Allowed : 17.66 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1194 helix: 1.36 (0.23), residues: 477 sheet: -1.05 (0.44), residues: 132 loop : -1.06 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 210 HIS 0.007 0.001 HIS A 230 PHE 0.035 0.002 PHE B 191 TYR 0.015 0.001 TYR C 94 ARG 0.006 0.000 ARG B 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 24) link_NAG-ASN : angle 1.92849 ( 72) link_BETA1-4 : bond 0.00230 ( 9) link_BETA1-4 : angle 1.40942 ( 27) link_ALPHA1-3 : bond 0.00032 ( 3) link_ALPHA1-3 : angle 1.60609 ( 9) hydrogen bonds : bond 0.03557 ( 481) hydrogen bonds : angle 5.30000 ( 1326) SS BOND : bond 0.00551 ( 18) SS BOND : angle 3.34348 ( 36) link_BETA1-3 : bond 0.01071 ( 3) link_BETA1-3 : angle 1.95546 ( 9) covalent geometry : bond 0.00327 (10602) covalent geometry : angle 0.64861 (14340) *********************** 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 : 1.084 Fit side-chains revert: symmetry clash REVERT: a 332 MET cc_start: 0.7688 (mmt) cc_final: 0.7342 (mmp) REVERT: a 410 MET cc_start: 0.6738 (OUTLIER) cc_final: 0.6433 (mtp) REVERT: b 332 MET cc_start: 0.7661 (mmp) cc_final: 0.7315 (mmt) REVERT: b 390 ASN cc_start: 0.7940 (t0) cc_final: 0.7303 (m110) REVERT: A 16 GLU cc_start: 0.6077 (pm20) cc_final: 0.5651 (pm20) REVERT: B 16 GLU cc_start: 0.6164 (pm20) cc_final: 0.5955 (pm20) REVERT: B 80 MET cc_start: 0.5826 (mmp) cc_final: 0.5565 (mmp) REVERT: B 146 ASN cc_start: 0.8100 (m-40) cc_final: 0.7809 (m-40) REVERT: B 164 VAL cc_start: 0.8056 (t) cc_final: 0.7854 (t) REVERT: C 16 GLU cc_start: 0.6139 (pm20) cc_final: 0.5902 (pm20) outliers start: 32 outliers final: 24 residues processed: 208 average time/residue: 0.2239 time to fit residues: 67.2668 Evaluate side-chains 207 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 410 MET 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 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 164 VAL Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 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 128 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 223 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 305 HIS ** 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** C 146 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.171070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.146629 restraints weight = 16017.805| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.33 r_work: 0.3815 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3762 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= 0.152 Angle : 0.737 17.287 14493 Z= 0.370 Chirality : 0.043 0.228 1728 Planarity : 0.005 0.063 1746 Dihedral : 6.271 42.061 2157 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.81 % Allowed : 17.93 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1194 helix: 1.36 (0.23), residues: 477 sheet: -1.25 (0.43), residues: 132 loop : -1.08 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 210 HIS 0.007 0.001 HIS A 230 PHE 0.032 0.002 PHE B 191 TYR 0.015 0.002 TYR C 94 ARG 0.005 0.000 ARG B 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 24) link_NAG-ASN : angle 1.97149 ( 72) link_BETA1-4 : bond 0.00172 ( 9) link_BETA1-4 : angle 1.53569 ( 27) link_ALPHA1-3 : bond 0.00055 ( 3) link_ALPHA1-3 : angle 1.62427 ( 9) hydrogen bonds : bond 0.03694 ( 481) hydrogen bonds : angle 5.26600 ( 1326) SS BOND : bond 0.00740 ( 18) SS BOND : angle 4.04893 ( 36) link_BETA1-3 : bond 0.01059 ( 3) link_BETA1-3 : angle 1.96810 ( 9) covalent geometry : bond 0.00352 (10602) covalent geometry : angle 0.69299 (14340) *********************** 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 222 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 332 MET cc_start: 0.7702 (mmt) cc_final: 0.7391 (mmp) REVERT: a 410 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6553 (mtp) REVERT: b 332 MET cc_start: 0.7777 (mmp) cc_final: 0.7399 (mmt) REVERT: b 390 ASN cc_start: 0.7917 (t0) cc_final: 0.7280 (m110) REVERT: A 16 GLU cc_start: 0.6056 (pm20) cc_final: 0.5631 (pm20) REVERT: B 16 GLU cc_start: 0.6369 (pm20) cc_final: 0.6144 (pm20) REVERT: B 80 MET cc_start: 0.5831 (mmp) cc_final: 0.5580 (mmp) REVERT: B 146 ASN cc_start: 0.8135 (m-40) cc_final: 0.7835 (m-40) outliers start: 31 outliers final: 24 residues processed: 212 average time/residue: 0.2041 time to fit residues: 63.2289 Evaluate side-chains 206 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 410 MET Chi-restraints excluded: chain a residue 430 LEU Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 385 CYS 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 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 128 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 223 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 52 optimal weight: 0.0670 chunk 99 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 7 optimal weight: 0.0980 chunk 102 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4239 r_free = 0.4239 target = 0.171363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.147316 restraints weight = 15677.155| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.29 r_work: 0.3841 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10659 Z= 0.133 Angle : 0.729 16.777 14493 Z= 0.367 Chirality : 0.044 0.372 1728 Planarity : 0.004 0.065 1746 Dihedral : 6.175 41.707 2157 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.54 % Allowed : 17.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.24), residues: 1194 helix: 1.39 (0.24), residues: 477 sheet: -1.32 (0.43), residues: 132 loop : -1.11 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 210 HIS 0.007 0.001 HIS A 230 PHE 0.031 0.002 PHE B 191 TYR 0.016 0.002 TYR C 94 ARG 0.005 0.000 ARG B 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 24) link_NAG-ASN : angle 1.86744 ( 72) link_BETA1-4 : bond 0.00236 ( 9) link_BETA1-4 : angle 1.40362 ( 27) link_ALPHA1-3 : bond 0.00090 ( 3) link_ALPHA1-3 : angle 1.58266 ( 9) hydrogen bonds : bond 0.03476 ( 481) hydrogen bonds : angle 5.22674 ( 1326) SS BOND : bond 0.00537 ( 18) SS BOND : angle 4.17947 ( 36) link_BETA1-3 : bond 0.01077 ( 3) link_BETA1-3 : angle 1.89100 ( 9) covalent geometry : bond 0.00300 (10602) covalent geometry : angle 0.68452 (14340) ********************** 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 220 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 332 MET cc_start: 0.7680 (mmt) cc_final: 0.7380 (mmp) REVERT: b 332 MET cc_start: 0.7727 (mmp) cc_final: 0.7469 (mmt) REVERT: b 390 ASN cc_start: 0.7910 (t0) cc_final: 0.7302 (m110) REVERT: A 16 GLU cc_start: 0.6025 (pm20) cc_final: 0.5581 (pm20) REVERT: B 16 GLU cc_start: 0.6349 (pm20) cc_final: 0.6118 (pm20) REVERT: B 80 MET cc_start: 0.5763 (mmp) cc_final: 0.5514 (mmp) REVERT: B 146 ASN cc_start: 0.8143 (m-40) cc_final: 0.7866 (m-40) REVERT: B 207 ARG cc_start: 0.5948 (mmm160) cc_final: 0.4759 (mmm160) REVERT: C 15 ILE cc_start: 0.8344 (tp) cc_final: 0.8143 (tp) REVERT: C 129 TYR cc_start: 0.8677 (p90) cc_final: 0.8467 (p90) outliers start: 28 outliers final: 25 residues processed: 208 average time/residue: 0.2438 time to fit residues: 74.5019 Evaluate side-chains 209 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 430 LEU Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 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 128 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 95 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4241 r_free = 0.4241 target = 0.171349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.146788 restraints weight = 15649.596| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.34 r_work: 0.3826 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10659 Z= 0.144 Angle : 0.732 18.496 14493 Z= 0.368 Chirality : 0.044 0.390 1728 Planarity : 0.004 0.065 1746 Dihedral : 6.087 39.960 2157 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.26 % Allowed : 18.75 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1194 helix: 1.38 (0.23), residues: 477 sheet: -1.37 (0.42), residues: 132 loop : -1.14 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 210 HIS 0.010 0.001 HIS A 93 PHE 0.030 0.002 PHE B 191 TYR 0.013 0.002 TYR C 94 ARG 0.005 0.000 ARG B 193 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 24) link_NAG-ASN : angle 1.87020 ( 72) link_BETA1-4 : bond 0.00206 ( 9) link_BETA1-4 : angle 1.46071 ( 27) link_ALPHA1-3 : bond 0.00079 ( 3) link_ALPHA1-3 : angle 1.59792 ( 9) hydrogen bonds : bond 0.03560 ( 481) hydrogen bonds : angle 5.24005 ( 1326) SS BOND : bond 0.00556 ( 18) SS BOND : angle 4.16551 ( 36) link_BETA1-3 : bond 0.01060 ( 3) link_BETA1-3 : angle 1.94166 ( 9) covalent geometry : bond 0.00335 (10602) covalent geometry : angle 0.68741 (14340) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7165.84 seconds wall clock time: 133 minutes 25.09 seconds (8005.09 seconds total)