Starting phenix.real_space_refine on Fri Feb 14 19:03:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7puy_13662/02_2025/7puy_13662.cif Found real_map, /net/cci-nas-00/data/ceres_data/7puy_13662/02_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_13662/02_2025/7puy_13662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7puy_13662/02_2025/7puy_13662.map" model { file = "/net/cci-nas-00/data/ceres_data/7puy_13662/02_2025/7puy_13662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7puy_13662/02_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-5592/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: 6.29, per 1000 atoms: 0.61 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: 2.75 Conformation dependent library (CDL) restraints added in 1.0 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: 1.06 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: 3.31 Time building geometry restraints manager: 3.10 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.940 Find NCS groups from input model: 0.490 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: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.060 ------------------------------------------------------------------------------- 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 10602 Z= 0.388 Angle : 0.738 6.952 14340 Z= 0.358 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 *********************** 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 : 1.251 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: 0.2468 time to fit residues: 99.1187 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 : 1.065 ------------------------------------------------------------------------------- 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: 0.1980 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: 0.7980 chunk 106 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.176100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.153693 restraints weight = 15471.832| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.18 r_work: 0.3882 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10602 Z= 0.257 Angle : 0.739 7.854 14340 Z= 0.368 Chirality : 0.047 0.208 1728 Planarity : 0.005 0.056 1746 Dihedral : 12.723 98.611 2160 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.54 % Allowed : 11.59 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.23 (0.22), residues: 1194 helix: 0.93 (0.23), residues: 471 sheet: -0.48 (0.45), residues: 135 loop : -0.94 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 210 HIS 0.007 0.001 HIS A 93 PHE 0.014 0.002 PHE C 233 TYR 0.020 0.002 TYR C 253 ARG 0.004 0.001 ARG C 256 *********************** 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 221 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 351 MET cc_start: 0.8323 (tpp) cc_final: 0.7996 (tpp) REVERT: a 410 MET cc_start: 0.6633 (mtp) cc_final: 0.6339 (mtp) REVERT: c 312 MET cc_start: 0.7703 (mmm) cc_final: 0.7042 (mmp) REVERT: B 16 GLU cc_start: 0.6609 (pm20) cc_final: 0.6393 (pm20) REVERT: B 191 PHE cc_start: 0.6951 (m-80) cc_final: 0.6380 (t80) REVERT: C 80 MET cc_start: 0.5619 (mmp) cc_final: 0.5362 (mmp) REVERT: C 253 TYR cc_start: 0.7804 (m-80) cc_final: 0.7574 (m-10) REVERT: C 256 ARG cc_start: 0.8292 (mtp85) cc_final: 0.8079 (mtm180) outliers start: 17 outliers final: 10 residues processed: 217 average time/residue: 0.2103 time to fit residues: 65.4592 Evaluate side-chains 192 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a 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 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: 2.9990 chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 54 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 305 HIS A 131 HIS A 209 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS C 146 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.168817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.143923 restraints weight = 16252.031| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.41 r_work: 0.3775 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10602 Z= 0.320 Angle : 0.720 7.581 14340 Z= 0.365 Chirality : 0.047 0.223 1728 Planarity : 0.005 0.060 1746 Dihedral : 9.387 60.469 2157 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.08 % Allowed : 12.32 % Favored : 84.60 % 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: -0.10 (0.23), residues: 1194 helix: 1.12 (0.23), residues: 453 sheet: -0.61 (0.45), residues: 144 loop : -0.83 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 210 HIS 0.010 0.002 HIS B 93 PHE 0.021 0.002 PHE A 191 TYR 0.024 0.002 TYR C 253 ARG 0.003 0.000 ARG C 256 *********************** 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 232 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 410 MET cc_start: 0.6626 (mtp) cc_final: 0.6313 (mtp) REVERT: b 390 ASN cc_start: 0.7747 (t0) cc_final: 0.7408 (t0) REVERT: c 428 LEU cc_start: 0.7056 (mp) cc_final: 0.6743 (mp) REVERT: B 80 MET cc_start: 0.5952 (mmp) cc_final: 0.5683 (mmp) REVERT: C 153 MET cc_start: 0.6993 (ttt) cc_final: 0.6731 (mtp) outliers start: 34 outliers final: 21 residues processed: 223 average time/residue: 0.2071 time to fit residues: 67.4494 Evaluate side-chains 199 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 b residue 431 VAL Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 5 VAL 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 110 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 110 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 190 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 60 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 305 HIS ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN B 209 ASN ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN C 209 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.165689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.141249 restraints weight = 16050.272| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.31 r_work: 0.3743 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10602 Z= 0.325 Angle : 0.721 8.065 14340 Z= 0.369 Chirality : 0.046 0.230 1728 Planarity : 0.005 0.064 1746 Dihedral : 8.341 51.427 2157 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.08 % Allowed : 14.86 % Favored : 82.07 % 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: -0.20 (0.23), residues: 1194 helix: 1.09 (0.23), residues: 453 sheet: -0.55 (0.45), residues: 138 loop : -0.97 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 210 HIS 0.007 0.001 HIS B 230 PHE 0.056 0.002 PHE B 191 TYR 0.011 0.002 TYR b 393 ARG 0.002 0.000 ARG c 325 *********************** 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 233 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 410 MET cc_start: 0.6898 (mtp) cc_final: 0.6599 (mtp) REVERT: b 390 ASN cc_start: 0.7949 (t0) cc_final: 0.7492 (t0) REVERT: b 410 MET cc_start: 0.7003 (mtp) cc_final: 0.6737 (mtp) REVERT: A 16 GLU cc_start: 0.6208 (pm20) cc_final: 0.5797 (pm20) REVERT: A 100 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7904 (mm-30) REVERT: B 66 TYR cc_start: 0.7499 (m-80) cc_final: 0.7279 (m-80) REVERT: B 80 MET cc_start: 0.6015 (mmp) cc_final: 0.5529 (mmp) REVERT: B 146 ASN cc_start: 0.8131 (m110) cc_final: 0.7839 (m-40) REVERT: C 80 MET cc_start: 0.5414 (mmp) cc_final: 0.5035 (mmp) outliers start: 34 outliers final: 23 residues processed: 221 average time/residue: 0.2119 time to fit residues: 67.4150 Evaluate side-chains 200 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 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 128 LEU Chi-restraints excluded: chain C residue 182 THR 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: 0.9990 chunk 8 optimal weight: 0.0770 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 335 GLN B 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.170153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.145835 restraints weight = 15847.091| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.33 r_work: 0.3806 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10602 Z= 0.206 Angle : 0.649 9.861 14340 Z= 0.335 Chirality : 0.043 0.288 1728 Planarity : 0.005 0.069 1746 Dihedral : 7.499 52.904 2157 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.81 % Allowed : 16.85 % Favored : 80.34 % 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: -0.09 (0.24), residues: 1194 helix: 1.33 (0.24), residues: 453 sheet: -0.66 (0.46), residues: 132 loop : -0.99 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 210 HIS 0.005 0.001 HIS A 230 PHE 0.030 0.002 PHE B 191 TYR 0.026 0.002 TYR C 253 ARG 0.003 0.000 ARG C 193 *********************** 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 238 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 410 MET cc_start: 0.6826 (mtp) cc_final: 0.6550 (mtp) REVERT: b 390 ASN cc_start: 0.8002 (t0) cc_final: 0.7600 (t0) REVERT: b 410 MET cc_start: 0.6693 (mtp) cc_final: 0.6434 (mtp) REVERT: A 16 GLU cc_start: 0.6338 (pm20) cc_final: 0.5953 (pm20) REVERT: C 15 ILE cc_start: 0.8440 (tp) cc_final: 0.8205 (tp) REVERT: C 207 ARG cc_start: 0.5050 (mmm160) cc_final: 0.4793 (mmm160) outliers start: 31 outliers final: 19 residues processed: 227 average time/residue: 0.2077 time to fit residues: 68.4753 Evaluate side-chains 206 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 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 A residue 4 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 128 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 305 HIS ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.170919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.146099 restraints weight = 15908.940| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.40 r_work: 0.3808 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10602 Z= 0.212 Angle : 0.662 13.866 14340 Z= 0.341 Chirality : 0.044 0.326 1728 Planarity : 0.005 0.071 1746 Dihedral : 7.200 52.977 2157 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.08 % Allowed : 17.66 % Favored : 79.26 % 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: 1.23 (0.23), residues: 486 sheet: -0.86 (0.45), residues: 132 loop : -0.97 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 210 HIS 0.007 0.001 HIS B 93 PHE 0.034 0.002 PHE B 191 TYR 0.024 0.002 TYR C 253 ARG 0.005 0.000 ARG B 193 *********************** 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 236 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 410 MET cc_start: 0.6789 (mtp) cc_final: 0.6519 (mtp) REVERT: b 390 ASN cc_start: 0.7997 (t0) cc_final: 0.7575 (t0) REVERT: A 16 GLU cc_start: 0.6341 (pm20) cc_final: 0.6113 (pm20) REVERT: B 16 GLU cc_start: 0.6224 (pm20) cc_final: 0.5995 (pm20) REVERT: B 146 ASN cc_start: 0.8065 (m110) cc_final: 0.7856 (m110) REVERT: C 191 PHE cc_start: 0.6741 (t80) cc_final: 0.5830 (t80) REVERT: C 207 ARG cc_start: 0.5050 (mmm160) cc_final: 0.4841 (mmm160) outliers start: 34 outliers final: 22 residues processed: 223 average time/residue: 0.2172 time to fit residues: 70.6030 Evaluate side-chains 205 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 430 LEU Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain A residue 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 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 223 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 78 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 335 GLN ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.162373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.137596 restraints weight = 16526.813| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.34 r_work: 0.3691 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 10602 Z= 0.391 Angle : 0.784 12.594 14340 Z= 0.405 Chirality : 0.048 0.278 1728 Planarity : 0.005 0.069 1746 Dihedral : 7.452 59.069 2157 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.08 % Allowed : 19.11 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.48 (0.23), residues: 1194 helix: 0.91 (0.22), residues: 471 sheet: -1.03 (0.43), residues: 138 loop : -1.14 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 210 HIS 0.009 0.002 HIS B 230 PHE 0.032 0.002 PHE B 191 TYR 0.021 0.002 TYR a 278 ARG 0.006 0.001 ARG B 193 *********************** 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 225 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: a 410 MET cc_start: 0.7030 (mtp) cc_final: 0.6634 (mtp) REVERT: b 390 ASN cc_start: 0.8025 (t0) cc_final: 0.7516 (t0) REVERT: A 16 GLU cc_start: 0.6397 (pm20) cc_final: 0.6096 (pm20) REVERT: C 146 ASN cc_start: 0.8013 (m110) cc_final: 0.7765 (m-40) REVERT: C 191 PHE cc_start: 0.6958 (t80) cc_final: 0.6385 (t80) REVERT: C 253 TYR cc_start: 0.8125 (m-10) cc_final: 0.7850 (m-10) outliers start: 34 outliers final: 26 residues processed: 214 average time/residue: 0.2034 time to fit residues: 63.2518 Evaluate side-chains 206 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 430 LEU Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain 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 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 182 THR Chi-restraints excluded: chain C residue 183 VAL 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: 6.9990 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 335 GLN ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.4166 r_free = 0.4166 target = 0.165322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.140487 restraints weight = 16062.090| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.34 r_work: 0.3726 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10602 Z= 0.290 Angle : 0.718 12.548 14340 Z= 0.370 Chirality : 0.044 0.234 1728 Planarity : 0.005 0.068 1746 Dihedral : 7.161 45.370 2157 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.81 % Allowed : 19.11 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -0.47 (0.24), residues: 1194 helix: 0.89 (0.22), residues: 486 sheet: -1.19 (0.44), residues: 132 loop : -1.12 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 210 HIS 0.007 0.001 HIS B 230 PHE 0.031 0.002 PHE B 191 TYR 0.027 0.002 TYR A 219 ARG 0.005 0.001 ARG B 193 *********************** 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 224 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: a 410 MET cc_start: 0.6930 (mtp) cc_final: 0.6641 (mtp) REVERT: b 390 ASN cc_start: 0.7908 (t0) cc_final: 0.7348 (t0) REVERT: C 191 PHE cc_start: 0.6798 (t80) cc_final: 0.6279 (t80) REVERT: C 253 TYR cc_start: 0.7936 (m-10) cc_final: 0.7552 (m-10) outliers start: 31 outliers final: 24 residues processed: 212 average time/residue: 0.2061 time to fit residues: 63.9610 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 : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 358 ILE 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 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 110 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 1 optimal weight: 0.0770 chunk 71 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.168917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.144187 restraints weight = 16144.506| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.39 r_work: 0.3778 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10602 Z= 0.206 Angle : 0.678 11.022 14340 Z= 0.347 Chirality : 0.043 0.252 1728 Planarity : 0.005 0.071 1746 Dihedral : 6.760 49.498 2157 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.26 % Allowed : 20.20 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -0.35 (0.24), residues: 1194 helix: 1.11 (0.23), residues: 486 sheet: -1.42 (0.42), residues: 132 loop : -1.11 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 210 HIS 0.006 0.001 HIS C 230 PHE 0.030 0.002 PHE B 191 TYR 0.016 0.002 TYR B 94 ARG 0.005 0.000 ARG a 282 *********************** 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 219 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 1.284 Fit side-chains REVERT: a 410 MET cc_start: 0.6852 (mtp) cc_final: 0.6599 (mtp) REVERT: b 390 ASN cc_start: 0.7968 (t0) cc_final: 0.7476 (t0) REVERT: A 16 GLU cc_start: 0.6291 (pm20) cc_final: 0.6029 (pm20) REVERT: B 104 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7202 (mm-30) REVERT: B 146 ASN cc_start: 0.8062 (m110) cc_final: 0.7834 (m-40) REVERT: C 191 PHE cc_start: 0.6788 (t80) cc_final: 0.6332 (t80) outliers start: 25 outliers final: 21 residues processed: 210 average time/residue: 0.2085 time to fit residues: 63.2018 Evaluate side-chains 199 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 430 LEU Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 430 LEU 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 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 223 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 99 optimal weight: 0.0170 chunk 20 optimal weight: 0.8980 chunk 63 optimal weight: 0.0170 chunk 116 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.171258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.148565 restraints weight = 15517.569| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.16 r_work: 0.3819 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10602 Z= 0.191 Angle : 0.706 15.527 14340 Z= 0.357 Chirality : 0.044 0.256 1728 Planarity : 0.005 0.070 1746 Dihedral : 6.499 59.379 2157 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.08 % Allowed : 20.56 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.28 (0.24), residues: 1194 helix: 1.38 (0.24), residues: 468 sheet: -1.53 (0.42), residues: 132 loop : -1.15 (0.25), residues: 594 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 0.028 0.002 PHE B 191 TYR 0.016 0.002 TYR B 94 ARG 0.005 0.000 ARG B 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 1.154 Fit side-chains REVERT: a 410 MET cc_start: 0.6752 (mtp) cc_final: 0.6511 (mtp) REVERT: b 325 ARG cc_start: 0.8045 (tpp-160) cc_final: 0.7818 (tpp-160) REVERT: b 390 ASN cc_start: 0.7914 (t0) cc_final: 0.7343 (m110) REVERT: A 16 GLU cc_start: 0.6213 (pm20) cc_final: 0.5855 (pm20) REVERT: B 104 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7185 (mm-30) REVERT: C 80 MET cc_start: 0.5420 (mmp) cc_final: 0.5142 (mmp) REVERT: C 191 PHE cc_start: 0.6825 (t80) cc_final: 0.6335 (t80) outliers start: 23 outliers final: 20 residues processed: 203 average time/residue: 0.2102 time to fit residues: 62.3764 Evaluate side-chains 193 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 361 ILE 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 b residue 414 MET Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain A residue 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 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 128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 95 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 75 optimal weight: 0.2980 chunk 46 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.168680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.144039 restraints weight = 15818.815| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.35 r_work: 0.3783 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10602 Z= 0.232 Angle : 0.698 11.094 14340 Z= 0.357 Chirality : 0.045 0.318 1728 Planarity : 0.005 0.066 1746 Dihedral : 6.365 48.718 2157 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.17 % Allowed : 20.56 % Favored : 77.26 % 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: -0.24 (0.24), residues: 1194 helix: 1.38 (0.24), residues: 474 sheet: -1.48 (0.43), residues: 132 loop : -1.13 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 210 HIS 0.010 0.001 HIS B 93 PHE 0.033 0.002 PHE B 191 TYR 0.014 0.002 TYR B 94 ARG 0.005 0.000 ARG B 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5563.46 seconds wall clock time: 99 minutes 52.28 seconds (5992.28 seconds total)