Starting phenix.real_space_refine on Fri Jul 3 07:06:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zj8_14744/07_2026/7zj8_14744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zj8_14744/07_2026/7zj8_14744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zj8_14744/07_2026/7zj8_14744.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zj8_14744/07_2026/7zj8_14744.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zj8_14744/07_2026/7zj8_14744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zj8_14744/07_2026/7zj8_14744.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zj8_14744/07_2026/7zj8_14744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zj8_14744/07_2026/7zj8_14744.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 57 5.16 5 C 7665 2.51 5 N 2088 2.21 5 O 2532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12342 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3889 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain: "B" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3889 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain: "C" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3889 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 474} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'BOG': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'BOG': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'BOG': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.01, per 1000 atoms: 0.24 Number of scatterers: 12342 At special positions: 0 Unit cell: (97.2, 93.96, 149.04, 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 57 16.00 O 2532 8.00 N 2088 7.00 C 7665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.05 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.07 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.05 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.05 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.11 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.05 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.05 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.07 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.05 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.05 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.10 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.05 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.05 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.07 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.05 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.05 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.10 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.05 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 " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA J 3 " - " MAN J 5 " " BMA N 3 " - " MAN N 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " BETA1-6 " NAG E 1 " - " FUC E 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 4 " " NAG M 1 " - " FUC M 4 " NAG-ASN " NAG A 601 " - " ASN A 483 " " NAG A 602 " - " ASN A 22 " " NAG B 602 " - " ASN B 483 " " NAG B 603 " - " ASN B 22 " " NAG C 602 " - " ASN C 483 " " NAG C 603 " - " ASN C 22 " " NAG D 1 " - " ASN A 38 " " NAG E 1 " - " ASN A 81 " " NAG F 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 285 " " NAG H 1 " - " ASN B 38 " " NAG I 1 " - " ASN B 81 " " NAG J 1 " - " ASN B 165 " " NAG K 1 " - " ASN B 285 " " NAG L 1 " - " ASN C 38 " " NAG M 1 " - " ASN C 81 " " NAG N 1 " - " ASN C 165 " " NAG O 1 " - " ASN C 285 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 463.4 milliseconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2730 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 39 sheets defined 27.7% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.736A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 79 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.569A pdb=" N GLY A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.696A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 386 removed outlier: 4.042A pdb=" N GLU A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 455 removed outlier: 3.517A pdb=" N VAL A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 448 " --> pdb=" O MET A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 487 through 490 Processing helix chain 'A' and resid 491 through 501 removed outlier: 3.627A pdb=" N GLN A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.737A pdb=" N ASP B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL B 78 " --> pdb=" O HIS B 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 79 " --> pdb=" O CYS B 76 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN B 80 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.567A pdb=" N GLY B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 removed outlier: 3.694A pdb=" N GLN B 191 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 removed outlier: 4.045A pdb=" N GLU B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 455 removed outlier: 3.514A pdb=" N VAL B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 487 through 490 Processing helix chain 'B' and resid 491 through 501 removed outlier: 3.627A pdb=" N GLN B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.736A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 79 " --> pdb=" O CYS C 76 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.569A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.695A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 386 removed outlier: 4.044A pdb=" N GLU C 386 " --> pdb=" O ASN C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 455 removed outlier: 3.515A pdb=" N VAL C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 448 " --> pdb=" O MET C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 484 Processing helix chain 'C' and resid 487 through 490 Processing helix chain 'C' and resid 491 through 501 removed outlier: 3.627A pdb=" N GLN C 501 " --> pdb=" O ASN C 497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 363 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.861A pdb=" N THR A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.722A pdb=" N GLN A 44 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.884A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.363A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.227A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 8.111A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 136 through 140 Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 removed outlier: 5.959A pdb=" N ARG A 201 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 281 through 283 removed outlier: 4.454A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.564A pdb=" N LYS A 391 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 361 through 363 Processing sheet with id=AB6, first strand: chain 'B' and resid 24 through 26 removed outlier: 3.861A pdb=" N THR B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB8, first strand: chain 'B' and resid 43 through 44 removed outlier: 3.723A pdb=" N GLN B 44 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 51 through 54 removed outlier: 5.883A pdb=" N ILE B 51 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS B 277 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN B 53 " --> pdb=" O CYS B 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.360A pdb=" N PHE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 101 removed outlier: 5.232A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 100 through 101 removed outlier: 8.117A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AC5, first strand: chain 'B' and resid 136 through 140 Processing sheet with id=AC6, first strand: chain 'B' and resid 164 through 169 removed outlier: 5.957A pdb=" N ARG B 201 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 281 through 283 removed outlier: 4.455A pdb=" N CYS B 281 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 303 through 304 removed outlier: 3.564A pdb=" N LYS B 391 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 361 through 363 Processing sheet with id=AD1, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.861A pdb=" N THR C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AD3, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.724A pdb=" N GLN C 44 " --> pdb=" O PHE C 294 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.883A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.361A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 100 through 101 removed outlier: 5.230A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 100 through 101 removed outlier: 8.116A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AD9, first strand: chain 'C' and resid 136 through 140 Processing sheet with id=AE1, first strand: chain 'C' and resid 164 through 169 removed outlier: 5.957A pdb=" N ARG C 201 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.456A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 303 through 304 removed outlier: 3.564A pdb=" N LYS C 391 " --> pdb=" O GLY C 303 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1395 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: 2.11 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2040 1.31 - 1.44: 3525 1.44 - 1.57: 6942 1.57 - 1.71: 0 1.71 - 1.84: 78 Bond restraints: 12585 Sorted by residual: bond pdb=" C GLN B 295 " pdb=" O GLN B 295 " ideal model delta sigma weight residual 1.234 1.180 0.054 1.22e-02 6.72e+03 1.95e+01 bond pdb=" C GLN A 295 " pdb=" O GLN A 295 " ideal model delta sigma weight residual 1.234 1.181 0.052 1.22e-02 6.72e+03 1.85e+01 bond pdb=" C GLN C 295 " pdb=" O GLN C 295 " ideal model delta sigma weight residual 1.234 1.182 0.052 1.22e-02 6.72e+03 1.80e+01 bond pdb=" C LEU A 42 " pdb=" O LEU A 42 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.33e-02 5.65e+03 1.77e+01 bond pdb=" C LEU B 42 " pdb=" O LEU B 42 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.33e-02 5.65e+03 1.74e+01 ... (remaining 12580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 13060 2.22 - 4.45: 3681 4.45 - 6.67: 285 6.67 - 8.89: 29 8.89 - 11.12: 6 Bond angle restraints: 17061 Sorted by residual: angle pdb=" CA GLN C 295 " pdb=" C GLN C 295 " pdb=" O GLN C 295 " ideal model delta sigma weight residual 121.33 114.58 6.75 1.08e+00 8.57e-01 3.90e+01 angle pdb=" CA GLN A 295 " pdb=" C GLN A 295 " pdb=" O GLN A 295 " ideal model delta sigma weight residual 121.33 114.60 6.73 1.08e+00 8.57e-01 3.88e+01 angle pdb=" CA GLN B 295 " pdb=" C GLN B 295 " pdb=" O GLN B 295 " ideal model delta sigma weight residual 121.33 114.67 6.66 1.08e+00 8.57e-01 3.81e+01 angle pdb=" CA PHE C 294 " pdb=" C PHE C 294 " pdb=" O PHE C 294 " ideal model delta sigma weight residual 121.73 114.28 7.45 1.35e+00 5.49e-01 3.04e+01 angle pdb=" CA ASN A 382 " pdb=" C ASN A 382 " pdb=" O ASN A 382 " ideal model delta sigma weight residual 120.70 115.07 5.63 1.03e+00 9.43e-01 2.99e+01 ... (remaining 17056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 6181 15.62 - 31.24: 791 31.24 - 46.86: 141 46.86 - 62.48: 60 62.48 - 78.10: 15 Dihedral angle restraints: 7188 sinusoidal: 2931 harmonic: 4257 Sorted by residual: dihedral pdb=" CA ASP B 60 " pdb=" C ASP B 60 " pdb=" N GLY B 61 " pdb=" CA GLY B 61 " ideal model delta harmonic sigma weight residual 180.00 154.57 25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA LEU B 455 " pdb=" C LEU B 455 " pdb=" N ARG B 456 " pdb=" CA ARG B 456 " ideal model delta harmonic sigma weight residual 180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ASP C 60 " pdb=" C ASP C 60 " pdb=" N GLY C 61 " pdb=" CA GLY C 61 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 7185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 1708 0.138 - 0.276: 304 0.276 - 0.414: 7 0.414 - 0.551: 3 0.551 - 0.689: 3 Chirality restraints: 2025 Sorted by residual: chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.85e+01 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.83e+01 chirality pdb=" C1 MAN F 5 " pdb=" O6 BMA F 3 " pdb=" C2 MAN F 5 " pdb=" O5 MAN F 5 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.58e+01 ... (remaining 2022 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.333 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG A 601 " -0.155 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.054 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.486 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " 0.255 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 602 " 0.331 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG B 602 " -0.153 2.00e-02 2.50e+03 pdb=" C8 NAG B 602 " 0.056 2.00e-02 2.50e+03 pdb=" N2 NAG B 602 " -0.485 2.00e-02 2.50e+03 pdb=" O7 NAG B 602 " 0.252 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 602 " 0.328 2.00e-02 2.50e+03 2.93e-01 1.08e+03 pdb=" C7 NAG C 602 " -0.154 2.00e-02 2.50e+03 pdb=" C8 NAG C 602 " 0.054 2.00e-02 2.50e+03 pdb=" N2 NAG C 602 " -0.482 2.00e-02 2.50e+03 pdb=" O7 NAG C 602 " 0.253 2.00e-02 2.50e+03 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 3 2.16 - 2.84: 2716 2.84 - 3.53: 15599 3.53 - 4.21: 28431 4.21 - 4.90: 46186 Nonbonded interactions: 92935 Sorted by model distance: nonbonded pdb=" O ASN B 8 " pdb=" NZ LYS B 472 " model vdw 1.471 3.120 nonbonded pdb=" O ASN A 8 " pdb=" NZ LYS A 472 " model vdw 1.473 3.120 nonbonded pdb=" O ASN C 8 " pdb=" NZ LYS C 472 " model vdw 1.474 3.120 nonbonded pdb=" N GLN C 295 " pdb=" O GLN C 295 " model vdw 2.412 2.496 nonbonded pdb=" N GLN B 295 " pdb=" O GLN B 295 " model vdw 2.412 2.496 ... (remaining 92930 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 501 or resid 602)) selection = (chain 'B' and (resid 8 through 501 or resid 602)) selection = (chain 'C' and (resid 8 through 501 or resid 602)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } 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: 2.110 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.610 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 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 : 0.014 0.074 12651 Z= 1.022 Angle : 1.882 11.117 17241 Z= 1.308 Chirality : 0.101 0.689 2025 Planarity : 0.017 0.296 2154 Dihedral : 15.099 78.095 4404 Min Nonbonded Distance : 1.471 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.23 % Allowed : 10.44 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.18), residues: 1476 helix: -1.26 (0.24), residues: 357 sheet: -0.93 (0.29), residues: 288 loop : -2.28 (0.16), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 229 TYR 0.040 0.006 TYR A 161 PHE 0.040 0.006 PHE A 258 TRP 0.041 0.007 TRP C 421 HIS 0.013 0.005 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.01386 / 1.02 (12585) covalent geometry : angle 1.87067 / 1.31 (17061) SS BOND : bond 0.03757 / 2.40 ( 18) SS BOND : angle 3.19769 / 2.24 ( 36) hydrogen bonds : bond 0.27963 / 19.34 ( 468) hydrogen bonds : angle 8.43537 / 5.96 ( 1395) link_ALPHA1-3 : bond 0.00663 / 0.33 ( 3) link_ALPHA1-3 : angle 1.98375 / 1.17 ( 9) link_ALPHA1-6 : bond 0.00072 / 0.04 ( 3) link_ALPHA1-6 : angle 0.31105 / 0.22 ( 9) link_BETA1-4 : bond 0.00745 / 0.51 ( 21) link_BETA1-4 : angle 1.94839 / 1.29 ( 63) link_BETA1-6 : bond 0.00299 / 0.15 ( 3) link_BETA1-6 : angle 1.05968 / 0.75 ( 9) link_NAG-ASN : bond 0.00913 / 0.62 ( 18) link_NAG-ASN : angle 3.57259 / 2.17 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 0.468 Fit side-chains REVERT: A 168 MET cc_start: 0.8954 (tpp) cc_final: 0.8361 (tpp) REVERT: A 199 SER cc_start: 0.9223 (t) cc_final: 0.8939 (p) REVERT: A 457 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8389 (mm-30) REVERT: A 462 MET cc_start: 0.8014 (mtm) cc_final: 0.7536 (mtm) REVERT: B 168 MET cc_start: 0.8836 (tpp) cc_final: 0.8299 (tpp) REVERT: B 199 SER cc_start: 0.9326 (t) cc_final: 0.9101 (p) REVERT: B 323 VAL cc_start: 0.8478 (t) cc_final: 0.8277 (p) REVERT: B 344 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7847 (tp30) REVERT: B 401 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8230 (mp0) REVERT: C 199 SER cc_start: 0.9269 (t) cc_final: 0.9014 (p) REVERT: C 320 MET cc_start: 0.8328 (ptp) cc_final: 0.8090 (ptp) REVERT: C 344 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8058 (tp30) REVERT: C 456 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.7945 (ttm170) outliers start: 3 outliers final: 0 residues processed: 158 average time/residue: 0.1472 time to fit residues: 31.2143 Evaluate side-chains 57 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0030 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN A 33 GLN A 54 ASN A 248 ASN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 ASN B 54 ASN B 248 ASN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 33 GLN C 54 ASN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 488 HIS ** C 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.080172 restraints weight = 22216.674| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.37 r_work: 0.2840 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12651 Z= 0.139 Angle : 0.639 8.326 17241 Z= 0.325 Chirality : 0.043 0.245 2025 Planarity : 0.004 0.031 2154 Dihedral : 5.514 26.756 1623 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.16 % Allowed : 11.68 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 1476 helix: 1.58 (0.26), residues: 366 sheet: 0.13 (0.30), residues: 288 loop : -1.59 (0.17), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 269 TYR 0.010 0.001 TYR C 486 PHE 0.010 0.001 PHE B 392 TRP 0.008 0.001 TRP A 180 HIS 0.007 0.002 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (12585) covalent geometry : angle 0.61701 / 0.32 (17061) SS BOND : bond 0.00245 / 0.17 ( 18) SS BOND : angle 1.03439 / 0.68 ( 36) hydrogen bonds : bond 0.07396 / 5.18 ( 468) hydrogen bonds : angle 5.14671 / 3.72 ( 1395) link_ALPHA1-3 : bond 0.00354 / 0.18 ( 3) link_ALPHA1-3 : angle 1.46651 / 0.98 ( 9) link_ALPHA1-6 : bond 0.00417 / 0.21 ( 3) link_ALPHA1-6 : angle 1.59013 / 0.95 ( 9) link_BETA1-4 : bond 0.00566 / 0.35 ( 21) link_BETA1-4 : angle 1.66680 / 1.10 ( 63) link_BETA1-6 : bond 0.00413 / 0.21 ( 3) link_BETA1-6 : angle 1.11473 / 0.74 ( 9) link_NAG-ASN : bond 0.00690 / 0.44 ( 18) link_NAG-ASN : angle 2.30883 / 1.48 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.504 Fit side-chains REVERT: A 168 MET cc_start: 0.8575 (tpp) cc_final: 0.7954 (tpp) REVERT: B 242 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8680 (p) REVERT: B 462 MET cc_start: 0.7783 (mtm) cc_final: 0.7579 (mtt) REVERT: C 242 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8589 (p) REVERT: C 491 TYR cc_start: 0.8249 (m-80) cc_final: 0.7998 (m-80) REVERT: C 500 PHE cc_start: 0.7609 (m-10) cc_final: 0.6943 (m-10) outliers start: 15 outliers final: 4 residues processed: 83 average time/residue: 0.1086 time to fit residues: 13.3346 Evaluate side-chains 53 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 20 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 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 = 0.3585 r_free = 0.3585 target = 0.110269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.076930 restraints weight = 22718.724| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.98 r_work: 0.2869 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12651 Z= 0.122 Angle : 0.597 9.619 17241 Z= 0.299 Chirality : 0.042 0.270 2025 Planarity : 0.004 0.039 2154 Dihedral : 4.882 31.791 1623 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.62 % Allowed : 12.45 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.21), residues: 1476 helix: 2.66 (0.27), residues: 363 sheet: 0.35 (0.29), residues: 306 loop : -1.24 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 452 TYR 0.009 0.001 TYR A 486 PHE 0.012 0.001 PHE C 258 TRP 0.007 0.001 TRP A 421 HIS 0.006 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (12585) covalent geometry : angle 0.57907 / 0.30 (17061) SS BOND : bond 0.00330 / 0.22 ( 18) SS BOND : angle 1.25314 / 0.80 ( 36) hydrogen bonds : bond 0.06265 / 4.35 ( 468) hydrogen bonds : angle 4.49200 / 3.23 ( 1395) link_ALPHA1-3 : bond 0.00408 / 0.20 ( 3) link_ALPHA1-3 : angle 1.40806 / 0.90 ( 9) link_ALPHA1-6 : bond 0.00417 / 0.21 ( 3) link_ALPHA1-6 : angle 1.51820 / 0.97 ( 9) link_BETA1-4 : bond 0.00510 / 0.33 ( 21) link_BETA1-4 : angle 1.56750 / 1.03 ( 63) link_BETA1-6 : bond 0.00288 / 0.14 ( 3) link_BETA1-6 : angle 1.19094 / 0.85 ( 9) link_NAG-ASN : bond 0.00408 / 0.27 ( 18) link_NAG-ASN : angle 1.76024 / 1.11 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.382 Fit side-chains REVERT: A 168 MET cc_start: 0.8505 (tpp) cc_final: 0.8205 (tpp) REVERT: A 242 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8600 (p) REVERT: A 449 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7321 (tp30) REVERT: A 462 MET cc_start: 0.8063 (mtm) cc_final: 0.7455 (mtm) REVERT: C 500 PHE cc_start: 0.7469 (m-10) cc_final: 0.6857 (m-10) outliers start: 8 outliers final: 3 residues processed: 57 average time/residue: 0.1320 time to fit residues: 10.5337 Evaluate side-chains 45 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 222 TRP Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain C residue 104 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 83 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN C 17 HIS C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.106282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.072802 restraints weight = 22777.692| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.95 r_work: 0.2791 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 12651 Z= 0.297 Angle : 0.747 9.935 17241 Z= 0.375 Chirality : 0.050 0.321 2025 Planarity : 0.005 0.049 2154 Dihedral : 5.525 49.083 1623 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.09 % Allowed : 12.14 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.21), residues: 1476 helix: 2.15 (0.27), residues: 360 sheet: 0.31 (0.29), residues: 306 loop : -1.42 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 321 TYR 0.014 0.002 TYR C 178 PHE 0.020 0.003 PHE C 258 TRP 0.010 0.002 TRP A 421 HIS 0.007 0.002 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00719 / 0.30 (12585) covalent geometry : angle 0.72647 / 0.37 (17061) SS BOND : bond 0.00456 / 0.26 ( 18) SS BOND : angle 1.56637 / 1.05 ( 36) hydrogen bonds : bond 0.07736 / 5.39 ( 468) hydrogen bonds : angle 4.84412 / 3.46 ( 1395) link_ALPHA1-3 : bond 0.00369 / 0.19 ( 3) link_ALPHA1-3 : angle 1.43773 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00163 / 0.08 ( 3) link_ALPHA1-6 : angle 1.93293 / 1.19 ( 9) link_BETA1-4 : bond 0.00491 / 0.31 ( 21) link_BETA1-4 : angle 2.01584 / 1.31 ( 63) link_BETA1-6 : bond 0.00123 / 0.06 ( 3) link_BETA1-6 : angle 1.43339 / 1.07 ( 9) link_NAG-ASN : bond 0.00697 / 0.47 ( 18) link_NAG-ASN : angle 1.90828 / 1.18 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 50 time to evaluate : 0.500 Fit side-chains REVERT: A 168 MET cc_start: 0.8794 (tpp) cc_final: 0.8510 (tpp) REVERT: A 462 MET cc_start: 0.8105 (mtm) cc_final: 0.7651 (mtm) REVERT: C 500 PHE cc_start: 0.7596 (m-10) cc_final: 0.6990 (m-10) outliers start: 27 outliers final: 18 residues processed: 75 average time/residue: 0.1178 time to fit residues: 12.7720 Evaluate side-chains 64 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 222 TRP Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 388 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.075952 restraints weight = 22686.496| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.95 r_work: 0.2853 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12651 Z= 0.113 Angle : 0.565 9.591 17241 Z= 0.279 Chirality : 0.041 0.270 2025 Planarity : 0.004 0.040 2154 Dihedral : 4.911 36.721 1623 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.62 % Allowed : 13.38 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.21), residues: 1476 helix: 2.94 (0.27), residues: 357 sheet: 0.31 (0.29), residues: 321 loop : -1.22 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 452 TYR 0.007 0.001 TYR C 105 PHE 0.009 0.001 PHE B 392 TRP 0.008 0.001 TRP A 421 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (12585) covalent geometry : angle 0.54445 / 0.27 (17061) SS BOND : bond 0.00202 / 0.14 ( 18) SS BOND : angle 1.59642 / 1.20 ( 36) hydrogen bonds : bond 0.05795 / 4.02 ( 468) hydrogen bonds : angle 4.43496 / 3.18 ( 1395) link_ALPHA1-3 : bond 0.00405 / 0.20 ( 3) link_ALPHA1-3 : angle 1.46597 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00268 / 0.13 ( 3) link_ALPHA1-6 : angle 1.55973 / 1.02 ( 9) link_BETA1-4 : bond 0.00446 / 0.29 ( 21) link_BETA1-4 : angle 1.66819 / 1.09 ( 63) link_BETA1-6 : bond 0.00203 / 0.10 ( 3) link_BETA1-6 : angle 1.19082 / 0.86 ( 9) link_NAG-ASN : bond 0.00391 / 0.26 ( 18) link_NAG-ASN : angle 1.53844 / 0.96 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.458 Fit side-chains REVERT: A 168 MET cc_start: 0.8560 (tpp) cc_final: 0.8212 (tpp) REVERT: A 462 MET cc_start: 0.8012 (mtm) cc_final: 0.7420 (mtm) outliers start: 8 outliers final: 7 residues processed: 52 average time/residue: 0.1423 time to fit residues: 10.6714 Evaluate side-chains 51 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain B residue 222 TRP Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 381 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 140 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 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 = 0.3552 r_free = 0.3552 target = 0.108121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.075033 restraints weight = 22670.171| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.91 r_work: 0.2832 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12651 Z= 0.152 Angle : 0.586 9.670 17241 Z= 0.289 Chirality : 0.043 0.280 2025 Planarity : 0.004 0.040 2154 Dihedral : 4.878 40.210 1623 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.77 % Allowed : 13.61 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.21), residues: 1476 helix: 2.89 (0.27), residues: 360 sheet: 0.34 (0.29), residues: 321 loop : -1.21 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 383 TYR 0.007 0.001 TYR C 491 PHE 0.012 0.002 PHE B 392 TRP 0.008 0.001 TRP A 421 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (12585) covalent geometry : angle 0.56548 / 0.28 (17061) SS BOND : bond 0.00239 / 0.16 ( 18) SS BOND : angle 1.57730 / 1.21 ( 36) hydrogen bonds : bond 0.06074 / 4.21 ( 468) hydrogen bonds : angle 4.41430 / 3.17 ( 1395) link_ALPHA1-3 : bond 0.00375 / 0.19 ( 3) link_ALPHA1-3 : angle 1.47057 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00306 / 0.15 ( 3) link_ALPHA1-6 : angle 1.59470 / 1.01 ( 9) link_BETA1-4 : bond 0.00437 / 0.28 ( 21) link_BETA1-4 : angle 1.72527 / 1.12 ( 63) link_BETA1-6 : bond 0.00085 / 0.04 ( 3) link_BETA1-6 : angle 1.34408 / 1.00 ( 9) link_NAG-ASN : bond 0.00434 / 0.29 ( 18) link_NAG-ASN : angle 1.51864 / 0.94 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.456 Fit side-chains REVERT: A 168 MET cc_start: 0.8550 (tpp) cc_final: 0.8209 (tpp) REVERT: A 462 MET cc_start: 0.8007 (mtm) cc_final: 0.7456 (mtm) REVERT: C 500 PHE cc_start: 0.7495 (m-10) cc_final: 0.6983 (m-10) outliers start: 10 outliers final: 8 residues processed: 56 average time/residue: 0.1348 time to fit residues: 10.7251 Evaluate side-chains 53 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 222 TRP Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 381 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 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 = 0.3549 r_free = 0.3549 target = 0.107919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.074964 restraints weight = 22522.435| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.90 r_work: 0.2828 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12651 Z= 0.160 Angle : 0.587 9.689 17241 Z= 0.290 Chirality : 0.044 0.279 2025 Planarity : 0.004 0.040 2154 Dihedral : 5.061 43.069 1623 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.24 % Allowed : 13.38 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.21), residues: 1476 helix: 2.97 (0.26), residues: 357 sheet: 0.28 (0.29), residues: 339 loop : -1.09 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 321 TYR 0.008 0.001 TYR C 491 PHE 0.011 0.002 PHE B 87 TRP 0.008 0.001 TRP A 421 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (12585) covalent geometry : angle 0.56759 / 0.29 (17061) SS BOND : bond 0.00250 / 0.16 ( 18) SS BOND : angle 1.45115 / 1.11 ( 36) hydrogen bonds : bond 0.06121 / 4.25 ( 468) hydrogen bonds : angle 4.44366 / 3.19 ( 1395) link_ALPHA1-3 : bond 0.00395 / 0.20 ( 3) link_ALPHA1-3 : angle 1.46346 / 0.93 ( 9) link_ALPHA1-6 : bond 0.00288 / 0.14 ( 3) link_ALPHA1-6 : angle 1.59256 / 1.03 ( 9) link_BETA1-4 : bond 0.00439 / 0.28 ( 21) link_BETA1-4 : angle 1.77892 / 1.16 ( 63) link_BETA1-6 : bond 0.00056 / 0.03 ( 3) link_BETA1-6 : angle 1.35979 / 1.02 ( 9) link_NAG-ASN : bond 0.00438 / 0.30 ( 18) link_NAG-ASN : angle 1.48829 / 0.92 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.382 Fit side-chains REVERT: A 168 MET cc_start: 0.8554 (tpp) cc_final: 0.8208 (tpp) REVERT: A 462 MET cc_start: 0.7992 (mtm) cc_final: 0.7447 (mtm) outliers start: 16 outliers final: 10 residues processed: 63 average time/residue: 0.1278 time to fit residues: 11.5721 Evaluate side-chains 58 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 222 TRP Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 295 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 133 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.106976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.074041 restraints weight = 22611.102| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.89 r_work: 0.2806 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12651 Z= 0.209 Angle : 0.639 9.771 17241 Z= 0.315 Chirality : 0.046 0.284 2025 Planarity : 0.004 0.040 2154 Dihedral : 5.451 45.733 1623 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.31 % Allowed : 13.61 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.21), residues: 1476 helix: 2.75 (0.27), residues: 351 sheet: 0.19 (0.28), residues: 339 loop : -1.08 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 269 TYR 0.010 0.002 TYR C 491 PHE 0.015 0.002 PHE B 392 TRP 0.007 0.001 TRP B 421 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (12585) covalent geometry : angle 0.61821 / 0.31 (17061) SS BOND : bond 0.00284 / 0.18 ( 18) SS BOND : angle 1.51524 / 1.16 ( 36) hydrogen bonds : bond 0.06630 / 4.61 ( 468) hydrogen bonds : angle 4.57563 / 3.28 ( 1395) link_ALPHA1-3 : bond 0.00366 / 0.18 ( 3) link_ALPHA1-3 : angle 1.48166 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00187 / 0.09 ( 3) link_ALPHA1-6 : angle 1.59239 / 1.02 ( 9) link_BETA1-4 : bond 0.00462 / 0.30 ( 21) link_BETA1-4 : angle 1.91279 / 1.24 ( 63) link_BETA1-6 : bond 0.00107 / 0.06 ( 3) link_BETA1-6 : angle 1.51795 / 1.14 ( 9) link_NAG-ASN : bond 0.00513 / 0.35 ( 18) link_NAG-ASN : angle 1.60831 / 1.00 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.485 Fit side-chains REVERT: A 168 MET cc_start: 0.8572 (tpp) cc_final: 0.8223 (tpp) REVERT: A 462 MET cc_start: 0.8008 (mtm) cc_final: 0.7464 (mtm) REVERT: B 295 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8532 (tm130) outliers start: 17 outliers final: 14 residues processed: 68 average time/residue: 0.1222 time to fit residues: 11.9548 Evaluate side-chains 63 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 222 TRP Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 381 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 86 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 33 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 110 optimal weight: 0.0670 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** 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 = 0.3562 r_free = 0.3562 target = 0.108759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.075978 restraints weight = 22594.416| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.90 r_work: 0.2847 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 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 : 0.002 0.033 12651 Z= 0.107 Angle : 0.550 9.577 17241 Z= 0.269 Chirality : 0.042 0.270 2025 Planarity : 0.003 0.039 2154 Dihedral : 5.029 44.529 1623 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.77 % Allowed : 14.15 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.22), residues: 1476 helix: 3.20 (0.26), residues: 357 sheet: 0.30 (0.28), residues: 345 loop : -1.05 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 452 TYR 0.007 0.001 TYR C 105 PHE 0.013 0.001 PHE B 294 TRP 0.006 0.001 TRP A 421 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (12585) covalent geometry : angle 0.53093 / 0.27 (17061) SS BOND : bond 0.00200 / 0.13 ( 18) SS BOND : angle 1.34575 / 1.03 ( 36) hydrogen bonds : bond 0.05567 / 3.86 ( 468) hydrogen bonds : angle 4.34080 / 3.11 ( 1395) link_ALPHA1-3 : bond 0.00406 / 0.20 ( 3) link_ALPHA1-3 : angle 1.46745 / 0.94 ( 9) link_ALPHA1-6 : bond 0.00347 / 0.17 ( 3) link_ALPHA1-6 : angle 1.46170 / 0.96 ( 9) link_BETA1-4 : bond 0.00414 / 0.27 ( 21) link_BETA1-4 : angle 1.70699 / 1.11 ( 63) link_BETA1-6 : bond 0.00222 / 0.11 ( 3) link_BETA1-6 : angle 1.13373 / 0.81 ( 9) link_NAG-ASN : bond 0.00392 / 0.26 ( 18) link_NAG-ASN : angle 1.38548 / 0.86 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.516 Fit side-chains REVERT: A 168 MET cc_start: 0.8549 (tpp) cc_final: 0.8209 (tpp) REVERT: A 462 MET cc_start: 0.7936 (mtm) cc_final: 0.7393 (mtm) REVERT: B 295 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8781 (tm-30) REVERT: B 346 MET cc_start: 0.7782 (tpp) cc_final: 0.7220 (mtp) outliers start: 10 outliers final: 8 residues processed: 60 average time/residue: 0.1150 time to fit residues: 10.0544 Evaluate side-chains 56 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 222 TRP Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 222 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 136 optimal weight: 0.4980 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** 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 = 0.3553 r_free = 0.3553 target = 0.108188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.075177 restraints weight = 22756.846| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.93 r_work: 0.2834 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12651 Z= 0.141 Angle : 0.569 9.614 17241 Z= 0.279 Chirality : 0.043 0.273 2025 Planarity : 0.004 0.039 2154 Dihedral : 5.071 45.848 1623 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.93 % Allowed : 14.54 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.22), residues: 1476 helix: 3.16 (0.26), residues: 357 sheet: 0.24 (0.28), residues: 348 loop : -1.02 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 499 TYR 0.007 0.001 TYR C 491 PHE 0.018 0.002 PHE A 500 TRP 0.007 0.001 TRP B 421 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (12585) covalent geometry : angle 0.55007 / 0.27 (17061) SS BOND : bond 0.00227 / 0.15 ( 18) SS BOND : angle 1.36421 / 1.05 ( 36) hydrogen bonds : bond 0.05800 / 4.03 ( 468) hydrogen bonds : angle 4.34562 / 3.12 ( 1395) link_ALPHA1-3 : bond 0.00394 / 0.20 ( 3) link_ALPHA1-3 : angle 1.47039 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00287 / 0.14 ( 3) link_ALPHA1-6 : angle 1.51555 / 0.99 ( 9) link_BETA1-4 : bond 0.00432 / 0.28 ( 21) link_BETA1-4 : angle 1.72848 / 1.12 ( 63) link_BETA1-6 : bond 0.00080 / 0.04 ( 3) link_BETA1-6 : angle 1.35822 / 1.00 ( 9) link_NAG-ASN : bond 0.00384 / 0.26 ( 18) link_NAG-ASN : angle 1.42385 / 0.88 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.504 Fit side-chains REVERT: A 168 MET cc_start: 0.8532 (tpp) cc_final: 0.8186 (tpp) REVERT: A 462 MET cc_start: 0.7954 (mtm) cc_final: 0.7392 (mtm) REVERT: B 295 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8753 (tm-30) outliers start: 12 outliers final: 10 residues processed: 60 average time/residue: 0.1226 time to fit residues: 10.6609 Evaluate side-chains 58 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 222 TRP Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 295 GLN Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 222 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.076314 restraints weight = 22522.180| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.92 r_work: 0.2858 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12651 Z= 0.101 Angle : 0.533 9.561 17241 Z= 0.261 Chirality : 0.041 0.271 2025 Planarity : 0.003 0.039 2154 Dihedral : 4.877 45.299 1623 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.93 % Allowed : 14.31 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.22), residues: 1476 helix: 3.39 (0.26), residues: 357 sheet: 0.28 (0.28), residues: 345 loop : -0.98 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 456 TYR 0.007 0.001 TYR C 105 PHE 0.015 0.001 PHE B 294 TRP 0.008 0.001 TRP B 421 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (12585) covalent geometry : angle 0.51545 / 0.26 (17061) SS BOND : bond 0.00185 / 0.12 ( 18) SS BOND : angle 1.27880 / 0.98 ( 36) hydrogen bonds : bond 0.05291 / 3.67 ( 468) hydrogen bonds : angle 4.22128 / 3.03 ( 1395) link_ALPHA1-3 : bond 0.00411 / 0.21 ( 3) link_ALPHA1-3 : angle 1.46049 / 0.94 ( 9) link_ALPHA1-6 : bond 0.00364 / 0.18 ( 3) link_ALPHA1-6 : angle 1.43772 / 0.95 ( 9) link_BETA1-4 : bond 0.00431 / 0.28 ( 21) link_BETA1-4 : angle 1.63228 / 1.06 ( 63) link_BETA1-6 : bond 0.00233 / 0.12 ( 3) link_BETA1-6 : angle 1.20196 / 0.86 ( 9) link_NAG-ASN : bond 0.00355 / 0.23 ( 18) link_NAG-ASN : angle 1.33595 / 0.83 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2605.13 seconds wall clock time: 45 minutes 33.49 seconds (2733.49 seconds total)