Starting phenix.real_space_refine on Wed Jul 30 21:04:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zj8_14744/07_2025/7zj8_14744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zj8_14744/07_2025/7zj8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zj8_14744/07_2025/7zj8_14744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zj8_14744/07_2025/7zj8_14744.map" model { file = "/net/cci-nas-00/data/ceres_data/7zj8_14744/07_2025/7zj8_14744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zj8_14744/07_2025/7zj8_14744.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.57, per 1000 atoms: 0.61 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: 4.06 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.18 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: 5.05 Time building geometry restraints manager: 4.53 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 - 21.35: 7409 21.35 - 42.69: 623 42.69 - 64.04: 95 64.04 - 85.38: 63 85.38 - 106.73: 36 Dihedral angle restraints: 8226 sinusoidal: 3969 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 8223 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: 0.06 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 35.140 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.180 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:3.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 : 18.143 106.728 5442 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.041 0.007 TRP C 421 HIS 0.013 0.005 HIS A 435 PHE 0.040 0.006 PHE A 258 TYR 0.040 0.006 TYR A 161 ARG 0.012 0.001 ARG B 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00913 ( 18) link_NAG-ASN : angle 3.57259 ( 54) link_ALPHA1-6 : bond 0.00072 ( 3) link_ALPHA1-6 : angle 0.31105 ( 9) link_BETA1-4 : bond 0.00745 ( 21) link_BETA1-4 : angle 1.94839 ( 63) link_ALPHA1-3 : bond 0.00663 ( 3) link_ALPHA1-3 : angle 1.98375 ( 9) hydrogen bonds : bond 0.27963 ( 468) hydrogen bonds : angle 8.43537 ( 1395) link_BETA1-6 : bond 0.00299 ( 3) link_BETA1-6 : angle 1.05968 ( 9) SS BOND : bond 0.03757 ( 18) SS BOND : angle 3.19769 ( 36) covalent geometry : bond 0.01386 (12585) covalent geometry : angle 1.87067 (17061) *********************** 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 : 1.459 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: 0.8600 (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: 0.3247 time to fit residues: 68.5118 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 : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.109906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.078678 restraints weight = 22292.531| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.37 r_work: 0.2809 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2009 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= 0.158 Angle : 0.688 9.225 17241 Z= 0.344 Chirality : 0.046 0.253 2025 Planarity : 0.004 0.033 2154 Dihedral : 12.785 78.090 2661 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.93 % Allowed : 11.60 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.19), residues: 1476 helix: 1.51 (0.26), residues: 366 sheet: 0.16 (0.30), residues: 288 loop : -1.64 (0.17), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 421 HIS 0.008 0.002 HIS A 75 PHE 0.013 0.002 PHE B 392 TYR 0.009 0.001 TYR C 486 ARG 0.003 0.000 ARG C 269 Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 18) link_NAG-ASN : angle 2.53936 ( 54) link_ALPHA1-6 : bond 0.00283 ( 3) link_ALPHA1-6 : angle 2.29923 ( 9) link_BETA1-4 : bond 0.00672 ( 21) link_BETA1-4 : angle 2.13752 ( 63) link_ALPHA1-3 : bond 0.00866 ( 3) link_ALPHA1-3 : angle 2.09484 ( 9) hydrogen bonds : bond 0.07765 ( 468) hydrogen bonds : angle 5.16034 ( 1395) link_BETA1-6 : bond 0.00682 ( 3) link_BETA1-6 : angle 1.22500 ( 9) SS BOND : bond 0.00196 ( 18) SS BOND : angle 1.03814 ( 36) covalent geometry : bond 0.00333 (12585) covalent geometry : angle 0.65767 (17061) *********************** 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 77 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 1.459 Fit side-chains REVERT: A 168 MET cc_start: 0.8633 (tpp) cc_final: 0.8021 (tpp) REVERT: B 462 MET cc_start: 0.7788 (mtm) cc_final: 0.7510 (mtt) REVERT: C 491 TYR cc_start: 0.8297 (m-80) cc_final: 0.8019 (m-80) REVERT: C 500 PHE cc_start: 0.7647 (m-10) cc_final: 0.6966 (m-10) outliers start: 12 outliers final: 4 residues processed: 76 average time/residue: 0.2898 time to fit residues: 31.8744 Evaluate side-chains 51 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 222 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 91 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.107210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.073742 restraints weight = 22914.315| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.99 r_work: 0.2806 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12651 Z= 0.224 Angle : 0.725 9.951 17241 Z= 0.360 Chirality : 0.048 0.300 2025 Planarity : 0.005 0.039 2154 Dihedral : 10.505 75.429 2661 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.47 % Allowed : 12.22 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1476 helix: 2.17 (0.27), residues: 360 sheet: 0.23 (0.28), residues: 312 loop : -1.49 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 421 HIS 0.006 0.002 HIS B 17 PHE 0.018 0.002 PHE A 258 TYR 0.011 0.002 TYR C 178 ARG 0.003 0.000 ARG B 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 18) link_NAG-ASN : angle 2.08962 ( 54) link_ALPHA1-6 : bond 0.00061 ( 3) link_ALPHA1-6 : angle 2.43331 ( 9) link_BETA1-4 : bond 0.00512 ( 21) link_BETA1-4 : angle 2.31876 ( 63) link_ALPHA1-3 : bond 0.00838 ( 3) link_ALPHA1-3 : angle 1.79325 ( 9) hydrogen bonds : bond 0.07470 ( 468) hydrogen bonds : angle 4.78140 ( 1395) link_BETA1-6 : bond 0.00073 ( 3) link_BETA1-6 : angle 1.38044 ( 9) SS BOND : bond 0.00413 ( 18) SS BOND : angle 1.64957 ( 36) covalent geometry : bond 0.00535 (12585) covalent geometry : angle 0.69678 (17061) *********************** 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 66 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 1.324 Fit side-chains REVERT: A 168 MET cc_start: 0.8608 (tpp) cc_final: 0.8299 (tpp) REVERT: A 449 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7366 (tp30) REVERT: A 462 MET cc_start: 0.8205 (mtm) cc_final: 0.7541 (mtm) REVERT: C 242 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8491 (p) outliers start: 19 outliers final: 13 residues processed: 66 average time/residue: 0.2903 time to fit residues: 27.4222 Evaluate side-chains 60 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 381 LEU 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 388 THR Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 242 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 95 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 130 optimal weight: 0.4980 chunk 75 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3556 r_free = 0.3556 target = 0.108132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.074949 restraints weight = 22864.928| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.01 r_work: 0.2834 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12651 Z= 0.153 Angle : 0.606 9.723 17241 Z= 0.298 Chirality : 0.044 0.271 2025 Planarity : 0.004 0.039 2154 Dihedral : 8.814 66.793 2661 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.39 % Allowed : 12.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1476 helix: 2.65 (0.27), residues: 360 sheet: 0.25 (0.28), residues: 321 loop : -1.33 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.006 0.001 HIS A 75 PHE 0.012 0.002 PHE A 258 TYR 0.007 0.001 TYR C 178 ARG 0.003 0.000 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 18) link_NAG-ASN : angle 1.76676 ( 54) link_ALPHA1-6 : bond 0.00291 ( 3) link_ALPHA1-6 : angle 2.31934 ( 9) link_BETA1-4 : bond 0.00419 ( 21) link_BETA1-4 : angle 2.05501 ( 63) link_ALPHA1-3 : bond 0.01034 ( 3) link_ALPHA1-3 : angle 1.79945 ( 9) hydrogen bonds : bond 0.06280 ( 468) hydrogen bonds : angle 4.53749 ( 1395) link_BETA1-6 : bond 0.00131 ( 3) link_BETA1-6 : angle 1.31900 ( 9) SS BOND : bond 0.00303 ( 18) SS BOND : angle 1.31149 ( 36) covalent geometry : bond 0.00355 (12585) covalent geometry : angle 0.58054 (17061) *********************** 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 67 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 1.606 Fit side-chains REVERT: A 168 MET cc_start: 0.8573 (tpp) cc_final: 0.8221 (tpp) REVERT: A 462 MET cc_start: 0.8256 (mtm) cc_final: 0.7625 (mtm) REVERT: C 242 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8536 (p) outliers start: 18 outliers final: 8 residues processed: 65 average time/residue: 0.3402 time to fit residues: 32.0225 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 : 1.440 ------------------------------------------------------------------------------- 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 196 VAL Chi-restraints excluded: chain B residue 222 TRP 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 242 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 57 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.107051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.074005 restraints weight = 22733.491| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.97 r_work: 0.2812 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12651 Z= 0.187 Angle : 0.638 9.901 17241 Z= 0.313 Chirality : 0.046 0.280 2025 Planarity : 0.004 0.040 2154 Dihedral : 8.696 64.637 2661 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.78 % Allowed : 13.30 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1476 helix: 2.62 (0.27), residues: 360 sheet: 0.25 (0.29), residues: 321 loop : -1.30 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.009 0.002 HIS C 17 PHE 0.014 0.002 PHE B 392 TYR 0.008 0.001 TYR A 178 ARG 0.003 0.000 ARG C 321 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 18) link_NAG-ASN : angle 1.75933 ( 54) link_ALPHA1-6 : bond 0.00225 ( 3) link_ALPHA1-6 : angle 2.21753 ( 9) link_BETA1-4 : bond 0.00471 ( 21) link_BETA1-4 : angle 1.94475 ( 63) link_ALPHA1-3 : bond 0.00852 ( 3) link_ALPHA1-3 : angle 1.82815 ( 9) hydrogen bonds : bond 0.06595 ( 468) hydrogen bonds : angle 4.58084 ( 1395) link_BETA1-6 : bond 0.00051 ( 3) link_BETA1-6 : angle 1.47721 ( 9) SS BOND : bond 0.00279 ( 18) SS BOND : angle 1.10430 ( 36) covalent geometry : bond 0.00445 (12585) covalent geometry : angle 0.61575 (17061) *********************** 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 71 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 1.361 Fit side-chains REVERT: A 168 MET cc_start: 0.8578 (tpp) cc_final: 0.8216 (tpp) REVERT: A 462 MET cc_start: 0.8244 (mtm) cc_final: 0.7629 (mtm) REVERT: B 295 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8540 (tm130) REVERT: C 500 PHE cc_start: 0.7373 (m-10) cc_final: 0.6856 (m-10) outliers start: 23 outliers final: 18 residues processed: 70 average time/residue: 0.3982 time to fit residues: 40.3444 Evaluate side-chains 64 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER 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 475 ASN Chi-restraints excluded: chain B residue 104 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 35 optimal weight: 0.4980 chunk 131 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** 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 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.106435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.073337 restraints weight = 23117.872| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.98 r_work: 0.2799 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12651 Z= 0.235 Angle : 0.661 9.919 17241 Z= 0.326 Chirality : 0.047 0.282 2025 Planarity : 0.004 0.041 2154 Dihedral : 8.839 63.398 2661 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.55 % Allowed : 13.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1476 helix: 2.51 (0.27), residues: 360 sheet: 0.22 (0.29), residues: 321 loop : -1.34 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 421 HIS 0.010 0.002 HIS B 17 PHE 0.015 0.002 PHE B 392 TYR 0.009 0.002 TYR C 178 ARG 0.003 0.000 ARG A 499 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 18) link_NAG-ASN : angle 1.80213 ( 54) link_ALPHA1-6 : bond 0.00121 ( 3) link_ALPHA1-6 : angle 2.24735 ( 9) link_BETA1-4 : bond 0.00440 ( 21) link_BETA1-4 : angle 2.02340 ( 63) link_ALPHA1-3 : bond 0.00949 ( 3) link_ALPHA1-3 : angle 1.78090 ( 9) hydrogen bonds : bond 0.06893 ( 468) hydrogen bonds : angle 4.66637 ( 1395) link_BETA1-6 : bond 0.00045 ( 3) link_BETA1-6 : angle 1.56935 ( 9) SS BOND : bond 0.00312 ( 18) SS BOND : angle 1.06689 ( 36) covalent geometry : bond 0.00565 (12585) covalent geometry : angle 0.63863 (17061) *********************** 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 68 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 1.902 Fit side-chains REVERT: A 168 MET cc_start: 0.8582 (tpp) cc_final: 0.8225 (tpp) REVERT: A 462 MET cc_start: 0.8261 (mtm) cc_final: 0.7662 (mtm) outliers start: 20 outliers final: 15 residues processed: 67 average time/residue: 0.3813 time to fit residues: 36.8595 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 : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain B residue 104 ASP 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 388 THR Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 388 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 49 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 295 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 ASN ** 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** C 497 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.107003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.074015 restraints weight = 22896.273| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.98 r_work: 0.2811 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12651 Z= 0.182 Angle : 0.610 9.769 17241 Z= 0.299 Chirality : 0.045 0.274 2025 Planarity : 0.004 0.040 2154 Dihedral : 8.598 59.834 2661 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.62 % Allowed : 14.08 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1476 helix: 2.79 (0.27), residues: 351 sheet: 0.15 (0.29), residues: 321 loop : -1.21 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 421 HIS 0.006 0.001 HIS B 17 PHE 0.013 0.002 PHE B 392 TYR 0.008 0.001 TYR A 178 ARG 0.004 0.000 ARG A 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 18) link_NAG-ASN : angle 1.68679 ( 54) link_ALPHA1-6 : bond 0.00187 ( 3) link_ALPHA1-6 : angle 2.09282 ( 9) link_BETA1-4 : bond 0.00401 ( 21) link_BETA1-4 : angle 1.92729 ( 63) link_ALPHA1-3 : bond 0.01003 ( 3) link_ALPHA1-3 : angle 1.79217 ( 9) hydrogen bonds : bond 0.06385 ( 468) hydrogen bonds : angle 4.55620 ( 1395) link_BETA1-6 : bond 0.00043 ( 3) link_BETA1-6 : angle 1.47102 ( 9) SS BOND : bond 0.00271 ( 18) SS BOND : angle 0.96362 ( 36) covalent geometry : bond 0.00430 (12585) covalent geometry : angle 0.58820 (17061) *********************** 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 71 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 3.774 Fit side-chains REVERT: A 168 MET cc_start: 0.8585 (tpp) cc_final: 0.8242 (tpp) REVERT: A 462 MET cc_start: 0.8222 (mtm) cc_final: 0.7644 (mtm) REVERT: B 295 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8414 (tm130) outliers start: 21 outliers final: 17 residues processed: 69 average time/residue: 0.4080 time to fit residues: 41.2696 Evaluate side-chains 66 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 2.309 ------------------------------------------------------------------------------- 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 295 GLN 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 104 ASP 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 187 THR Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain C residue 388 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 13 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.075152 restraints weight = 23120.205| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.02 r_work: 0.2834 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3468 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= 0.112 Angle : 0.560 9.662 17241 Z= 0.272 Chirality : 0.043 0.268 2025 Planarity : 0.003 0.039 2154 Dihedral : 8.205 59.614 2661 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.08 % Allowed : 14.46 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1476 helix: 3.12 (0.26), residues: 357 sheet: 0.18 (0.29), residues: 321 loop : -1.11 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 421 HIS 0.006 0.001 HIS B 17 PHE 0.011 0.001 PHE B 294 TYR 0.007 0.001 TYR C 105 ARG 0.003 0.000 ARG A 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 18) link_NAG-ASN : angle 1.55408 ( 54) link_ALPHA1-6 : bond 0.00371 ( 3) link_ALPHA1-6 : angle 1.84176 ( 9) link_BETA1-4 : bond 0.00416 ( 21) link_BETA1-4 : angle 1.78973 ( 63) link_ALPHA1-3 : bond 0.00899 ( 3) link_ALPHA1-3 : angle 1.68759 ( 9) hydrogen bonds : bond 0.05746 ( 468) hydrogen bonds : angle 4.39530 ( 1395) link_BETA1-6 : bond 0.00224 ( 3) link_BETA1-6 : angle 1.25622 ( 9) SS BOND : bond 0.00191 ( 18) SS BOND : angle 0.88464 ( 36) covalent geometry : bond 0.00243 (12585) covalent geometry : angle 0.53988 (17061) *********************** 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 66 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 1.462 Fit side-chains REVERT: A 168 MET cc_start: 0.8547 (tpp) cc_final: 0.8216 (tpp) REVERT: A 462 MET cc_start: 0.8205 (mtm) cc_final: 0.7622 (mtm) REVERT: C 242 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8555 (p) outliers start: 14 outliers final: 12 residues processed: 64 average time/residue: 0.2838 time to fit residues: 26.6062 Evaluate side-chains 61 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 310 LYS 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 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 187 THR Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 242 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 107 optimal weight: 0.0470 chunk 62 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** 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** B 407 GLN B 454 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.105502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.072392 restraints weight = 23141.816| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.94 r_work: 0.2777 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 12651 Z= 0.335 Angle : 0.739 9.972 17241 Z= 0.366 Chirality : 0.051 0.306 2025 Planarity : 0.005 0.045 2154 Dihedral : 8.848 59.752 2661 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.16 % Allowed : 14.46 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1476 helix: 2.45 (0.27), residues: 351 sheet: -0.07 (0.28), residues: 342 loop : -1.24 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 421 HIS 0.007 0.002 HIS B 17 PHE 0.020 0.003 PHE C 392 TYR 0.012 0.002 TYR C 178 ARG 0.005 0.001 ARG A 499 Details of bonding type rmsd link_NAG-ASN : bond 0.00591 ( 18) link_NAG-ASN : angle 1.97342 ( 54) link_ALPHA1-6 : bond 0.00165 ( 3) link_ALPHA1-6 : angle 2.21392 ( 9) link_BETA1-4 : bond 0.00469 ( 21) link_BETA1-4 : angle 2.15063 ( 63) link_ALPHA1-3 : bond 0.00963 ( 3) link_ALPHA1-3 : angle 1.78079 ( 9) hydrogen bonds : bond 0.07476 ( 468) hydrogen bonds : angle 4.78438 ( 1395) link_BETA1-6 : bond 0.00200 ( 3) link_BETA1-6 : angle 1.88952 ( 9) SS BOND : bond 0.00418 ( 18) SS BOND : angle 1.11140 ( 36) covalent geometry : bond 0.00813 (12585) covalent geometry : angle 0.71626 (17061) *********************** 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 63 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 1.535 Fit side-chains REVERT: A 168 MET cc_start: 0.8600 (tpp) cc_final: 0.8247 (tpp) REVERT: A 462 MET cc_start: 0.8231 (mtm) cc_final: 0.7627 (mtm) outliers start: 15 outliers final: 12 residues processed: 61 average time/residue: 0.2972 time to fit residues: 26.2044 Evaluate side-chains 59 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 310 LYS 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 295 GLN Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 310 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 23 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 29 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.107960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.075074 restraints weight = 22759.919| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.98 r_work: 0.2831 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3559 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= 0.110 Angle : 0.566 9.650 17241 Z= 0.275 Chirality : 0.043 0.268 2025 Planarity : 0.004 0.040 2154 Dihedral : 8.109 59.657 2661 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.93 % Allowed : 14.77 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.22), residues: 1476 helix: 3.01 (0.27), residues: 351 sheet: 0.05 (0.29), residues: 324 loop : -1.11 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 421 HIS 0.007 0.001 HIS B 17 PHE 0.010 0.001 PHE B 294 TYR 0.007 0.001 TYR C 105 ARG 0.003 0.000 ARG A 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 18) link_NAG-ASN : angle 1.57741 ( 54) link_ALPHA1-6 : bond 0.00281 ( 3) link_ALPHA1-6 : angle 1.78822 ( 9) link_BETA1-4 : bond 0.00407 ( 21) link_BETA1-4 : angle 1.87049 ( 63) link_ALPHA1-3 : bond 0.00959 ( 3) link_ALPHA1-3 : angle 1.64731 ( 9) hydrogen bonds : bond 0.05850 ( 468) hydrogen bonds : angle 4.44636 ( 1395) link_BETA1-6 : bond 0.00269 ( 3) link_BETA1-6 : angle 1.23978 ( 9) SS BOND : bond 0.00187 ( 18) SS BOND : angle 0.87757 ( 36) covalent geometry : bond 0.00233 (12585) covalent geometry : angle 0.54541 (17061) ********************** 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 60 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 1.362 Fit side-chains REVERT: A 168 MET cc_start: 0.8547 (tpp) cc_final: 0.8220 (tpp) REVERT: A 462 MET cc_start: 0.8183 (mtm) cc_final: 0.7602 (mtm) REVERT: B 295 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8515 (tm130) outliers start: 12 outliers final: 9 residues processed: 58 average time/residue: 0.2901 time to fit residues: 24.3935 Evaluate side-chains 56 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain B residue 78 VAL 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 187 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 65 optimal weight: 0.0870 chunk 121 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 146 optimal weight: 8.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** B 295 GLN B 296 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.108610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.075838 restraints weight = 22742.564| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.99 r_work: 0.2850 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12651 Z= 0.102 Angle : 0.543 9.599 17241 Z= 0.262 Chirality : 0.042 0.264 2025 Planarity : 0.003 0.039 2154 Dihedral : 7.570 58.690 2661 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.93 % Allowed : 15.00 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.22), residues: 1476 helix: 3.36 (0.27), residues: 357 sheet: 0.17 (0.28), residues: 348 loop : -1.00 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 421 HIS 0.008 0.001 HIS B 17 PHE 0.012 0.001 PHE B 294 TYR 0.007 0.001 TYR C 105 ARG 0.003 0.000 ARG A 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 18) link_NAG-ASN : angle 1.50864 ( 54) link_ALPHA1-6 : bond 0.00398 ( 3) link_ALPHA1-6 : angle 1.77042 ( 9) link_BETA1-4 : bond 0.00443 ( 21) link_BETA1-4 : angle 1.76072 ( 63) link_ALPHA1-3 : bond 0.01030 ( 3) link_ALPHA1-3 : angle 1.72891 ( 9) hydrogen bonds : bond 0.05405 ( 468) hydrogen bonds : angle 4.27996 ( 1395) link_BETA1-6 : bond 0.00286 ( 3) link_BETA1-6 : angle 1.23824 ( 9) SS BOND : bond 0.00187 ( 18) SS BOND : angle 0.80349 ( 36) covalent geometry : bond 0.00216 (12585) covalent geometry : angle 0.52295 (17061) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6044.22 seconds wall clock time: 111 minutes 22.31 seconds (6682.31 seconds total)