Starting phenix.real_space_refine on Sat Aug 23 11:21:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wis_37567/08_2025/8wis_37567.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wis_37567/08_2025/8wis_37567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wis_37567/08_2025/8wis_37567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wis_37567/08_2025/8wis_37567.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wis_37567/08_2025/8wis_37567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wis_37567/08_2025/8wis_37567.map" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.144 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 54 5.16 5 C 7245 2.51 5 N 1929 2.21 5 O 2388 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11616 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3685 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3685 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3685 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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 Time building chain proxies: 2.74, per 1000 atoms: 0.24 Number of scatterers: 11616 At special positions: 0 Unit cell: (95.2, 90.95, 141.95, 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 54 16.00 O 2388 8.00 N 1929 7.00 C 7245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 87 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 75 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 75 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 495 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-2 " BMA E 5 " - " BMA E 6 " " BMA H 5 " - " BMA H 6 " " BMA K 5 " - " BMA K 6 " BETA1-3 " BMA E 4 " - " BMA E 5 " " BMA H 4 " - " BMA H 5 " " BMA K 4 " - " BMA K 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " BETA1-6 " BMA E 3 " - " BMA E 4 " " BMA H 3 " - " BMA H 4 " " BMA K 3 " - " BMA K 4 " BETA2-6 " GAL D 1 " - " SIA D 2 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL G 1 " - " SIA G 2 " " GAL J 1 " - " SIA J 2 " NAG-ASN " NAG A 601 " - " ASN A 35 " " NAG A 602 " - " ASN A 105 " " NAG A 603 " - " ASN A 203 " " NAG A 604 " - " ASN A 486 " " NAG B 601 " - " ASN B 35 " " NAG B 602 " - " ASN B 105 " " NAG B 603 " - " ASN B 203 " " NAG B 604 " - " ASN B 486 " " NAG C 601 " - " ASN C 35 " " NAG C 602 " - " ASN C 105 " " NAG C 603 " - " ASN C 203 " " NAG C 604 " - " ASN C 486 " " NAG E 1 " - " ASN A 124 " " NAG F 1 " - " ASN A 307 " " NAG H 1 " - " ASN B 124 " " NAG I 1 " - " ASN B 307 " " NAG K 1 " - " ASN C 124 " " NAG L 1 " - " ASN C 307 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 520.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2598 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 33 sheets defined 32.3% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 76 through 83 removed outlier: 3.720A pdb=" N HIS A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 removed outlier: 4.337A pdb=" N ILE A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 removed outlier: 3.507A pdb=" N LEU A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.746A pdb=" N GLY A 153 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 154 " --> pdb=" O SER A 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 154' Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.592A pdb=" N TYR A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 415 removed outlier: 4.060A pdb=" N THR A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.664A pdb=" N LEU A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 474 removed outlier: 3.514A pdb=" N GLU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 448 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.899A pdb=" N ILE A 499 " --> pdb=" O CYS A 495 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 510 removed outlier: 3.573A pdb=" N ILE A 510 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 83 removed outlier: 3.707A pdb=" N HIS B 81 " --> pdb=" O ILE B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 116 through 127 removed outlier: 4.180A pdb=" N ILE B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.703A pdb=" N GLY B 153 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B 154 " --> pdb=" O SER B 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 150 through 154' Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.666A pdb=" N TYR B 233 " --> pdb=" O PRO B 229 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 415 removed outlier: 4.066A pdb=" N THR B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.732A pdb=" N LEU B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 474 removed outlier: 3.739A pdb=" N ILE B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 501 removed outlier: 3.605A pdb=" N SER B 500 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 removed outlier: 3.826A pdb=" N ILE B 510 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 83 removed outlier: 3.522A pdb=" N HIS C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 127 removed outlier: 4.401A pdb=" N ILE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 145 removed outlier: 3.572A pdb=" N LEU C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.686A pdb=" N GLY C 153 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 154 " --> pdb=" O SER C 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 150 through 154' Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 229 through 237 removed outlier: 3.501A pdb=" N TYR C 233 " --> pdb=" O PRO C 229 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE C 235 " --> pdb=" O GLU C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 415 removed outlier: 4.194A pdb=" N THR C 388 " --> pdb=" O ASP C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 428 removed outlier: 3.610A pdb=" N LEU C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 474 removed outlier: 3.633A pdb=" N GLU C 437 " --> pdb=" O ASP C 433 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE C 448 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 474 " --> pdb=" O LYS C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 501 removed outlier: 3.500A pdb=" N ILE C 499 " --> pdb=" O CYS C 495 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER C 500 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG C 501 " --> pdb=" O ASN C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 510 removed outlier: 3.547A pdb=" N TYR C 509 " --> pdb=" O ARG C 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.027A pdb=" N ILE A 362 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS A 29 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.027A pdb=" N ILE A 362 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS A 29 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 39 Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 62 removed outlier: 5.725A pdb=" N ILE A 61 " --> pdb=" O ASP A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 68 through 71 Processing sheet with id=AA7, first strand: chain 'A' and resid 112 through 115 removed outlier: 6.649A pdb=" N ASN A 112 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU A 251 " --> pdb=" O ASN A 112 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TYR A 114 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N SER A 253 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 112 through 115 removed outlier: 6.649A pdb=" N ASN A 112 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU A 251 " --> pdb=" O ASN A 112 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TYR A 114 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N SER A 253 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 182 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 171 through 176 removed outlier: 4.048A pdb=" N ARG A 211 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 303 through 305 removed outlier: 3.869A pdb=" N GLY A 303 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N CYS A 298 " --> pdb=" O PHE A 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 312 through 313 removed outlier: 5.810A pdb=" N ILE A 312 " --> pdb=" O ILE A 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.875A pdb=" N ILE B 362 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS B 29 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.875A pdb=" N ILE B 362 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS B 29 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 36 through 39 Processing sheet with id=AB6, first strand: chain 'B' and resid 50 through 52 Processing sheet with id=AB7, first strand: chain 'B' and resid 61 through 62 removed outlier: 5.634A pdb=" N ILE B 61 " --> pdb=" O ASP B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AB9, first strand: chain 'B' and resid 112 through 115 removed outlier: 6.584A pdb=" N ASN B 112 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LEU B 251 " --> pdb=" O ASN B 112 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR B 114 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N SER B 253 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AC2, first strand: chain 'B' and resid 171 through 176 removed outlier: 4.095A pdb=" N ARG B 211 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 298 through 299 removed outlier: 4.663A pdb=" N CYS B 298 " --> pdb=" O PHE B 305 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 312 through 313 removed outlier: 5.767A pdb=" N ILE B 312 " --> pdb=" O ILE B 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.996A pdb=" N ILE C 362 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS C 29 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.996A pdb=" N ILE C 362 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS C 29 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 36 through 39 Processing sheet with id=AC8, first strand: chain 'C' and resid 50 through 52 Processing sheet with id=AC9, first strand: chain 'C' and resid 61 through 62 removed outlier: 5.751A pdb=" N ILE C 61 " --> pdb=" O ASP C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AD2, first strand: chain 'C' and resid 112 through 115 removed outlier: 6.655A pdb=" N ASN C 112 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU C 251 " --> pdb=" O ASN C 112 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR C 114 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N SER C 253 " --> pdb=" O TYR C 114 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 112 through 115 removed outlier: 6.655A pdb=" N ASN C 112 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU C 251 " --> pdb=" O ASN C 112 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR C 114 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N SER C 253 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR C 182 " --> pdb=" O PHE C 277 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 171 through 176 removed outlier: 4.178A pdb=" N ARG C 211 " --> pdb=" O SER C 265 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 303 through 305 removed outlier: 4.590A pdb=" N CYS C 298 " --> pdb=" O PHE C 305 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 312 through 313 removed outlier: 5.786A pdb=" N ILE C 312 " --> pdb=" O ILE C 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 450 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3727 1.34 - 1.46: 2733 1.46 - 1.58: 5294 1.58 - 1.69: 6 1.69 - 1.81: 72 Bond restraints: 11832 Sorted by residual: bond pdb=" C1 BMA K 5 " pdb=" C2 BMA K 5 " ideal model delta sigma weight residual 1.519 1.588 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 BMA H 5 " pdb=" C2 BMA H 5 " ideal model delta sigma weight residual 1.519 1.583 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C2 BMA E 5 " pdb=" O2 BMA E 5 " ideal model delta sigma weight residual 1.402 1.464 -0.062 2.00e-02 2.50e+03 9.69e+00 bond pdb=" C2 BMA H 5 " pdb=" O2 BMA H 5 " ideal model delta sigma weight residual 1.402 1.463 -0.061 2.00e-02 2.50e+03 9.33e+00 bond pdb=" C1 BMA E 5 " pdb=" C2 BMA E 5 " ideal model delta sigma weight residual 1.519 1.580 -0.061 2.00e-02 2.50e+03 9.18e+00 ... (remaining 11827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 15353 1.43 - 2.87: 502 2.87 - 4.30: 110 4.30 - 5.73: 31 5.73 - 7.17: 24 Bond angle restraints: 16020 Sorted by residual: angle pdb=" C1 BMA K 5 " pdb=" C2 BMA K 5 " pdb=" O2 BMA K 5 " ideal model delta sigma weight residual 108.40 115.57 -7.17 3.00e+00 1.11e-01 5.71e+00 angle pdb=" N GLU C 142 " pdb=" CA GLU C 142 " pdb=" CB GLU C 142 " ideal model delta sigma weight residual 110.16 113.68 -3.52 1.48e+00 4.57e-01 5.67e+00 angle pdb=" N GLY C 186 " pdb=" CA GLY C 186 " pdb=" C GLY C 186 " ideal model delta sigma weight residual 110.20 113.28 -3.08 1.32e+00 5.74e-01 5.45e+00 angle pdb=" C ASN B 112 " pdb=" N PHE B 113 " pdb=" CA PHE B 113 " ideal model delta sigma weight residual 122.62 119.01 3.61 1.56e+00 4.11e-01 5.36e+00 angle pdb=" C1 BMA K 4 " pdb=" O5 BMA K 4 " pdb=" C5 BMA K 4 " ideal model delta sigma weight residual 118.82 111.90 6.92 3.00e+00 1.11e-01 5.32e+00 ... (remaining 16015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 6979 22.41 - 44.83: 447 44.83 - 67.24: 48 67.24 - 89.65: 89 89.65 - 112.06: 45 Dihedral angle restraints: 7608 sinusoidal: 3528 harmonic: 4080 Sorted by residual: dihedral pdb=" O4 BMA K 5 " pdb=" C4 BMA K 5 " pdb=" C5 BMA K 5 " pdb=" O5 BMA K 5 " ideal model delta sinusoidal sigma weight residual 288.71 176.65 112.06 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" O4 BMA H 5 " pdb=" C4 BMA H 5 " pdb=" C5 BMA H 5 " pdb=" O5 BMA H 5 " ideal model delta sinusoidal sigma weight residual 288.71 177.36 111.35 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C3 BMA K 5 " pdb=" C4 BMA K 5 " pdb=" C5 BMA K 5 " pdb=" O5 BMA K 5 " ideal model delta sinusoidal sigma weight residual 47.62 -63.05 110.67 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 7605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1635 0.066 - 0.132: 249 0.132 - 0.199: 13 0.199 - 0.265: 9 0.265 - 0.331: 8 Chirality restraints: 1914 Sorted by residual: chirality pdb=" C2 SIA G 2 " pdb=" O6 GAL G 1 " pdb=" C1 SIA G 2 " pdb=" O6 SIA G 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.61 0.11 2.00e-02 2.50e+03 3.05e+01 chirality pdb=" C2 SIA J 2 " pdb=" O6 GAL J 1 " pdb=" C1 SIA J 2 " pdb=" O6 SIA J 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.59 0.09 2.00e-02 2.50e+03 1.92e+01 chirality pdb=" C2 SIA D 2 " pdb=" O6 GAL D 1 " pdb=" C1 SIA D 2 " pdb=" O6 SIA D 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.58 0.08 2.00e-02 2.50e+03 1.60e+01 ... (remaining 1911 not shown) Planarity restraints: 2025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 324 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO C 325 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 325 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 325 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 324 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 325 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 325 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 325 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 138 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C ASP C 138 " -0.024 2.00e-02 2.50e+03 pdb=" O ASP C 138 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN C 139 " 0.008 2.00e-02 2.50e+03 ... (remaining 2022 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1848 2.76 - 3.30: 10610 3.30 - 3.83: 18498 3.83 - 4.37: 21021 4.37 - 4.90: 37913 Nonbonded interactions: 89890 Sorted by model distance: nonbonded pdb=" OE1 GLN C 84 " pdb=" OG1 THR C 109 " model vdw 2.228 3.040 nonbonded pdb=" OD1 ASP A 209 " pdb=" OG SER A 221 " model vdw 2.251 3.040 nonbonded pdb=" OE1 GLN B 84 " pdb=" OG1 THR B 109 " model vdw 2.268 3.040 nonbonded pdb=" O GLN B 408 " pdb=" NE2 GLN B 412 " model vdw 2.282 3.120 nonbonded pdb=" OG1 THR C 126 " pdb=" OH TYR C 184 " model vdw 2.301 3.040 ... (remaining 89885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.750 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 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 : 0.004 0.069 11886 Z= 0.204 Angle : 0.713 21.770 16167 Z= 0.323 Chirality : 0.051 0.331 1914 Planarity : 0.003 0.048 2007 Dihedral : 19.080 112.065 4965 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.22), residues: 1425 helix: 2.61 (0.28), residues: 399 sheet: -0.78 (0.33), residues: 234 loop : -1.54 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 501 TYR 0.014 0.001 TYR B 410 PHE 0.012 0.001 PHE A 282 TRP 0.014 0.001 TRP A 208 HIS 0.003 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00423 (11832) covalent geometry : angle 0.67172 (16020) SS BOND : bond 0.00198 ( 15) SS BOND : angle 0.83770 ( 30) hydrogen bonds : bond 0.13277 ( 434) hydrogen bonds : angle 6.01581 ( 1263) glycosidic custom : bond 0.00106 ( 3) glycosidic custom : angle 7.33991 ( 9) link_BETA1-2 : bond 0.00584 ( 3) link_BETA1-2 : angle 4.45595 ( 9) link_BETA1-3 : bond 0.00691 ( 3) link_BETA1-3 : angle 3.33233 ( 9) link_BETA1-4 : bond 0.00452 ( 9) link_BETA1-4 : angle 1.49587 ( 27) link_BETA1-6 : bond 0.01582 ( 3) link_BETA1-6 : angle 1.01514 ( 9) link_NAG-ASN : bond 0.00328 ( 18) link_NAG-ASN : angle 1.55872 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.7811 (ptt) cc_final: 0.7466 (ptm) REVERT: A 64 LYS cc_start: 0.7195 (tttp) cc_final: 0.6857 (tttt) REVERT: A 114 TYR cc_start: 0.7080 (t80) cc_final: 0.6770 (t80) REVERT: A 146 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6627 (tt0) REVERT: A 157 LYS cc_start: 0.7682 (mtmm) cc_final: 0.7251 (mtmt) REVERT: A 204 VAL cc_start: 0.6202 (m) cc_final: 0.5904 (t) REVERT: A 260 GLU cc_start: 0.6830 (mp0) cc_final: 0.6400 (mp0) REVERT: A 263 SER cc_start: 0.6793 (p) cc_final: 0.6356 (t) REVERT: A 289 GLN cc_start: 0.6981 (tt0) cc_final: 0.6686 (tt0) REVERT: A 291 ASP cc_start: 0.6592 (t0) cc_final: 0.6270 (OUTLIER) REVERT: A 404 GLU cc_start: 0.5577 (tp30) cc_final: 0.5319 (tp30) REVERT: A 419 THR cc_start: 0.6003 (m) cc_final: 0.5316 (p) REVERT: A 423 LEU cc_start: 0.4778 (mp) cc_final: 0.4538 (mp) REVERT: A 430 GLU cc_start: 0.5729 (tp30) cc_final: 0.5436 (tt0) REVERT: A 467 GLU cc_start: 0.4873 (tm-30) cc_final: 0.4574 (tt0) REVERT: B 46 LYS cc_start: 0.7153 (mtmt) cc_final: 0.6543 (mttm) REVERT: B 59 GLN cc_start: 0.7178 (mm110) cc_final: 0.6911 (mm-40) REVERT: B 60 LYS cc_start: 0.6323 (pttm) cc_final: 0.5952 (pttp) REVERT: B 104 MET cc_start: 0.7523 (tpp) cc_final: 0.7188 (tpp) REVERT: B 174 GLU cc_start: 0.6667 (mm-30) cc_final: 0.6158 (mt-10) REVERT: B 175 LYS cc_start: 0.5827 (tttp) cc_final: 0.5350 (ttpp) REVERT: B 203 ASN cc_start: 0.6402 (m-40) cc_final: 0.5992 (m-40) REVERT: B 211 ARG cc_start: 0.7092 (mtt180) cc_final: 0.6817 (mtt-85) REVERT: B 215 SER cc_start: 0.6718 (t) cc_final: 0.6377 (p) REVERT: B 218 SER cc_start: 0.7155 (m) cc_final: 0.6746 (t) REVERT: B 260 GLU cc_start: 0.5820 (mp0) cc_final: 0.4241 (pp20) REVERT: B 264 ILE cc_start: 0.6428 (mt) cc_final: 0.6227 (mt) REVERT: B 265 SER cc_start: 0.8022 (t) cc_final: 0.7819 (m) REVERT: B 408 GLN cc_start: 0.4496 (tt0) cc_final: 0.3715 (tp40) REVERT: C 91 PHE cc_start: 0.7096 (m-80) cc_final: 0.6279 (m-80) REVERT: C 94 ASN cc_start: 0.8016 (m-40) cc_final: 0.7811 (m-40) REVERT: C 132 GLU cc_start: 0.6533 (tt0) cc_final: 0.6277 (tt0) REVERT: C 155 THR cc_start: 0.7241 (m) cc_final: 0.7015 (p) REVERT: C 206 GLU cc_start: 0.5991 (mt-10) cc_final: 0.5452 (tt0) REVERT: C 291 ASP cc_start: 0.6835 (t0) cc_final: 0.6510 (t70) REVERT: C 401 GLU cc_start: 0.6224 (mt-10) cc_final: 0.5822 (mt-10) REVERT: C 422 GLU cc_start: 0.6516 (pt0) cc_final: 0.6093 (pp20) REVERT: C 430 GLU cc_start: 0.5942 (tt0) cc_final: 0.5278 (tp30) REVERT: C 464 LYS cc_start: 0.5609 (ttmm) cc_final: 0.5297 (mmtm) REVERT: C 467 GLU cc_start: 0.4783 (tm-30) cc_final: 0.4524 (tt0) REVERT: C 468 GLU cc_start: 0.5860 (tt0) cc_final: 0.5220 (mm-30) outliers start: 0 outliers final: 3 residues processed: 191 average time/residue: 0.5065 time to fit residues: 105.5529 Evaluate side-chains 120 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain C residue 243 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.0370 chunk 55 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 84 GLN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN B 412 GLN ** B 476 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 = 0.3864 r_free = 0.3864 target = 0.165358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.124980 restraints weight = 11954.158| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.84 r_work: 0.3156 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11886 Z= 0.124 Angle : 0.629 10.786 16167 Z= 0.293 Chirality : 0.050 0.454 1914 Planarity : 0.003 0.035 2007 Dihedral : 14.215 84.878 2425 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.90 % Allowed : 8.35 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.22), residues: 1425 helix: 2.63 (0.27), residues: 396 sheet: -0.62 (0.33), residues: 237 loop : -1.57 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.012 0.001 TYR A 184 PHE 0.015 0.001 PHE A 282 TRP 0.014 0.001 TRP A 208 HIS 0.004 0.001 HIS C 375 Details of bonding type rmsd covalent geometry : bond 0.00269 (11832) covalent geometry : angle 0.57677 (16020) SS BOND : bond 0.00202 ( 15) SS BOND : angle 0.77367 ( 30) hydrogen bonds : bond 0.03871 ( 434) hydrogen bonds : angle 4.54381 ( 1263) glycosidic custom : bond 0.00099 ( 3) glycosidic custom : angle 0.64331 ( 9) link_BETA1-2 : bond 0.00731 ( 3) link_BETA1-2 : angle 6.99903 ( 9) link_BETA1-3 : bond 0.00420 ( 3) link_BETA1-3 : angle 5.87847 ( 9) link_BETA1-4 : bond 0.00516 ( 9) link_BETA1-4 : angle 2.13657 ( 27) link_BETA1-6 : bond 0.00649 ( 3) link_BETA1-6 : angle 1.65279 ( 9) link_NAG-ASN : bond 0.00606 ( 18) link_NAG-ASN : angle 1.65091 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.7928 (m-30) cc_final: 0.7696 (m-30) REVERT: A 157 LYS cc_start: 0.8270 (mtmm) cc_final: 0.8068 (mtmt) REVERT: A 423 LEU cc_start: 0.6939 (mp) cc_final: 0.6678 (mp) REVERT: A 467 GLU cc_start: 0.6279 (tm-30) cc_final: 0.5847 (tt0) REVERT: B 46 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7946 (mttm) REVERT: B 175 LYS cc_start: 0.7726 (tttp) cc_final: 0.7509 (ttpp) REVERT: B 203 ASN cc_start: 0.7768 (m-40) cc_final: 0.7423 (m-40) REVERT: B 230 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6371 (ttm) REVERT: B 260 GLU cc_start: 0.6621 (mp0) cc_final: 0.5923 (pp20) REVERT: B 408 GLN cc_start: 0.7293 (tt0) cc_final: 0.6380 (tp40) REVERT: C 91 PHE cc_start: 0.8060 (m-80) cc_final: 0.7831 (m-80) REVERT: C 329 ARG cc_start: 0.7453 (ptp90) cc_final: 0.7232 (mtm-85) REVERT: C 401 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7722 (mt-10) REVERT: C 405 ASN cc_start: 0.7327 (m-40) cc_final: 0.6998 (m-40) REVERT: C 430 GLU cc_start: 0.7016 (tt0) cc_final: 0.6759 (tp30) REVERT: C 464 LYS cc_start: 0.7269 (ttmm) cc_final: 0.6902 (mmtm) REVERT: C 467 GLU cc_start: 0.6075 (tm-30) cc_final: 0.5686 (tt0) REVERT: C 468 GLU cc_start: 0.7180 (tt0) cc_final: 0.6358 (mm-30) outliers start: 23 outliers final: 15 residues processed: 136 average time/residue: 0.4654 time to fit residues: 69.5125 Evaluate side-chains 109 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 230 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 476 ASN A 512 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.157725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.116732 restraints weight = 12186.441| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.83 r_work: 0.3069 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11886 Z= 0.214 Angle : 0.714 10.536 16167 Z= 0.346 Chirality : 0.056 0.481 1914 Planarity : 0.005 0.038 2007 Dihedral : 13.451 87.261 2421 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.05 % Allowed : 10.92 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.21), residues: 1425 helix: 2.06 (0.27), residues: 396 sheet: -1.11 (0.30), residues: 264 loop : -1.67 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 211 TYR 0.023 0.003 TYR B 410 PHE 0.023 0.002 PHE C 282 TRP 0.024 0.002 TRP A 208 HIS 0.007 0.001 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00539 (11832) covalent geometry : angle 0.67033 (16020) SS BOND : bond 0.00343 ( 15) SS BOND : angle 1.04564 ( 30) hydrogen bonds : bond 0.05416 ( 434) hydrogen bonds : angle 4.72446 ( 1263) glycosidic custom : bond 0.00454 ( 3) glycosidic custom : angle 0.91573 ( 9) link_BETA1-2 : bond 0.00727 ( 3) link_BETA1-2 : angle 6.32343 ( 9) link_BETA1-3 : bond 0.00106 ( 3) link_BETA1-3 : angle 4.74918 ( 9) link_BETA1-4 : bond 0.00633 ( 9) link_BETA1-4 : angle 2.47300 ( 27) link_BETA1-6 : bond 0.00833 ( 3) link_BETA1-6 : angle 2.06584 ( 9) link_NAG-ASN : bond 0.00826 ( 18) link_NAG-ASN : angle 2.12871 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 109 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6110 (tm-30) REVERT: A 291 ASP cc_start: 0.7717 (t70) cc_final: 0.7206 (t0) REVERT: A 423 LEU cc_start: 0.7080 (mp) cc_final: 0.6763 (mp) REVERT: B 46 LYS cc_start: 0.8392 (mtmt) cc_final: 0.8155 (mtmm) REVERT: B 142 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7859 (pt0) REVERT: B 203 ASN cc_start: 0.7843 (m-40) cc_final: 0.7350 (m-40) REVERT: B 230 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.6442 (ttm) REVERT: B 232 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6960 (pt0) REVERT: B 448 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7036 (mt) REVERT: C 91 PHE cc_start: 0.8091 (m-80) cc_final: 0.7766 (m-80) REVERT: C 260 GLU cc_start: 0.7689 (mp0) cc_final: 0.6338 (mm-30) REVERT: C 430 GLU cc_start: 0.7116 (tt0) cc_final: 0.6892 (tp30) REVERT: C 464 LYS cc_start: 0.7183 (ttmm) cc_final: 0.6788 (mmtm) REVERT: C 467 GLU cc_start: 0.5965 (tm-30) cc_final: 0.5592 (tt0) REVERT: C 468 GLU cc_start: 0.7111 (tt0) cc_final: 0.6251 (mm-30) outliers start: 49 outliers final: 24 residues processed: 143 average time/residue: 0.4349 time to fit residues: 69.4041 Evaluate side-chains 126 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 300 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.149533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.107325 restraints weight = 12416.684| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.87 r_work: 0.3062 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11886 Z= 0.157 Angle : 0.636 11.051 16167 Z= 0.304 Chirality : 0.053 0.496 1914 Planarity : 0.004 0.038 2007 Dihedral : 11.808 86.916 2421 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.39 % Allowed : 14.64 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.21), residues: 1425 helix: 2.20 (0.27), residues: 396 sheet: -0.85 (0.31), residues: 240 loop : -1.66 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 409 TYR 0.015 0.002 TYR C 414 PHE 0.020 0.002 PHE A 282 TRP 0.014 0.002 TRP A 208 HIS 0.005 0.001 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00379 (11832) covalent geometry : angle 0.58224 (16020) SS BOND : bond 0.00283 ( 15) SS BOND : angle 0.91043 ( 30) hydrogen bonds : bond 0.04591 ( 434) hydrogen bonds : angle 4.47060 ( 1263) glycosidic custom : bond 0.00267 ( 3) glycosidic custom : angle 0.57741 ( 9) link_BETA1-2 : bond 0.00692 ( 3) link_BETA1-2 : angle 6.72957 ( 9) link_BETA1-3 : bond 0.00179 ( 3) link_BETA1-3 : angle 5.47752 ( 9) link_BETA1-4 : bond 0.00552 ( 9) link_BETA1-4 : angle 2.31488 ( 27) link_BETA1-6 : bond 0.00708 ( 3) link_BETA1-6 : angle 1.78965 ( 9) link_NAG-ASN : bond 0.00589 ( 18) link_NAG-ASN : angle 2.05029 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLU cc_start: 0.7923 (mp0) cc_final: 0.7624 (mp0) REVERT: A 291 ASP cc_start: 0.7779 (t70) cc_final: 0.7414 (t0) REVERT: A 423 LEU cc_start: 0.7108 (mp) cc_final: 0.6682 (mp) REVERT: A 457 GLU cc_start: 0.6842 (tp30) cc_final: 0.6513 (mm-30) REVERT: B 46 LYS cc_start: 0.8433 (mtmt) cc_final: 0.8188 (mtmm) REVERT: B 142 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7850 (pt0) REVERT: B 157 LYS cc_start: 0.8177 (mtmm) cc_final: 0.7566 (mttm) REVERT: B 203 ASN cc_start: 0.7798 (m-40) cc_final: 0.7292 (m-40) REVERT: B 230 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6445 (ttm) REVERT: B 260 GLU cc_start: 0.7177 (mp0) cc_final: 0.6727 (mt-10) REVERT: C 91 PHE cc_start: 0.8041 (m-80) cc_final: 0.7759 (m-80) REVERT: C 93 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8074 (tt) REVERT: C 260 GLU cc_start: 0.7762 (mp0) cc_final: 0.6182 (mm-30) REVERT: C 416 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6766 (tt) REVERT: C 430 GLU cc_start: 0.7101 (tt0) cc_final: 0.6875 (tp30) REVERT: C 464 LYS cc_start: 0.7056 (ttmm) cc_final: 0.6684 (mmtm) REVERT: C 467 GLU cc_start: 0.6017 (tm-30) cc_final: 0.5626 (tt0) REVERT: C 468 GLU cc_start: 0.7009 (tt0) cc_final: 0.6208 (mm-30) outliers start: 41 outliers final: 24 residues processed: 136 average time/residue: 0.4113 time to fit residues: 62.5682 Evaluate side-chains 128 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 416 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 137 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.147394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.104841 restraints weight = 12284.815| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.88 r_work: 0.3024 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11886 Z= 0.200 Angle : 0.689 11.285 16167 Z= 0.330 Chirality : 0.055 0.513 1914 Planarity : 0.004 0.038 2007 Dihedral : 12.035 86.177 2421 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.47 % Allowed : 14.89 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.21), residues: 1425 helix: 2.01 (0.27), residues: 396 sheet: -0.96 (0.31), residues: 240 loop : -1.75 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.020 0.002 TYR A 410 PHE 0.019 0.002 PHE C 282 TRP 0.017 0.002 TRP A 208 HIS 0.007 0.001 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00502 (11832) covalent geometry : angle 0.63834 (16020) SS BOND : bond 0.00362 ( 15) SS BOND : angle 0.73699 ( 30) hydrogen bonds : bond 0.05219 ( 434) hydrogen bonds : angle 4.55842 ( 1263) glycosidic custom : bond 0.00197 ( 3) glycosidic custom : angle 0.69233 ( 9) link_BETA1-2 : bond 0.00663 ( 3) link_BETA1-2 : angle 6.70524 ( 9) link_BETA1-3 : bond 0.00254 ( 3) link_BETA1-3 : angle 5.13197 ( 9) link_BETA1-4 : bond 0.00569 ( 9) link_BETA1-4 : angle 2.57943 ( 27) link_BETA1-6 : bond 0.00687 ( 3) link_BETA1-6 : angle 2.06863 ( 9) link_NAG-ASN : bond 0.00553 ( 18) link_NAG-ASN : angle 2.21013 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 102 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6265 (tm-30) REVERT: A 260 GLU cc_start: 0.8022 (mp0) cc_final: 0.7690 (mp0) REVERT: A 291 ASP cc_start: 0.7758 (t70) cc_final: 0.7354 (t0) REVERT: A 423 LEU cc_start: 0.7058 (mp) cc_final: 0.6732 (mt) REVERT: A 457 GLU cc_start: 0.6879 (tp30) cc_final: 0.6503 (mm-30) REVERT: B 46 LYS cc_start: 0.8457 (mtmt) cc_final: 0.8205 (mtmm) REVERT: B 142 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7864 (pt0) REVERT: B 157 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7532 (mttm) REVERT: B 230 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.6398 (ttm) REVERT: B 232 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6975 (pt0) REVERT: B 448 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7130 (mt) REVERT: C 91 PHE cc_start: 0.8071 (m-80) cc_final: 0.7780 (m-80) REVERT: C 93 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8013 (tt) REVERT: C 416 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6890 (tt) REVERT: C 430 GLU cc_start: 0.7124 (tt0) cc_final: 0.6897 (tp30) REVERT: C 464 LYS cc_start: 0.6976 (ttmm) cc_final: 0.6596 (mmtm) REVERT: C 467 GLU cc_start: 0.5993 (tm-30) cc_final: 0.5591 (tt0) REVERT: C 468 GLU cc_start: 0.6906 (tt0) cc_final: 0.6071 (mm-30) outliers start: 54 outliers final: 31 residues processed: 141 average time/residue: 0.4317 time to fit residues: 68.1655 Evaluate side-chains 140 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 416 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 7 optimal weight: 4.9990 chunk 61 optimal weight: 0.0970 chunk 136 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN B 112 ASN B 247 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.148574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.108673 restraints weight = 12328.793| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.86 r_work: 0.3103 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11886 Z= 0.120 Angle : 0.602 11.465 16167 Z= 0.287 Chirality : 0.051 0.515 1914 Planarity : 0.004 0.040 2007 Dihedral : 11.142 85.927 2421 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.39 % Allowed : 16.71 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.22), residues: 1425 helix: 2.31 (0.27), residues: 396 sheet: -0.96 (0.30), residues: 270 loop : -1.59 (0.19), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 246 TYR 0.011 0.001 TYR C 414 PHE 0.013 0.001 PHE A 282 TRP 0.013 0.001 TRP A 208 HIS 0.003 0.001 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00279 (11832) covalent geometry : angle 0.54773 (16020) SS BOND : bond 0.00201 ( 15) SS BOND : angle 0.53992 ( 30) hydrogen bonds : bond 0.04271 ( 434) hydrogen bonds : angle 4.34069 ( 1263) glycosidic custom : bond 0.00167 ( 3) glycosidic custom : angle 0.55488 ( 9) link_BETA1-2 : bond 0.00779 ( 3) link_BETA1-2 : angle 6.92834 ( 9) link_BETA1-3 : bond 0.00150 ( 3) link_BETA1-3 : angle 5.24651 ( 9) link_BETA1-4 : bond 0.00591 ( 9) link_BETA1-4 : angle 2.13262 ( 27) link_BETA1-6 : bond 0.00883 ( 3) link_BETA1-6 : angle 1.48192 ( 9) link_NAG-ASN : bond 0.00593 ( 18) link_NAG-ASN : angle 2.05758 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6321 (tm-30) REVERT: A 227 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: A 260 GLU cc_start: 0.7941 (mp0) cc_final: 0.7627 (mp0) REVERT: A 291 ASP cc_start: 0.7779 (t70) cc_final: 0.7420 (t0) REVERT: A 423 LEU cc_start: 0.7036 (mp) cc_final: 0.6708 (mt) REVERT: A 457 GLU cc_start: 0.6904 (tp30) cc_final: 0.6549 (mm-30) REVERT: B 46 LYS cc_start: 0.8448 (mtmt) cc_final: 0.8240 (mtmm) REVERT: B 142 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: B 230 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.6393 (ttm) REVERT: B 232 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6813 (pt0) REVERT: B 242 VAL cc_start: 0.7632 (OUTLIER) cc_final: 0.7409 (m) REVERT: C 93 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8048 (tt) REVERT: C 416 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6865 (tt) REVERT: C 464 LYS cc_start: 0.6982 (ttmm) cc_final: 0.6652 (mmtm) REVERT: C 467 GLU cc_start: 0.6060 (tm-30) cc_final: 0.5625 (tt0) outliers start: 41 outliers final: 22 residues processed: 129 average time/residue: 0.4136 time to fit residues: 59.5586 Evaluate side-chains 125 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 416 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 65 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 114 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 137 optimal weight: 0.0670 chunk 120 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 123 optimal weight: 0.0170 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 497 ASN B 112 ASN ** B 476 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 = 0.3825 r_free = 0.3825 target = 0.161272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124472 restraints weight = 12151.616| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.76 r_work: 0.3157 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11886 Z= 0.094 Angle : 0.551 11.554 16167 Z= 0.260 Chirality : 0.050 0.516 1914 Planarity : 0.003 0.040 2007 Dihedral : 9.725 91.459 2421 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.73 % Allowed : 17.54 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.22), residues: 1425 helix: 2.70 (0.28), residues: 396 sheet: -0.89 (0.29), residues: 282 loop : -1.47 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 246 TYR 0.011 0.001 TYR C 504 PHE 0.011 0.001 PHE A 262 TRP 0.009 0.001 TRP B 127 HIS 0.004 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00202 (11832) covalent geometry : angle 0.49273 (16020) SS BOND : bond 0.00119 ( 15) SS BOND : angle 0.44706 ( 30) hydrogen bonds : bond 0.03352 ( 434) hydrogen bonds : angle 4.11607 ( 1263) glycosidic custom : bond 0.00108 ( 3) glycosidic custom : angle 0.55065 ( 9) link_BETA1-2 : bond 0.00846 ( 3) link_BETA1-2 : angle 7.25025 ( 9) link_BETA1-3 : bond 0.00218 ( 3) link_BETA1-3 : angle 5.12692 ( 9) link_BETA1-4 : bond 0.00575 ( 9) link_BETA1-4 : angle 1.68391 ( 27) link_BETA1-6 : bond 0.01078 ( 3) link_BETA1-6 : angle 0.99818 ( 9) link_NAG-ASN : bond 0.00560 ( 18) link_NAG-ASN : angle 1.97533 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7248 (mt-10) REVERT: A 227 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7666 (mp10) REVERT: A 260 GLU cc_start: 0.7799 (mp0) cc_final: 0.7580 (mp0) REVERT: A 291 ASP cc_start: 0.7796 (t70) cc_final: 0.7482 (t0) REVERT: A 423 LEU cc_start: 0.7050 (mp) cc_final: 0.6702 (mp) REVERT: A 457 GLU cc_start: 0.6918 (tp30) cc_final: 0.6557 (mm-30) REVERT: A 467 GLU cc_start: 0.6187 (tm-30) cc_final: 0.5492 (mm-30) REVERT: B 142 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7891 (pt0) REVERT: B 230 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6315 (ttm) REVERT: B 242 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7472 (m) REVERT: B 260 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6066 (pp20) REVERT: B 408 GLN cc_start: 0.7486 (tt0) cc_final: 0.6552 (tp40) REVERT: C 416 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6929 (tt) REVERT: C 464 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6553 (mmtm) REVERT: C 467 GLU cc_start: 0.6067 (tm-30) cc_final: 0.5610 (tt0) outliers start: 33 outliers final: 18 residues processed: 127 average time/residue: 0.4088 time to fit residues: 58.2318 Evaluate side-chains 121 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 416 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 89 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS A 497 ASN B 247 ASN ** B 476 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 = 0.3767 r_free = 0.3767 target = 0.155438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.115184 restraints weight = 12257.847| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.76 r_work: 0.3040 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11886 Z= 0.246 Angle : 0.761 11.327 16167 Z= 0.368 Chirality : 0.058 0.527 1914 Planarity : 0.005 0.045 2007 Dihedral : 11.278 90.934 2421 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.31 % Allowed : 17.62 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.21), residues: 1425 helix: 1.98 (0.27), residues: 396 sheet: -1.06 (0.31), residues: 252 loop : -1.72 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 211 TYR 0.025 0.003 TYR A 410 PHE 0.022 0.003 PHE C 282 TRP 0.024 0.002 TRP A 208 HIS 0.008 0.002 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00623 (11832) covalent geometry : angle 0.71413 (16020) SS BOND : bond 0.00448 ( 15) SS BOND : angle 0.79842 ( 30) hydrogen bonds : bond 0.05663 ( 434) hydrogen bonds : angle 4.61870 ( 1263) glycosidic custom : bond 0.00326 ( 3) glycosidic custom : angle 0.76945 ( 9) link_BETA1-2 : bond 0.00680 ( 3) link_BETA1-2 : angle 6.89160 ( 9) link_BETA1-3 : bond 0.00341 ( 3) link_BETA1-3 : angle 4.81103 ( 9) link_BETA1-4 : bond 0.00597 ( 9) link_BETA1-4 : angle 2.87952 ( 27) link_BETA1-6 : bond 0.00790 ( 3) link_BETA1-6 : angle 2.13448 ( 9) link_NAG-ASN : bond 0.00528 ( 18) link_NAG-ASN : angle 2.22212 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 103 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.7806 (mp10) REVERT: A 291 ASP cc_start: 0.7827 (t70) cc_final: 0.7402 (t0) REVERT: A 423 LEU cc_start: 0.7168 (mp) cc_final: 0.6829 (mp) REVERT: A 457 GLU cc_start: 0.6941 (tp30) cc_final: 0.6547 (mm-30) REVERT: B 230 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6607 (ttm) REVERT: C 93 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8135 (tt) REVERT: C 294 CYS cc_start: 0.8150 (p) cc_final: 0.7786 (p) REVERT: C 464 LYS cc_start: 0.6974 (ttmm) cc_final: 0.6610 (mmtm) REVERT: C 467 GLU cc_start: 0.6099 (tm-30) cc_final: 0.5652 (tt0) outliers start: 40 outliers final: 26 residues processed: 130 average time/residue: 0.3544 time to fit residues: 52.0063 Evaluate side-chains 130 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 312 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 125 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 497 ASN B 112 ASN ** B 476 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 = 0.3800 r_free = 0.3800 target = 0.158639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.118814 restraints weight = 12077.897| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.75 r_work: 0.3064 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11886 Z= 0.118 Angle : 0.606 11.663 16167 Z= 0.290 Chirality : 0.051 0.530 1914 Planarity : 0.004 0.039 2007 Dihedral : 10.207 94.410 2421 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.56 % Allowed : 18.69 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.22), residues: 1425 helix: 2.38 (0.27), residues: 396 sheet: -1.10 (0.29), residues: 282 loop : -1.57 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 418 TYR 0.012 0.001 TYR A 184 PHE 0.016 0.002 PHE C 311 TRP 0.014 0.001 TRP A 208 HIS 0.004 0.001 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00268 (11832) covalent geometry : angle 0.55116 (16020) SS BOND : bond 0.00174 ( 15) SS BOND : angle 0.49697 ( 30) hydrogen bonds : bond 0.04109 ( 434) hydrogen bonds : angle 4.28055 ( 1263) glycosidic custom : bond 0.00095 ( 3) glycosidic custom : angle 0.56039 ( 9) link_BETA1-2 : bond 0.00814 ( 3) link_BETA1-2 : angle 7.19256 ( 9) link_BETA1-3 : bond 0.00150 ( 3) link_BETA1-3 : angle 5.04342 ( 9) link_BETA1-4 : bond 0.00635 ( 9) link_BETA1-4 : angle 2.11062 ( 27) link_BETA1-6 : bond 0.01036 ( 3) link_BETA1-6 : angle 1.27923 ( 9) link_NAG-ASN : bond 0.00733 ( 18) link_NAG-ASN : angle 2.03013 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7807 (mp10) REVERT: A 291 ASP cc_start: 0.7798 (t70) cc_final: 0.7393 (t0) REVERT: A 416 LEU cc_start: 0.8116 (mp) cc_final: 0.7856 (mp) REVERT: A 423 LEU cc_start: 0.7156 (mp) cc_final: 0.6783 (mp) REVERT: A 457 GLU cc_start: 0.6922 (tp30) cc_final: 0.6572 (mm-30) REVERT: B 230 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.6567 (ttm) REVERT: B 242 VAL cc_start: 0.7781 (OUTLIER) cc_final: 0.7526 (m) REVERT: C 93 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8149 (tt) REVERT: C 464 LYS cc_start: 0.6893 (ttmm) cc_final: 0.6596 (mmtm) REVERT: C 467 GLU cc_start: 0.6070 (tm-30) cc_final: 0.5618 (tt0) outliers start: 31 outliers final: 20 residues processed: 119 average time/residue: 0.3286 time to fit residues: 44.3823 Evaluate side-chains 119 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 155 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 17 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN B 112 ASN B 247 ASN ** B 476 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 = 0.3803 r_free = 0.3803 target = 0.158886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119024 restraints weight = 12178.236| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.76 r_work: 0.3070 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11886 Z= 0.126 Angle : 0.608 11.615 16167 Z= 0.293 Chirality : 0.051 0.526 1914 Planarity : 0.004 0.039 2007 Dihedral : 10.000 96.140 2421 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.32 % Allowed : 19.11 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.22), residues: 1425 helix: 2.43 (0.27), residues: 396 sheet: -1.10 (0.29), residues: 282 loop : -1.53 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 501 TYR 0.013 0.001 TYR C 414 PHE 0.014 0.002 PHE C 282 TRP 0.015 0.001 TRP A 208 HIS 0.004 0.001 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00295 (11832) covalent geometry : angle 0.55561 (16020) SS BOND : bond 0.00213 ( 15) SS BOND : angle 0.47575 ( 30) hydrogen bonds : bond 0.04118 ( 434) hydrogen bonds : angle 4.25873 ( 1263) glycosidic custom : bond 0.00146 ( 3) glycosidic custom : angle 0.57862 ( 9) link_BETA1-2 : bond 0.00797 ( 3) link_BETA1-2 : angle 7.20406 ( 9) link_BETA1-3 : bond 0.00176 ( 3) link_BETA1-3 : angle 4.93934 ( 9) link_BETA1-4 : bond 0.00594 ( 9) link_BETA1-4 : angle 2.13732 ( 27) link_BETA1-6 : bond 0.01071 ( 3) link_BETA1-6 : angle 1.16858 ( 9) link_NAG-ASN : bond 0.00620 ( 18) link_NAG-ASN : angle 1.96213 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.7765 (mp10) REVERT: A 291 ASP cc_start: 0.7804 (t70) cc_final: 0.7439 (t0) REVERT: A 423 LEU cc_start: 0.7136 (mp) cc_final: 0.6775 (mp) REVERT: A 457 GLU cc_start: 0.6936 (tp30) cc_final: 0.6547 (mm-30) REVERT: B 230 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.6362 (ttm) REVERT: B 260 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6065 (pp20) REVERT: C 93 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8120 (tt) REVERT: C 464 LYS cc_start: 0.6857 (ttmm) cc_final: 0.6550 (mmtm) REVERT: C 467 GLU cc_start: 0.6142 (tm-30) cc_final: 0.5683 (tt0) outliers start: 28 outliers final: 22 residues processed: 114 average time/residue: 0.3527 time to fit residues: 45.9190 Evaluate side-chains 118 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 155 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 1 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN B 112 ASN ** B 476 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 = 0.3800 r_free = 0.3800 target = 0.158639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.118626 restraints weight = 12139.893| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.76 r_work: 0.3089 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 11886 Z= 0.206 Angle : 0.855 59.198 16167 Z= 0.487 Chirality : 0.053 0.549 1914 Planarity : 0.004 0.039 2007 Dihedral : 10.027 96.134 2421 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.65 % Allowed : 18.94 % Favored : 78.41 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.22), residues: 1425 helix: 2.43 (0.27), residues: 396 sheet: -1.10 (0.29), residues: 282 loop : -1.54 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 211 TYR 0.013 0.002 TYR C 414 PHE 0.014 0.002 PHE C 282 TRP 0.014 0.001 TRP A 208 HIS 0.004 0.001 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00409 (11832) covalent geometry : angle 0.82068 (16020) SS BOND : bond 0.00233 ( 15) SS BOND : angle 0.48118 ( 30) hydrogen bonds : bond 0.04168 ( 434) hydrogen bonds : angle 4.26025 ( 1263) glycosidic custom : bond 0.00290 ( 3) glycosidic custom : angle 0.73784 ( 9) link_BETA1-2 : bond 0.00780 ( 3) link_BETA1-2 : angle 7.20040 ( 9) link_BETA1-3 : bond 0.00182 ( 3) link_BETA1-3 : angle 4.92375 ( 9) link_BETA1-4 : bond 0.00618 ( 9) link_BETA1-4 : angle 2.14918 ( 27) link_BETA1-6 : bond 0.01109 ( 3) link_BETA1-6 : angle 1.18993 ( 9) link_NAG-ASN : bond 0.00657 ( 18) link_NAG-ASN : angle 1.95289 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3786.35 seconds wall clock time: 65 minutes 27.63 seconds (3927.63 seconds total)