Starting phenix.real_space_refine on Wed May 14 11:09:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wis_37567/05_2025/8wis_37567.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wis_37567/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wis_37567/05_2025/8wis_37567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wis_37567/05_2025/8wis_37567.map" model { file = "/net/cci-nas-00/data/ceres_data/8wis_37567/05_2025/8wis_37567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wis_37567/05_2025/8wis_37567.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.144 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.72, per 1000 atoms: 0.66 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: 3.19 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.69 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: 4.18 Time building geometry restraints manager: 3.70 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: 0.00 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.110 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.530 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (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 TRP 0.014 0.001 TRP A 208 HIS 0.003 0.001 HIS B 314 PHE 0.012 0.001 PHE A 282 TYR 0.014 0.001 TYR B 410 ARG 0.005 0.000 ARG C 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 18) link_NAG-ASN : angle 1.55872 ( 54) link_BETA1-2 : bond 0.00584 ( 3) link_BETA1-2 : angle 4.45595 ( 9) link_BETA1-4 : bond 0.00452 ( 9) link_BETA1-4 : angle 1.49587 ( 27) hydrogen bonds : bond 0.13277 ( 434) hydrogen bonds : angle 6.01581 ( 1263) link_BETA1-6 : bond 0.01582 ( 3) link_BETA1-6 : angle 1.01514 ( 9) SS BOND : bond 0.00198 ( 15) SS BOND : angle 0.83770 ( 30) glycosidic custom : bond 0.00106 ( 3) glycosidic custom : angle 7.33991 ( 9) link_BETA1-3 : bond 0.00691 ( 3) link_BETA1-3 : angle 3.33233 ( 9) covalent geometry : bond 0.00423 (11832) covalent geometry : angle 0.67172 (16020) *********************** 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 : 1.227 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: 1.1017 time to fit residues: 229.8871 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 : 1.186 ------------------------------------------------------------------------------- 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 119 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 247 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113865 restraints weight = 12094.247| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.88 r_work: 0.3106 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11886 Z= 0.158 Angle : 0.693 12.346 16167 Z= 0.324 Chirality : 0.053 0.452 1914 Planarity : 0.004 0.036 2007 Dihedral : 14.387 88.167 2425 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.89 % Allowed : 8.27 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.21), residues: 1425 helix: 2.35 (0.27), residues: 396 sheet: -1.01 (0.32), residues: 249 loop : -1.60 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 208 HIS 0.004 0.001 HIS B 314 PHE 0.023 0.002 PHE A 282 TYR 0.017 0.002 TYR A 414 ARG 0.004 0.000 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 18) link_NAG-ASN : angle 1.81860 ( 54) link_BETA1-2 : bond 0.00713 ( 3) link_BETA1-2 : angle 7.08408 ( 9) link_BETA1-4 : bond 0.00558 ( 9) link_BETA1-4 : angle 2.36038 ( 27) hydrogen bonds : bond 0.04429 ( 434) hydrogen bonds : angle 4.63233 ( 1263) link_BETA1-6 : bond 0.00654 ( 3) link_BETA1-6 : angle 1.66575 ( 9) SS BOND : bond 0.00407 ( 15) SS BOND : angle 0.84912 ( 30) glycosidic custom : bond 0.00403 ( 3) glycosidic custom : angle 0.69093 ( 9) link_BETA1-3 : bond 0.00400 ( 3) link_BETA1-3 : angle 5.85312 ( 9) covalent geometry : bond 0.00368 (11832) covalent geometry : angle 0.64350 (16020) *********************** 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 152 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8754 (ptt) cc_final: 0.8495 (ptm) REVERT: A 64 LYS cc_start: 0.8106 (tttp) cc_final: 0.7867 (tttt) REVERT: A 138 ASP cc_start: 0.7965 (m-30) cc_final: 0.7625 (m-30) REVERT: A 157 LYS cc_start: 0.8381 (mtmm) cc_final: 0.8109 (mtmt) REVERT: A 260 GLU cc_start: 0.7857 (mp0) cc_final: 0.7612 (mp0) REVERT: A 291 ASP cc_start: 0.7561 (t0) cc_final: 0.7250 (OUTLIER) REVERT: A 423 LEU cc_start: 0.7024 (mp) cc_final: 0.6739 (mp) REVERT: A 430 GLU cc_start: 0.6647 (tp30) cc_final: 0.6357 (tt0) REVERT: A 467 GLU cc_start: 0.6192 (tm-30) cc_final: 0.5353 (mm-30) REVERT: B 46 LYS cc_start: 0.8297 (mtmt) cc_final: 0.7925 (mttm) REVERT: B 104 MET cc_start: 0.8589 (tpp) cc_final: 0.8321 (tpp) REVERT: B 142 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7663 (pt0) REVERT: B 175 LYS cc_start: 0.7754 (tttp) cc_final: 0.7482 (ttpp) REVERT: B 184 TYR cc_start: 0.8110 (m-80) cc_final: 0.7902 (m-80) REVERT: B 203 ASN cc_start: 0.7755 (m-40) cc_final: 0.7313 (m-40) REVERT: B 230 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.6444 (ttm) REVERT: B 260 GLU cc_start: 0.6734 (mp0) cc_final: 0.5925 (pp20) REVERT: B 408 GLN cc_start: 0.7255 (tt0) cc_final: 0.6270 (tp40) REVERT: C 91 PHE cc_start: 0.8032 (m-80) cc_final: 0.7756 (m-80) REVERT: C 405 ASN cc_start: 0.7331 (m-40) cc_final: 0.7005 (m110) REVERT: C 430 GLU cc_start: 0.7036 (tt0) cc_final: 0.6685 (tp30) REVERT: C 464 LYS cc_start: 0.7135 (ttmm) cc_final: 0.6726 (mmtm) REVERT: C 467 GLU cc_start: 0.5847 (tm-30) cc_final: 0.5475 (tt0) REVERT: C 468 GLU cc_start: 0.7022 (tt0) cc_final: 0.6157 (mm-30) outliers start: 35 outliers final: 22 residues processed: 139 average time/residue: 0.9643 time to fit residues: 148.7485 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 : 1.212 ------------------------------------------------------------------------------- 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 293 ASP 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 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 37 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 151 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 29 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.159740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119095 restraints weight = 12178.816| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.81 r_work: 0.3100 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11886 Z= 0.128 Angle : 0.595 10.230 16167 Z= 0.283 Chirality : 0.052 0.522 1914 Planarity : 0.004 0.037 2007 Dihedral : 12.237 82.106 2421 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.89 % Allowed : 11.75 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1425 helix: 2.53 (0.27), residues: 396 sheet: -0.64 (0.33), residues: 225 loop : -1.59 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 208 HIS 0.003 0.001 HIS B 314 PHE 0.017 0.002 PHE A 282 TYR 0.013 0.001 TYR A 410 ARG 0.002 0.000 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00681 ( 18) link_NAG-ASN : angle 1.98306 ( 54) link_BETA1-2 : bond 0.00773 ( 3) link_BETA1-2 : angle 6.47467 ( 9) link_BETA1-4 : bond 0.00595 ( 9) link_BETA1-4 : angle 1.93180 ( 27) hydrogen bonds : bond 0.04090 ( 434) hydrogen bonds : angle 4.46246 ( 1263) link_BETA1-6 : bond 0.00861 ( 3) link_BETA1-6 : angle 1.65398 ( 9) SS BOND : bond 0.00206 ( 15) SS BOND : angle 0.66109 ( 30) glycosidic custom : bond 0.00289 ( 3) glycosidic custom : angle 0.62644 ( 9) link_BETA1-3 : bond 0.00279 ( 3) link_BETA1-3 : angle 5.14318 ( 9) covalent geometry : bond 0.00299 (11832) covalent geometry : angle 0.54449 (16020) *********************** 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 144 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8825 (ptt) cc_final: 0.8556 (ptm) REVERT: A 64 LYS cc_start: 0.8172 (tttp) cc_final: 0.7949 (tttt) REVERT: A 138 ASP cc_start: 0.7960 (m-30) cc_final: 0.7621 (m-30) REVERT: A 157 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8209 (mtmt) REVERT: A 227 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7480 (mp10) REVERT: A 260 GLU cc_start: 0.7863 (mp0) cc_final: 0.7630 (mp0) REVERT: A 291 ASP cc_start: 0.7695 (t0) cc_final: 0.7318 (t0) REVERT: A 423 LEU cc_start: 0.7084 (mp) cc_final: 0.6694 (mp) REVERT: A 430 GLU cc_start: 0.6713 (tp30) cc_final: 0.6418 (tt0) REVERT: A 467 GLU cc_start: 0.6238 (tm-30) cc_final: 0.5734 (tt0) REVERT: B 46 LYS cc_start: 0.8378 (mtmt) cc_final: 0.8152 (mtmm) REVERT: B 157 LYS cc_start: 0.8279 (mtmm) cc_final: 0.7505 (mttm) REVERT: B 175 LYS cc_start: 0.7795 (tttp) cc_final: 0.7570 (ttpp) REVERT: B 203 ASN cc_start: 0.7809 (m-40) cc_final: 0.7313 (m-40) REVERT: B 230 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.6383 (ttm) REVERT: B 260 GLU cc_start: 0.6876 (mp0) cc_final: 0.5851 (pp20) REVERT: B 408 GLN cc_start: 0.7457 (tt0) cc_final: 0.6475 (tp40) REVERT: B 448 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.6969 (mt) REVERT: C 91 PHE cc_start: 0.8015 (m-80) cc_final: 0.7738 (m-80) REVERT: C 260 GLU cc_start: 0.7617 (mp0) cc_final: 0.6313 (mm-30) REVERT: C 405 ASN cc_start: 0.7431 (m-40) cc_final: 0.7156 (m110) REVERT: C 430 GLU cc_start: 0.7067 (tt0) cc_final: 0.6768 (tp30) REVERT: C 464 LYS cc_start: 0.7070 (ttmm) cc_final: 0.6649 (mmtm) REVERT: C 467 GLU cc_start: 0.5891 (tm-30) cc_final: 0.5493 (tt0) REVERT: C 468 GLU cc_start: 0.7105 (tt0) cc_final: 0.6280 (mm-30) outliers start: 35 outliers final: 15 residues processed: 136 average time/residue: 0.9126 time to fit residues: 138.2000 Evaluate side-chains 119 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 312 ILE 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 178 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 310 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 155 THR Chi-restraints excluded: chain C residue 230 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 108 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 87 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.158701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117592 restraints weight = 12160.857| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.84 r_work: 0.3066 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11886 Z= 0.157 Angle : 0.636 10.829 16167 Z= 0.305 Chirality : 0.053 0.476 1914 Planarity : 0.004 0.037 2007 Dihedral : 11.707 83.616 2421 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.72 % Allowed : 13.40 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.21), residues: 1425 helix: 2.35 (0.27), residues: 396 sheet: -0.75 (0.32), residues: 240 loop : -1.63 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 208 HIS 0.005 0.001 HIS C 81 PHE 0.018 0.002 PHE A 282 TYR 0.016 0.002 TYR A 410 ARG 0.002 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 18) link_NAG-ASN : angle 1.98057 ( 54) link_BETA1-2 : bond 0.00780 ( 3) link_BETA1-2 : angle 6.71678 ( 9) link_BETA1-4 : bond 0.00564 ( 9) link_BETA1-4 : angle 2.27892 ( 27) hydrogen bonds : bond 0.04527 ( 434) hydrogen bonds : angle 4.50061 ( 1263) link_BETA1-6 : bond 0.00764 ( 3) link_BETA1-6 : angle 1.69332 ( 9) SS BOND : bond 0.00270 ( 15) SS BOND : angle 0.71258 ( 30) glycosidic custom : bond 0.00120 ( 3) glycosidic custom : angle 0.59805 ( 9) link_BETA1-3 : bond 0.00151 ( 3) link_BETA1-3 : angle 5.23835 ( 9) covalent geometry : bond 0.00383 (11832) covalent geometry : angle 0.58488 (16020) *********************** 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 153 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 108 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8852 (ptt) cc_final: 0.8649 (ptm) REVERT: A 64 LYS cc_start: 0.8236 (tttp) cc_final: 0.7987 (tttt) REVERT: A 217 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6153 (tm-30) REVERT: A 227 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7760 (mp10) REVERT: A 260 GLU cc_start: 0.7944 (mp0) cc_final: 0.7675 (mp0) REVERT: A 291 ASP cc_start: 0.7867 (t0) cc_final: 0.7427 (t0) REVERT: A 423 LEU cc_start: 0.6992 (mp) cc_final: 0.6661 (mt) REVERT: A 430 GLU cc_start: 0.6718 (tp30) cc_final: 0.6380 (tt0) REVERT: B 46 LYS cc_start: 0.8419 (mtmt) cc_final: 0.8179 (mtmm) REVERT: B 203 ASN cc_start: 0.7832 (m-40) cc_final: 0.7319 (m-40) REVERT: B 230 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.6439 (ttm) REVERT: B 260 GLU cc_start: 0.7165 (mp0) cc_final: 0.6939 (mp0) REVERT: B 408 GLN cc_start: 0.7595 (tt0) cc_final: 0.6529 (tp40) REVERT: C 91 PHE cc_start: 0.8067 (m-80) cc_final: 0.7783 (m-80) REVERT: C 260 GLU cc_start: 0.7824 (mp0) cc_final: 0.6335 (mm-30) REVERT: C 416 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6790 (tt) REVERT: C 430 GLU cc_start: 0.7102 (tt0) cc_final: 0.6849 (tp30) REVERT: C 464 LYS cc_start: 0.7038 (ttmm) cc_final: 0.6643 (mmtm) REVERT: C 467 GLU cc_start: 0.5980 (tm-30) cc_final: 0.5573 (tt0) REVERT: C 468 GLU cc_start: 0.6925 (tt0) cc_final: 0.6117 (mm-30) outliers start: 45 outliers final: 25 residues processed: 138 average time/residue: 0.8877 time to fit residues: 136.7230 Evaluate side-chains 127 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 155 THR Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 293 ASP 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 93 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 271 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 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 226 LYS Chi-restraints excluded: chain C residue 230 MET 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 111 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.106811 restraints weight = 12266.246| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.87 r_work: 0.3043 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11886 Z= 0.173 Angle : 0.654 11.075 16167 Z= 0.314 Chirality : 0.054 0.509 1914 Planarity : 0.004 0.038 2007 Dihedral : 11.560 84.619 2421 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.97 % Allowed : 14.97 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1425 helix: 2.23 (0.27), residues: 396 sheet: -0.87 (0.32), residues: 240 loop : -1.68 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 208 HIS 0.006 0.001 HIS C 81 PHE 0.019 0.002 PHE A 282 TYR 0.018 0.002 TYR A 410 ARG 0.002 0.000 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 18) link_NAG-ASN : angle 2.16849 ( 54) link_BETA1-2 : bond 0.00699 ( 3) link_BETA1-2 : angle 6.75696 ( 9) link_BETA1-4 : bond 0.00592 ( 9) link_BETA1-4 : angle 2.37435 ( 27) hydrogen bonds : bond 0.04868 ( 434) hydrogen bonds : angle 4.52154 ( 1263) link_BETA1-6 : bond 0.00791 ( 3) link_BETA1-6 : angle 1.80666 ( 9) SS BOND : bond 0.00317 ( 15) SS BOND : angle 0.64048 ( 30) glycosidic custom : bond 0.00175 ( 3) glycosidic custom : angle 0.62861 ( 9) link_BETA1-3 : bond 0.00207 ( 3) link_BETA1-3 : angle 5.07980 ( 9) covalent geometry : bond 0.00426 (11832) covalent geometry : angle 0.60308 (16020) *********************** 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 154 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 106 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8171 (tttp) cc_final: 0.7911 (tttt) REVERT: A 217 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6185 (tm-30) REVERT: A 227 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7842 (mp10) REVERT: A 260 GLU cc_start: 0.7944 (mp0) cc_final: 0.7644 (mp0) REVERT: A 291 ASP cc_start: 0.7983 (t0) cc_final: 0.7498 (t0) REVERT: A 423 LEU cc_start: 0.7075 (mp) cc_final: 0.6715 (mp) REVERT: A 430 GLU cc_start: 0.6529 (tp30) cc_final: 0.6147 (tt0) REVERT: A 457 GLU cc_start: 0.6873 (tp30) cc_final: 0.6524 (mm-30) REVERT: B 46 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8198 (mtmm) REVERT: B 157 LYS cc_start: 0.8191 (mtmm) cc_final: 0.7562 (mttm) REVERT: B 203 ASN cc_start: 0.7797 (m-40) cc_final: 0.7316 (m-40) REVERT: B 230 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.6404 (ttm) REVERT: B 232 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6898 (pt0) REVERT: B 260 GLU cc_start: 0.7371 (mp0) cc_final: 0.7062 (mp0) REVERT: B 448 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7118 (mt) REVERT: C 260 GLU cc_start: 0.7801 (mp0) cc_final: 0.6229 (mm-30) REVERT: C 416 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6766 (tt) REVERT: C 430 GLU cc_start: 0.7110 (tt0) cc_final: 0.6853 (tp30) REVERT: C 464 LYS cc_start: 0.7002 (ttmm) cc_final: 0.6621 (mmtm) REVERT: C 467 GLU cc_start: 0.6021 (tm-30) cc_final: 0.5598 (tt0) outliers start: 48 outliers final: 27 residues processed: 138 average time/residue: 0.8563 time to fit residues: 132.8193 Evaluate side-chains 135 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 53 VAL 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 B residue 73 SER Chi-restraints excluded: chain B residue 93 LEU 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 271 VAL Chi-restraints excluded: chain B residue 284 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 B residue 448 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 230 MET 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 94 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 0.0030 chunk 20 optimal weight: 0.1980 chunk 131 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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** C 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.158668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117621 restraints weight = 12076.397| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.83 r_work: 0.3097 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11886 Z= 0.100 Angle : 0.561 11.450 16167 Z= 0.266 Chirality : 0.050 0.511 1914 Planarity : 0.003 0.039 2007 Dihedral : 10.391 87.922 2421 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.56 % Allowed : 17.20 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1425 helix: 2.60 (0.28), residues: 396 sheet: -0.86 (0.30), residues: 270 loop : -1.48 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 208 HIS 0.003 0.001 HIS B 69 PHE 0.011 0.001 PHE A 262 TYR 0.010 0.001 TYR A 184 ARG 0.001 0.000 ARG B 128 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 18) link_NAG-ASN : angle 1.87694 ( 54) link_BETA1-2 : bond 0.00828 ( 3) link_BETA1-2 : angle 7.15335 ( 9) link_BETA1-4 : bond 0.00596 ( 9) link_BETA1-4 : angle 1.87445 ( 27) hydrogen bonds : bond 0.03708 ( 434) hydrogen bonds : angle 4.24531 ( 1263) link_BETA1-6 : bond 0.00989 ( 3) link_BETA1-6 : angle 1.21617 ( 9) SS BOND : bond 0.00139 ( 15) SS BOND : angle 0.46406 ( 30) glycosidic custom : bond 0.00118 ( 3) glycosidic custom : angle 0.52265 ( 9) link_BETA1-3 : bond 0.00165 ( 3) link_BETA1-3 : angle 5.20300 ( 9) covalent geometry : bond 0.00219 (11832) covalent geometry : angle 0.50422 (16020) *********************** 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 138 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8159 (tttp) cc_final: 0.7911 (tttt) REVERT: A 227 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7725 (mp10) REVERT: A 260 GLU cc_start: 0.7838 (mp0) cc_final: 0.7584 (mp0) REVERT: A 291 ASP cc_start: 0.7866 (t0) cc_final: 0.7415 (t0) REVERT: A 423 LEU cc_start: 0.6999 (mp) cc_final: 0.6640 (mp) REVERT: A 430 GLU cc_start: 0.6567 (tp30) cc_final: 0.6222 (tt0) REVERT: A 457 GLU cc_start: 0.6849 (tp30) cc_final: 0.6513 (mm-30) REVERT: B 46 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8202 (mtmm) REVERT: B 142 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: B 230 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6377 (ttm) REVERT: B 291 ASP cc_start: 0.7924 (t70) cc_final: 0.7675 (t0) REVERT: B 408 GLN cc_start: 0.7364 (tt0) cc_final: 0.6351 (tp40) REVERT: C 260 GLU cc_start: 0.7756 (mp0) cc_final: 0.6192 (mm-30) REVERT: C 416 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6763 (tt) REVERT: C 430 GLU cc_start: 0.7077 (tt0) cc_final: 0.6854 (tp30) REVERT: C 464 LYS cc_start: 0.6965 (ttmm) cc_final: 0.6682 (mmtm) REVERT: C 467 GLU cc_start: 0.6094 (tm-30) cc_final: 0.5652 (tt0) outliers start: 31 outliers final: 12 residues processed: 128 average time/residue: 0.8285 time to fit residues: 120.0275 Evaluate side-chains 117 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 227 GLN Chi-restraints excluded: chain A residue 312 ILE 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 93 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 230 MET 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 416 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 107 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS A 476 ASN A 497 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 314 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.155439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115246 restraints weight = 12350.774| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.76 r_work: 0.3040 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11886 Z= 0.248 Angle : 0.751 11.236 16167 Z= 0.362 Chirality : 0.058 0.525 1914 Planarity : 0.005 0.039 2007 Dihedral : 11.844 89.739 2421 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.72 % Allowed : 16.63 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1425 helix: 1.92 (0.26), residues: 396 sheet: -1.11 (0.30), residues: 252 loop : -1.73 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 208 HIS 0.007 0.001 HIS C 81 PHE 0.020 0.003 PHE C 282 TYR 0.025 0.003 TYR A 410 ARG 0.004 0.001 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 18) link_NAG-ASN : angle 2.28399 ( 54) link_BETA1-2 : bond 0.00639 ( 3) link_BETA1-2 : angle 6.82810 ( 9) link_BETA1-4 : bond 0.00622 ( 9) link_BETA1-4 : angle 2.95860 ( 27) hydrogen bonds : bond 0.05820 ( 434) hydrogen bonds : angle 4.70500 ( 1263) link_BETA1-6 : bond 0.00763 ( 3) link_BETA1-6 : angle 2.23746 ( 9) SS BOND : bond 0.00480 ( 15) SS BOND : angle 0.75473 ( 30) glycosidic custom : bond 0.00294 ( 3) glycosidic custom : angle 0.80681 ( 9) link_BETA1-3 : bond 0.00357 ( 3) link_BETA1-3 : angle 4.85583 ( 9) covalent geometry : bond 0.00626 (11832) covalent geometry : angle 0.70208 (16020) *********************** 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 151 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 106 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8181 (tttp) cc_final: 0.7969 (tttt) REVERT: A 217 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6309 (tm-30) REVERT: A 227 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.7931 (mp10) REVERT: A 260 GLU cc_start: 0.8047 (mp0) cc_final: 0.7746 (mp0) REVERT: A 291 ASP cc_start: 0.7989 (t0) cc_final: 0.7492 (t0) REVERT: A 423 LEU cc_start: 0.7229 (mp) cc_final: 0.6897 (mp) REVERT: A 430 GLU cc_start: 0.6605 (tp30) cc_final: 0.6164 (tt0) REVERT: A 457 GLU cc_start: 0.6956 (tp30) cc_final: 0.6572 (mm-30) REVERT: B 46 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8310 (mtmm) REVERT: B 230 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.6632 (ttm) REVERT: B 232 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6884 (pt0) REVERT: B 291 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7691 (t0) REVERT: C 294 CYS cc_start: 0.8134 (p) cc_final: 0.7778 (p) REVERT: C 416 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6926 (tt) REVERT: C 464 LYS cc_start: 0.6976 (ttmm) cc_final: 0.6573 (mmtm) outliers start: 45 outliers final: 27 residues processed: 136 average time/residue: 0.8380 time to fit residues: 128.8502 Evaluate side-chains 136 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 155 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 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 156 LEU 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 244 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 291 ASP 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 73 SER Chi-restraints excluded: chain C residue 226 LYS 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 104 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 0.0870 overall best weight: 1.0960 ------------------------------------------------------------------------------- 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 247 ASN ** 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 = 0.3788 r_free = 0.3788 target = 0.157505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117151 restraints weight = 12197.800| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.79 r_work: 0.3056 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11886 Z= 0.136 Angle : 0.625 11.597 16167 Z= 0.299 Chirality : 0.053 0.526 1914 Planarity : 0.004 0.039 2007 Dihedral : 10.905 92.256 2421 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.06 % Allowed : 17.78 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.21), residues: 1425 helix: 2.20 (0.27), residues: 396 sheet: -1.09 (0.31), residues: 252 loop : -1.67 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 208 HIS 0.004 0.001 HIS C 81 PHE 0.016 0.002 PHE A 282 TYR 0.014 0.002 TYR C 414 ARG 0.002 0.000 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 18) link_NAG-ASN : angle 2.18347 ( 54) link_BETA1-2 : bond 0.00764 ( 3) link_BETA1-2 : angle 7.07047 ( 9) link_BETA1-4 : bond 0.00630 ( 9) link_BETA1-4 : angle 2.35885 ( 27) hydrogen bonds : bond 0.04591 ( 434) hydrogen bonds : angle 4.43345 ( 1263) link_BETA1-6 : bond 0.00961 ( 3) link_BETA1-6 : angle 1.56482 ( 9) SS BOND : bond 0.00239 ( 15) SS BOND : angle 0.53642 ( 30) glycosidic custom : bond 0.00124 ( 3) glycosidic custom : angle 0.57208 ( 9) link_BETA1-3 : bond 0.00187 ( 3) link_BETA1-3 : angle 5.08100 ( 9) covalent geometry : bond 0.00324 (11832) covalent geometry : angle 0.56920 (16020) *********************** 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 140 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8178 (tttp) cc_final: 0.7939 (tttt) REVERT: A 217 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6383 (tm-30) REVERT: A 227 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.7931 (mp10) REVERT: A 260 GLU cc_start: 0.7991 (mp0) cc_final: 0.7698 (mp0) REVERT: A 291 ASP cc_start: 0.8024 (t0) cc_final: 0.7537 (t0) REVERT: A 423 LEU cc_start: 0.7123 (mp) cc_final: 0.6789 (mt) REVERT: A 430 GLU cc_start: 0.6602 (tp30) cc_final: 0.6133 (tt0) REVERT: A 457 GLU cc_start: 0.6937 (tp30) cc_final: 0.6587 (mm-30) REVERT: B 46 LYS cc_start: 0.8466 (mtmt) cc_final: 0.8251 (mtmm) REVERT: B 157 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7518 (mmtm) REVERT: B 230 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6430 (ttm) REVERT: B 242 VAL cc_start: 0.7656 (OUTLIER) cc_final: 0.7419 (m) REVERT: B 448 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7184 (mt) REVERT: B 456 GLU cc_start: 0.7901 (tp30) cc_final: 0.7628 (tp30) REVERT: C 416 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6893 (tt) REVERT: C 464 LYS cc_start: 0.6982 (ttmm) cc_final: 0.6644 (mmtm) REVERT: C 467 GLU cc_start: 0.6121 (tm-30) cc_final: 0.5629 (tt0) outliers start: 37 outliers final: 21 residues processed: 129 average time/residue: 0.8406 time to fit residues: 122.1548 Evaluate side-chains 125 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 470 LYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 156 LEU 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 271 VAL Chi-restraints excluded: chain B residue 290 ILE 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 448 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 416 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 108 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 128 optimal weight: 0.0970 chunk 49 optimal weight: 0.0270 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 109 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.160795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121022 restraints weight = 12146.544| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.77 r_work: 0.3087 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11886 Z= 0.098 Angle : 0.559 11.663 16167 Z= 0.266 Chirality : 0.050 0.527 1914 Planarity : 0.003 0.040 2007 Dihedral : 9.545 96.301 2421 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.90 % Allowed : 19.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.22), residues: 1425 helix: 2.63 (0.28), residues: 396 sheet: -1.00 (0.29), residues: 282 loop : -1.50 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 127 HIS 0.004 0.001 HIS B 69 PHE 0.012 0.001 PHE A 136 TYR 0.010 0.001 TYR C 504 ARG 0.002 0.000 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 18) link_NAG-ASN : angle 1.94352 ( 54) link_BETA1-2 : bond 0.00842 ( 3) link_BETA1-2 : angle 7.36786 ( 9) link_BETA1-4 : bond 0.00594 ( 9) link_BETA1-4 : angle 1.78376 ( 27) hydrogen bonds : bond 0.03495 ( 434) hydrogen bonds : angle 4.18016 ( 1263) link_BETA1-6 : bond 0.01111 ( 3) link_BETA1-6 : angle 0.93681 ( 9) SS BOND : bond 0.00150 ( 15) SS BOND : angle 0.48466 ( 30) glycosidic custom : bond 0.00132 ( 3) glycosidic custom : angle 0.57864 ( 9) link_BETA1-3 : bond 0.00211 ( 3) link_BETA1-3 : angle 5.03328 ( 9) covalent geometry : bond 0.00215 (11832) covalent geometry : angle 0.50128 (16020) *********************** 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 129 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8173 (tttp) cc_final: 0.7930 (tttt) REVERT: A 227 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7745 (mp10) REVERT: A 260 GLU cc_start: 0.7851 (mp0) cc_final: 0.7593 (mp0) REVERT: A 291 ASP cc_start: 0.8016 (t0) cc_final: 0.7581 (t0) REVERT: A 423 LEU cc_start: 0.7100 (mp) cc_final: 0.6745 (mp) REVERT: A 430 GLU cc_start: 0.6597 (tp30) cc_final: 0.6127 (tt0) REVERT: A 457 GLU cc_start: 0.6939 (tp30) cc_final: 0.6559 (mm-30) REVERT: A 467 GLU cc_start: 0.6034 (tm-30) cc_final: 0.5328 (mm-30) REVERT: B 46 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8210 (mtmm) REVERT: B 230 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.6344 (ttm) REVERT: B 242 VAL cc_start: 0.7666 (OUTLIER) cc_final: 0.7457 (m) REVERT: B 408 GLN cc_start: 0.7437 (tt0) cc_final: 0.6468 (tp40) REVERT: C 416 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6876 (tt) REVERT: C 464 LYS cc_start: 0.6841 (ttmm) cc_final: 0.6562 (mmtm) REVERT: C 467 GLU cc_start: 0.6212 (tm-30) cc_final: 0.5645 (tt0) outliers start: 23 outliers final: 14 residues processed: 123 average time/residue: 0.7353 time to fit residues: 103.4488 Evaluate side-chains 117 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 227 GLN Chi-restraints excluded: chain A residue 312 ILE 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 93 LEU 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 271 VAL Chi-restraints excluded: chain B residue 284 VAL 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 155 THR Chi-restraints excluded: chain C residue 416 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 134 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 432 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.155912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.115653 restraints weight = 12254.765| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.77 r_work: 0.3042 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11886 Z= 0.220 Angle : 0.719 11.648 16167 Z= 0.347 Chirality : 0.056 0.526 1914 Planarity : 0.004 0.038 2007 Dihedral : 10.712 97.771 2421 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.56 % Allowed : 18.61 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1425 helix: 2.06 (0.27), residues: 396 sheet: -1.07 (0.31), residues: 252 loop : -1.70 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 208 HIS 0.006 0.001 HIS C 81 PHE 0.019 0.002 PHE A 282 TYR 0.022 0.003 TYR A 410 ARG 0.003 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 18) link_NAG-ASN : angle 2.28620 ( 54) link_BETA1-2 : bond 0.00682 ( 3) link_BETA1-2 : angle 7.09906 ( 9) link_BETA1-4 : bond 0.00648 ( 9) link_BETA1-4 : angle 2.79271 ( 27) hydrogen bonds : bond 0.05350 ( 434) hydrogen bonds : angle 4.56817 ( 1263) link_BETA1-6 : bond 0.00926 ( 3) link_BETA1-6 : angle 1.89528 ( 9) SS BOND : bond 0.00389 ( 15) SS BOND : angle 0.65713 ( 30) glycosidic custom : bond 0.00191 ( 3) glycosidic custom : angle 0.73230 ( 9) link_BETA1-3 : bond 0.00300 ( 3) link_BETA1-3 : angle 4.78993 ( 9) covalent geometry : bond 0.00556 (11832) covalent geometry : angle 0.66787 (16020) ********************** 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 136 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8149 (tttp) cc_final: 0.7924 (tttt) REVERT: A 227 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: A 260 GLU cc_start: 0.8034 (mp0) cc_final: 0.7728 (mp0) REVERT: A 291 ASP cc_start: 0.7999 (t0) cc_final: 0.7425 (t0) REVERT: A 416 LEU cc_start: 0.8116 (mp) cc_final: 0.7853 (mt) REVERT: A 423 LEU cc_start: 0.7168 (mp) cc_final: 0.6805 (mp) REVERT: A 430 GLU cc_start: 0.6588 (tp30) cc_final: 0.6018 (tt0) REVERT: A 457 GLU cc_start: 0.6913 (tp30) cc_final: 0.6543 (mm-30) REVERT: B 46 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8262 (mtmm) REVERT: B 230 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.6661 (ttm) REVERT: B 242 VAL cc_start: 0.7789 (OUTLIER) cc_final: 0.7491 (m) REVERT: B 456 GLU cc_start: 0.7899 (tp30) cc_final: 0.7618 (tp30) REVERT: C 294 CYS cc_start: 0.8186 (p) cc_final: 0.7847 (p) REVERT: C 416 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6856 (tt) REVERT: C 464 LYS cc_start: 0.6898 (ttmm) cc_final: 0.6574 (mmtm) REVERT: C 467 GLU cc_start: 0.6212 (tm-30) cc_final: 0.5665 (tt0) outliers start: 31 outliers final: 20 residues processed: 126 average time/residue: 0.7442 time to fit residues: 107.0906 Evaluate side-chains 128 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 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 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 230 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 271 VAL 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 155 THR Chi-restraints excluded: chain C residue 416 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 112 optimal weight: 0.1980 chunk 93 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.156283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116133 restraints weight = 12212.717| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.77 r_work: 0.3046 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.200 11886 Z= 0.268 Angle : 0.944 59.158 16167 Z= 0.529 Chirality : 0.056 0.618 1914 Planarity : 0.004 0.043 2007 Dihedral : 10.720 97.807 2421 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.65 % Allowed : 18.53 % Favored : 78.83 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1425 helix: 2.04 (0.27), residues: 396 sheet: -1.08 (0.31), residues: 252 loop : -1.71 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 208 HIS 0.005 0.001 HIS C 81 PHE 0.019 0.002 PHE C 282 TYR 0.021 0.002 TYR A 410 ARG 0.002 0.000 ARG C 207 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 18) link_NAG-ASN : angle 2.28576 ( 54) link_BETA1-2 : bond 0.00751 ( 3) link_BETA1-2 : angle 7.09543 ( 9) link_BETA1-4 : bond 0.00532 ( 9) link_BETA1-4 : angle 2.77274 ( 27) hydrogen bonds : bond 0.05169 ( 434) hydrogen bonds : angle 4.55948 ( 1263) link_BETA1-6 : bond 0.00964 ( 3) link_BETA1-6 : angle 1.88933 ( 9) SS BOND : bond 0.00261 ( 15) SS BOND : angle 0.59980 ( 30) glycosidic custom : bond 0.00406 ( 3) glycosidic custom : angle 0.68319 ( 9) link_BETA1-3 : bond 0.00227 ( 3) link_BETA1-3 : angle 4.84701 ( 9) covalent geometry : bond 0.00566 (11832) covalent geometry : angle 0.90843 (16020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7803.37 seconds wall clock time: 135 minutes 41.90 seconds (8141.90 seconds total)