Starting phenix.real_space_refine on Tue Jul 29 21:59:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wis_37567/07_2025/8wis_37567.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wis_37567/07_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_37567/07_2025/8wis_37567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wis_37567/07_2025/8wis_37567.map" model { file = "/net/cci-nas-00/data/ceres_data/8wis_37567/07_2025/8wis_37567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wis_37567/07_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-5711/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: 7.83, per 1000 atoms: 0.67 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: 3.31 Conformation dependent library (CDL) restraints added in 1.6 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: 1.94 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: 4.05 Time building geometry restraints manager: 3.88 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 31.220 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.180 ------------------------------------------------------------------------------- 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 : 1.350 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: 1.1635 time to fit residues: 242.1292 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 : 1.333 ------------------------------------------------------------------------------- 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 = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113873 restraints weight = 12094.247| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.88 r_work: 0.3121 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8764 (ptt) cc_final: 0.8516 (ptm) REVERT: A 64 LYS cc_start: 0.8126 (tttp) cc_final: 0.7906 (tttt) REVERT: A 138 ASP cc_start: 0.7995 (m-30) cc_final: 0.7683 (m-30) REVERT: A 157 LYS cc_start: 0.8372 (mtmm) cc_final: 0.8120 (mtmt) REVERT: A 260 GLU cc_start: 0.7877 (mp0) cc_final: 0.7657 (mp0) REVERT: A 291 ASP cc_start: 0.7549 (t0) cc_final: 0.7263 (OUTLIER) REVERT: A 423 LEU cc_start: 0.7100 (mp) cc_final: 0.6823 (mp) REVERT: A 430 GLU cc_start: 0.6667 (tp30) cc_final: 0.6424 (tt0) REVERT: A 467 GLU cc_start: 0.6255 (tm-30) cc_final: 0.5417 (mm-30) REVERT: B 46 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7970 (mttm) REVERT: B 104 MET cc_start: 0.8593 (tpp) cc_final: 0.8338 (tpp) REVERT: B 142 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7699 (pt0) REVERT: B 175 LYS cc_start: 0.7768 (tttp) cc_final: 0.7517 (ttpp) REVERT: B 203 ASN cc_start: 0.7783 (m-40) cc_final: 0.7359 (m-40) REVERT: B 230 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.6466 (ttm) REVERT: B 260 GLU cc_start: 0.6732 (mp0) cc_final: 0.5984 (pp20) REVERT: B 408 GLN cc_start: 0.7364 (tt0) cc_final: 0.6428 (tp40) REVERT: C 91 PHE cc_start: 0.8054 (m-80) cc_final: 0.7796 (m-80) REVERT: C 405 ASN cc_start: 0.7387 (m-40) cc_final: 0.7049 (m110) REVERT: C 430 GLU cc_start: 0.7052 (tt0) cc_final: 0.6753 (tp30) REVERT: C 464 LYS cc_start: 0.7227 (ttmm) cc_final: 0.6844 (mmtm) REVERT: C 467 GLU cc_start: 0.5926 (tm-30) cc_final: 0.5551 (tt0) REVERT: C 468 GLU cc_start: 0.7112 (tt0) cc_final: 0.6250 (mm-30) outliers start: 35 outliers final: 22 residues processed: 139 average time/residue: 1.0451 time to fit residues: 161.2363 Evaluate side-chains 120 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.160651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.119414 restraints weight = 12082.368| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.86 r_work: 0.3089 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2563 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= 0.139 Angle : 0.605 9.959 16167 Z= 0.289 Chirality : 0.053 0.561 1914 Planarity : 0.004 0.038 2007 Dihedral : 12.206 81.958 2421 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.31 % Allowed : 11.91 % Favored : 84.78 % 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: -0.38 (0.22), residues: 1425 helix: 2.48 (0.27), residues: 396 sheet: -0.74 (0.32), residues: 240 loop : -1.62 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 208 HIS 0.004 0.001 HIS B 314 PHE 0.018 0.002 PHE A 282 TYR 0.014 0.002 TYR B 410 ARG 0.002 0.000 ARG C 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00684 ( 18) link_NAG-ASN : angle 1.97670 ( 54) link_BETA1-2 : bond 0.00824 ( 3) link_BETA1-2 : angle 6.28832 ( 9) link_BETA1-4 : bond 0.00635 ( 9) link_BETA1-4 : angle 1.94841 ( 27) hydrogen bonds : bond 0.04323 ( 434) hydrogen bonds : angle 4.49009 ( 1263) link_BETA1-6 : bond 0.00926 ( 3) link_BETA1-6 : angle 1.61876 ( 9) SS BOND : bond 0.00213 ( 15) SS BOND : angle 0.74807 ( 30) glycosidic custom : bond 0.00243 ( 3) glycosidic custom : angle 0.79761 ( 9) link_BETA1-3 : bond 0.00397 ( 3) link_BETA1-3 : angle 5.02985 ( 9) covalent geometry : bond 0.00329 (11832) covalent geometry : angle 0.55716 (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 147 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8827 (ptt) cc_final: 0.8591 (ptm) REVERT: A 64 LYS cc_start: 0.8188 (tttp) cc_final: 0.7949 (tttt) REVERT: A 138 ASP cc_start: 0.8027 (m-30) cc_final: 0.7704 (m-30) REVERT: A 157 LYS cc_start: 0.8500 (mtmm) cc_final: 0.8218 (mtmt) REVERT: A 217 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6144 (tm-30) REVERT: A 227 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: A 260 GLU cc_start: 0.7882 (mp0) cc_final: 0.7570 (mp0) REVERT: A 291 ASP cc_start: 0.7730 (t0) cc_final: 0.7368 (t0) REVERT: A 423 LEU cc_start: 0.7109 (mp) cc_final: 0.6729 (mp) REVERT: A 430 GLU cc_start: 0.6731 (tp30) cc_final: 0.6413 (tt0) REVERT: A 467 GLU cc_start: 0.6175 (tm-30) cc_final: 0.5714 (tt0) REVERT: B 46 LYS cc_start: 0.8377 (mtmt) cc_final: 0.8155 (mtmm) REVERT: B 157 LYS cc_start: 0.8280 (mtmm) cc_final: 0.7485 (mttm) REVERT: B 203 ASN cc_start: 0.7802 (m-40) cc_final: 0.7275 (m-40) REVERT: B 230 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.6298 (ttm) REVERT: B 260 GLU cc_start: 0.6918 (mp0) cc_final: 0.5890 (pp20) REVERT: B 408 GLN cc_start: 0.7526 (tt0) cc_final: 0.6519 (tp40) REVERT: B 448 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7002 (mt) REVERT: C 91 PHE cc_start: 0.8030 (m-80) cc_final: 0.7779 (m-80) REVERT: C 260 GLU cc_start: 0.7695 (mp0) cc_final: 0.6318 (mm-30) REVERT: C 430 GLU cc_start: 0.7069 (tt0) cc_final: 0.6772 (tp30) REVERT: C 464 LYS cc_start: 0.7068 (ttmm) cc_final: 0.6660 (mmtm) REVERT: C 467 GLU cc_start: 0.5884 (tm-30) cc_final: 0.5508 (tt0) REVERT: C 468 GLU cc_start: 0.7093 (tt0) cc_final: 0.6265 (mm-30) outliers start: 40 outliers final: 17 residues processed: 137 average time/residue: 0.9917 time to fit residues: 150.5717 Evaluate side-chains 119 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 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 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 271 VAL 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: 0.6980 chunk 33 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 79 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3827 r_free = 0.3827 target = 0.161237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120549 restraints weight = 12122.113| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.83 r_work: 0.3090 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2813 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= 0.111 Angle : 0.576 10.831 16167 Z= 0.273 Chirality : 0.050 0.471 1914 Planarity : 0.003 0.037 2007 Dihedral : 11.120 80.704 2421 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.89 % Allowed : 14.31 % Favored : 82.80 % 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: -0.20 (0.22), residues: 1425 helix: 2.62 (0.27), residues: 396 sheet: -0.74 (0.30), residues: 270 loop : -1.47 (0.19), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 208 HIS 0.003 0.001 HIS C 81 PHE 0.015 0.001 PHE A 282 TYR 0.010 0.001 TYR A 184 ARG 0.001 0.000 ARG A 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 18) link_NAG-ASN : angle 1.93583 ( 54) link_BETA1-2 : bond 0.00821 ( 3) link_BETA1-2 : angle 6.84946 ( 9) link_BETA1-4 : bond 0.00544 ( 9) link_BETA1-4 : angle 1.94011 ( 27) hydrogen bonds : bond 0.03783 ( 434) hydrogen bonds : angle 4.34384 ( 1263) link_BETA1-6 : bond 0.00833 ( 3) link_BETA1-6 : angle 1.36990 ( 9) SS BOND : bond 0.00171 ( 15) SS BOND : angle 0.59436 ( 30) glycosidic custom : bond 0.00070 ( 3) glycosidic custom : angle 0.49977 ( 9) link_BETA1-3 : bond 0.00154 ( 3) link_BETA1-3 : angle 5.34698 ( 9) covalent geometry : bond 0.00255 (11832) covalent geometry : angle 0.52057 (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 140 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8817 (ptt) cc_final: 0.8604 (ptm) REVERT: A 64 LYS cc_start: 0.8206 (tttp) cc_final: 0.7978 (tttt) REVERT: A 135 ASP cc_start: 0.7476 (t0) cc_final: 0.7275 (t0) REVERT: A 138 ASP cc_start: 0.7993 (m-30) cc_final: 0.7710 (m-30) REVERT: A 157 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8229 (mtmt) REVERT: A 227 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: A 260 GLU cc_start: 0.7875 (mp0) cc_final: 0.7586 (mp0) REVERT: A 291 ASP cc_start: 0.7776 (t0) cc_final: 0.7338 (t0) REVERT: A 423 LEU cc_start: 0.6940 (mp) cc_final: 0.6592 (mp) REVERT: A 430 GLU cc_start: 0.6755 (tp30) cc_final: 0.6442 (tt0) REVERT: A 467 GLU cc_start: 0.6234 (tm-30) cc_final: 0.5793 (tt0) REVERT: B 46 LYS cc_start: 0.8382 (mtmt) cc_final: 0.8145 (mtmm) REVERT: B 157 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7594 (mttm) REVERT: B 203 ASN cc_start: 0.7825 (m-40) cc_final: 0.7344 (m-40) REVERT: B 230 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.6464 (ttm) REVERT: B 408 GLN cc_start: 0.7543 (tt0) cc_final: 0.6622 (tp40) REVERT: B 464 LYS cc_start: 0.7070 (mttp) cc_final: 0.6852 (mttp) REVERT: C 91 PHE cc_start: 0.8010 (m-80) cc_final: 0.7760 (m-80) REVERT: C 260 GLU cc_start: 0.7696 (mp0) cc_final: 0.6303 (mm-30) REVERT: C 416 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6817 (tt) REVERT: C 430 GLU cc_start: 0.7068 (tt0) cc_final: 0.6785 (tp30) REVERT: C 464 LYS cc_start: 0.7025 (ttmm) cc_final: 0.6675 (mmtm) REVERT: C 467 GLU cc_start: 0.5998 (tm-30) cc_final: 0.5575 (tt0) REVERT: C 468 GLU cc_start: 0.6984 (tt0) cc_final: 0.6198 (mm-30) outliers start: 35 outliers final: 14 residues processed: 130 average time/residue: 0.9495 time to fit residues: 137.5950 Evaluate side-chains 117 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 227 GLN 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 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 310 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 416 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 111 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 247 ASN B 412 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.148042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.105556 restraints weight = 12278.987| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.89 r_work: 0.3045 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11886 Z= 0.167 Angle : 0.653 10.966 16167 Z= 0.314 Chirality : 0.054 0.510 1914 Planarity : 0.004 0.037 2007 Dihedral : 11.338 87.014 2421 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.31 % Allowed : 15.22 % Favored : 81.47 % 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: -0.46 (0.21), residues: 1425 helix: 2.31 (0.27), residues: 396 sheet: -0.78 (0.32), residues: 240 loop : -1.61 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 208 HIS 0.005 0.001 HIS C 81 PHE 0.019 0.002 PHE A 282 TYR 0.018 0.002 TYR A 410 ARG 0.003 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 18) link_NAG-ASN : angle 2.08572 ( 54) link_BETA1-2 : bond 0.00872 ( 3) link_BETA1-2 : angle 6.73849 ( 9) link_BETA1-4 : bond 0.00656 ( 9) link_BETA1-4 : angle 2.38125 ( 27) hydrogen bonds : bond 0.04802 ( 434) hydrogen bonds : angle 4.51578 ( 1263) link_BETA1-6 : bond 0.00984 ( 3) link_BETA1-6 : angle 1.71579 ( 9) SS BOND : bond 0.00270 ( 15) SS BOND : angle 0.61745 ( 30) glycosidic custom : bond 0.00288 ( 3) glycosidic custom : angle 0.74579 ( 9) link_BETA1-3 : bond 0.00224 ( 3) link_BETA1-3 : angle 4.90004 ( 9) covalent geometry : bond 0.00411 (11832) covalent geometry : angle 0.60406 (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 152 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8164 (tttp) cc_final: 0.7895 (tttt) REVERT: A 138 ASP cc_start: 0.7917 (m-30) cc_final: 0.7716 (m-30) REVERT: A 217 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6146 (tm-30) REVERT: A 227 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.7827 (mp10) REVERT: A 260 GLU cc_start: 0.7926 (mp0) cc_final: 0.7604 (mp0) REVERT: A 291 ASP cc_start: 0.7944 (t0) cc_final: 0.7385 (t0) REVERT: A 423 LEU cc_start: 0.6999 (mp) cc_final: 0.6631 (mp) REVERT: A 430 GLU cc_start: 0.6567 (tp30) cc_final: 0.6165 (tt0) REVERT: A 457 GLU cc_start: 0.6848 (tp30) cc_final: 0.6495 (mm-30) REVERT: B 46 LYS cc_start: 0.8447 (mtmt) cc_final: 0.8184 (mtmm) REVERT: B 157 LYS cc_start: 0.8175 (mtmm) cc_final: 0.7515 (mttm) REVERT: B 203 ASN cc_start: 0.7790 (m-40) cc_final: 0.7290 (m-40) REVERT: B 230 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.6404 (ttm) REVERT: B 464 LYS cc_start: 0.6816 (mttp) cc_final: 0.6572 (mttp) REVERT: C 220 ILE cc_start: 0.7325 (tt) cc_final: 0.7120 (tt) REVERT: C 260 GLU cc_start: 0.7753 (mp0) cc_final: 0.6163 (mm-30) REVERT: C 416 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6756 (tt) REVERT: C 430 GLU cc_start: 0.7111 (tt0) cc_final: 0.6845 (tp30) REVERT: C 464 LYS cc_start: 0.6973 (ttmm) cc_final: 0.6610 (mmtm) REVERT: C 467 GLU cc_start: 0.5996 (tm-30) cc_final: 0.5599 (tt0) REVERT: C 468 GLU cc_start: 0.6873 (tt0) cc_final: 0.6064 (mm-30) outliers start: 40 outliers final: 22 residues processed: 139 average time/residue: 0.8737 time to fit residues: 135.9393 Evaluate side-chains 135 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 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 217 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 310 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 226 LYS 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: 6.9990 chunk 43 optimal weight: 0.0670 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 86 optimal weight: 0.0170 overall best weight: 0.9158 ------------------------------------------------------------------------------- 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 112 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.155991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.114079 restraints weight = 12096.939| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.87 r_work: 0.3055 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11886 Z= 0.118 Angle : 0.581 11.425 16167 Z= 0.276 Chirality : 0.051 0.510 1914 Planarity : 0.003 0.038 2007 Dihedral : 10.452 90.086 2421 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.81 % Allowed : 16.63 % Favored : 80.56 % 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: -0.30 (0.22), residues: 1425 helix: 2.52 (0.27), residues: 396 sheet: -0.94 (0.29), residues: 282 loop : -1.46 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 208 HIS 0.004 0.001 HIS C 81 PHE 0.013 0.001 PHE A 282 TYR 0.012 0.001 TYR C 414 ARG 0.001 0.000 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 18) link_NAG-ASN : angle 1.95096 ( 54) link_BETA1-2 : bond 0.00796 ( 3) link_BETA1-2 : angle 7.12106 ( 9) link_BETA1-4 : bond 0.00589 ( 9) link_BETA1-4 : angle 2.02305 ( 27) hydrogen bonds : bond 0.04011 ( 434) hydrogen bonds : angle 4.28745 ( 1263) link_BETA1-6 : bond 0.00948 ( 3) link_BETA1-6 : angle 1.29778 ( 9) SS BOND : bond 0.00190 ( 15) SS BOND : angle 0.49937 ( 30) glycosidic custom : bond 0.00095 ( 3) glycosidic custom : angle 0.53492 ( 9) link_BETA1-3 : bond 0.00143 ( 3) link_BETA1-3 : angle 5.11607 ( 9) covalent geometry : bond 0.00277 (11832) covalent geometry : angle 0.52531 (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 142 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.8000 (m) REVERT: A 64 LYS cc_start: 0.8156 (tttp) cc_final: 0.7914 (tttt) REVERT: A 227 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: A 260 GLU cc_start: 0.7864 (mp0) cc_final: 0.7577 (mp0) REVERT: A 291 ASP cc_start: 0.7938 (t0) cc_final: 0.7400 (t0) REVERT: A 423 LEU cc_start: 0.7012 (mp) cc_final: 0.6663 (mp) REVERT: A 430 GLU cc_start: 0.6594 (tp30) cc_final: 0.6225 (tt0) REVERT: A 457 GLU cc_start: 0.6863 (tp30) cc_final: 0.6515 (mm-30) REVERT: B 46 LYS cc_start: 0.8421 (mtmt) cc_final: 0.8188 (mtmm) REVERT: B 230 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.6412 (ttm) REVERT: C 260 GLU cc_start: 0.7756 (mp0) cc_final: 0.7475 (mp0) REVERT: C 416 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6774 (tt) REVERT: C 430 GLU cc_start: 0.7067 (tt0) cc_final: 0.6831 (tp30) REVERT: C 464 LYS cc_start: 0.6908 (ttmm) cc_final: 0.6578 (mmtm) REVERT: C 467 GLU cc_start: 0.6037 (tm-30) cc_final: 0.5585 (tt0) outliers start: 34 outliers final: 19 residues processed: 133 average time/residue: 1.2231 time to fit residues: 184.2924 Evaluate side-chains 123 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 1.682 ------------------------------------------------------------------------------- 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 116 THR Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 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 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 73 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 226 LYS 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: 3.9990 chunk 42 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 121 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN B 247 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 = 0.3769 r_free = 0.3769 target = 0.155564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.115077 restraints weight = 12355.059| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.78 r_work: 0.3035 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11886 Z= 0.234 Angle : 0.742 11.278 16167 Z= 0.357 Chirality : 0.057 0.524 1914 Planarity : 0.005 0.040 2007 Dihedral : 11.691 92.026 2421 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.80 % Allowed : 16.54 % 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: -0.77 (0.21), residues: 1425 helix: 1.92 (0.26), residues: 396 sheet: -1.06 (0.30), residues: 252 loop : -1.70 (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 0.003 0.001 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 18) link_NAG-ASN : angle 2.30311 ( 54) link_BETA1-2 : bond 0.00628 ( 3) link_BETA1-2 : angle 6.87804 ( 9) link_BETA1-4 : bond 0.00658 ( 9) link_BETA1-4 : angle 2.95844 ( 27) hydrogen bonds : bond 0.05758 ( 434) hydrogen bonds : angle 4.68437 ( 1263) link_BETA1-6 : bond 0.00816 ( 3) link_BETA1-6 : angle 2.23537 ( 9) SS BOND : bond 0.00458 ( 15) SS BOND : angle 0.74975 ( 30) glycosidic custom : bond 0.00261 ( 3) glycosidic custom : angle 0.77628 ( 9) link_BETA1-3 : bond 0.00339 ( 3) link_BETA1-3 : angle 4.83596 ( 9) covalent geometry : bond 0.00590 (11832) covalent geometry : angle 0.69197 (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 154 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 108 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8189 (tttp) cc_final: 0.7949 (tttt) REVERT: A 217 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6306 (tm-30) REVERT: A 227 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.7940 (mp10) REVERT: A 260 GLU cc_start: 0.8030 (mp0) cc_final: 0.7718 (mp0) REVERT: A 291 ASP cc_start: 0.7997 (t0) cc_final: 0.7500 (t0) REVERT: A 423 LEU cc_start: 0.7207 (mp) cc_final: 0.6879 (mt) REVERT: A 430 GLU cc_start: 0.6603 (tp30) cc_final: 0.6166 (tt0) REVERT: A 457 GLU cc_start: 0.6986 (tp30) cc_final: 0.6601 (mm-30) REVERT: B 46 LYS cc_start: 0.8514 (mtmt) cc_final: 0.8304 (mtmm) REVERT: B 230 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6618 (ttm) REVERT: B 232 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6915 (pt0) REVERT: B 448 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7177 (mt) REVERT: B 456 GLU cc_start: 0.7927 (tp30) cc_final: 0.7630 (tp30) REVERT: C 416 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6907 (tt) REVERT: C 464 LYS cc_start: 0.6991 (ttmm) cc_final: 0.6588 (mmtm) outliers start: 46 outliers final: 27 residues processed: 137 average time/residue: 0.9334 time to fit residues: 144.0397 Evaluate side-chains 137 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 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 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 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 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: 1.9990 chunk 105 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 497 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 = 0.3801 r_free = 0.3801 target = 0.158724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118321 restraints weight = 12173.366| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.80 r_work: 0.3126 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11886 Z= 0.118 Angle : 0.594 11.669 16167 Z= 0.283 Chirality : 0.051 0.527 1914 Planarity : 0.003 0.038 2007 Dihedral : 10.347 96.415 2421 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.73 % Allowed : 18.20 % 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: -0.46 (0.22), residues: 1425 helix: 2.38 (0.27), residues: 396 sheet: -1.08 (0.29), residues: 282 loop : -1.53 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 208 HIS 0.004 0.001 HIS C 81 PHE 0.013 0.001 PHE A 262 TYR 0.012 0.001 TYR B 184 ARG 0.002 0.000 ARG C 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00491 ( 18) link_NAG-ASN : angle 2.10429 ( 54) link_BETA1-2 : bond 0.00763 ( 3) link_BETA1-2 : angle 7.22497 ( 9) link_BETA1-4 : bond 0.00608 ( 9) link_BETA1-4 : angle 2.15502 ( 27) hydrogen bonds : bond 0.04178 ( 434) hydrogen bonds : angle 4.33984 ( 1263) link_BETA1-6 : bond 0.00964 ( 3) link_BETA1-6 : angle 1.37044 ( 9) SS BOND : bond 0.00194 ( 15) SS BOND : angle 0.50261 ( 30) glycosidic custom : bond 0.00131 ( 3) glycosidic custom : angle 0.55794 ( 9) link_BETA1-3 : bond 0.00154 ( 3) link_BETA1-3 : angle 5.10527 ( 9) covalent geometry : bond 0.00272 (11832) covalent geometry : angle 0.53647 (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 135 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8188 (tttp) cc_final: 0.7944 (tttt) REVERT: A 227 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: A 260 GLU cc_start: 0.7907 (mp0) cc_final: 0.7628 (mp0) REVERT: A 291 ASP cc_start: 0.7987 (t0) cc_final: 0.7532 (t0) REVERT: A 423 LEU cc_start: 0.7130 (mp) cc_final: 0.6741 (mp) REVERT: A 430 GLU cc_start: 0.6658 (tp30) cc_final: 0.6212 (tt0) REVERT: A 457 GLU cc_start: 0.6865 (tp30) cc_final: 0.6498 (mm-30) REVERT: B 46 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8249 (mtmm) REVERT: B 142 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7937 (pt0) REVERT: B 230 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.6405 (ttm) REVERT: B 242 VAL cc_start: 0.7700 (OUTLIER) cc_final: 0.7480 (m) REVERT: C 416 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6806 (tt) REVERT: C 464 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6586 (mmtm) REVERT: C 467 GLU cc_start: 0.6135 (tm-30) cc_final: 0.5611 (tt0) outliers start: 33 outliers final: 21 residues processed: 127 average time/residue: 1.0603 time to fit residues: 151.5765 Evaluate side-chains 121 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 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 142 GLU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 284 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 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 416 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 108 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 247 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 = 0.3760 r_free = 0.3760 target = 0.154782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114349 restraints weight = 12257.996| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.78 r_work: 0.3021 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11886 Z= 0.252 Angle : 0.767 11.625 16167 Z= 0.370 Chirality : 0.059 0.532 1914 Planarity : 0.005 0.043 2007 Dihedral : 11.515 100.020 2421 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.98 % Allowed : 17.95 % 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: -0.92 (0.21), residues: 1425 helix: 1.78 (0.26), residues: 396 sheet: -1.20 (0.30), residues: 252 loop : -1.76 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 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 C 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 18) link_NAG-ASN : angle 2.52910 ( 54) link_BETA1-2 : bond 0.00662 ( 3) link_BETA1-2 : angle 7.03244 ( 9) link_BETA1-4 : bond 0.00698 ( 9) link_BETA1-4 : angle 3.12271 ( 27) hydrogen bonds : bond 0.05980 ( 434) hydrogen bonds : angle 4.74698 ( 1263) link_BETA1-6 : bond 0.00795 ( 3) link_BETA1-6 : angle 2.23591 ( 9) SS BOND : bond 0.00448 ( 15) SS BOND : angle 0.78619 ( 30) glycosidic custom : bond 0.00293 ( 3) glycosidic custom : angle 0.81714 ( 9) link_BETA1-3 : bond 0.00425 ( 3) link_BETA1-3 : angle 4.91478 ( 9) covalent geometry : bond 0.00639 (11832) covalent geometry : angle 0.71468 (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 139 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8176 (tttp) cc_final: 0.7941 (tttt) REVERT: A 217 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6420 (tm-30) REVERT: A 227 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.7956 (mp10) REVERT: A 260 GLU cc_start: 0.7992 (mp0) cc_final: 0.7682 (mp0) REVERT: A 291 ASP cc_start: 0.7992 (t0) cc_final: 0.7490 (t0) REVERT: A 423 LEU cc_start: 0.7250 (mp) cc_final: 0.6937 (mt) REVERT: A 430 GLU cc_start: 0.6594 (tp30) cc_final: 0.6063 (tt0) REVERT: B 46 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8330 (mtmm) REVERT: B 157 LYS cc_start: 0.8169 (mtmm) cc_final: 0.7562 (mmtm) REVERT: B 230 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6618 (ttm) REVERT: B 232 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6917 (pt0) REVERT: B 242 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7576 (m) REVERT: B 243 ASP cc_start: 0.8085 (m-30) cc_final: 0.7863 (t0) REVERT: B 456 GLU cc_start: 0.7914 (tp30) cc_final: 0.7645 (tp30) REVERT: C 294 CYS cc_start: 0.8205 (p) cc_final: 0.7810 (p) REVERT: C 416 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6838 (tt) REVERT: C 464 LYS cc_start: 0.6969 (ttmm) cc_final: 0.6623 (mmtm) REVERT: C 467 GLU cc_start: 0.6218 (tm-30) cc_final: 0.5659 (tt0) outliers start: 36 outliers final: 25 residues processed: 128 average time/residue: 0.8427 time to fit residues: 121.8674 Evaluate side-chains 133 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 217 GLU Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 284 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 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 416 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 134 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 497 ASN B 112 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.156460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.116076 restraints weight = 12181.426| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.77 r_work: 0.3154 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11886 Z= 0.122 Angle : 0.618 11.882 16167 Z= 0.296 Chirality : 0.052 0.533 1914 Planarity : 0.004 0.039 2007 Dihedral : 10.539 103.600 2421 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.73 % Allowed : 18.36 % Favored : 78.91 % 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: -0.69 (0.22), residues: 1425 helix: 2.18 (0.27), residues: 396 sheet: -1.15 (0.31), residues: 252 loop : -1.71 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 208 HIS 0.004 0.001 HIS C 314 PHE 0.013 0.002 PHE C 282 TYR 0.013 0.001 TYR C 414 ARG 0.001 0.000 ARG C 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00611 ( 18) link_NAG-ASN : angle 2.11897 ( 54) link_BETA1-2 : bond 0.00799 ( 3) link_BETA1-2 : angle 7.20193 ( 9) link_BETA1-4 : bond 0.00665 ( 9) link_BETA1-4 : angle 2.34130 ( 27) hydrogen bonds : bond 0.04447 ( 434) hydrogen bonds : angle 4.41103 ( 1263) link_BETA1-6 : bond 0.01056 ( 3) link_BETA1-6 : angle 1.46210 ( 9) SS BOND : bond 0.00218 ( 15) SS BOND : angle 0.55638 ( 30) glycosidic custom : bond 0.00174 ( 3) glycosidic custom : angle 0.60616 ( 9) link_BETA1-3 : bond 0.00182 ( 3) link_BETA1-3 : angle 5.10041 ( 9) covalent geometry : bond 0.00282 (11832) covalent geometry : angle 0.56158 (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: 33 poor density : 103 time to evaluate : 1.498 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8179 (tttp) cc_final: 0.7941 (tttt) REVERT: A 217 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6467 (tm-30) REVERT: A 227 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.7991 (mp10) REVERT: A 260 GLU cc_start: 0.7981 (mp0) cc_final: 0.7687 (mp0) REVERT: A 291 ASP cc_start: 0.7959 (t0) cc_final: 0.7431 (t0) REVERT: A 423 LEU cc_start: 0.7133 (mp) cc_final: 0.6803 (mt) REVERT: A 430 GLU cc_start: 0.6646 (tp30) cc_final: 0.6105 (tt0) REVERT: A 457 GLU cc_start: 0.6843 (tp30) cc_final: 0.6469 (mm-30) REVERT: B 46 LYS cc_start: 0.8530 (mtmt) cc_final: 0.8325 (mtmm) REVERT: B 157 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7616 (mmtt) REVERT: B 230 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.6407 (ttm) REVERT: B 242 VAL cc_start: 0.7859 (OUTLIER) cc_final: 0.7559 (m) REVERT: B 291 ASP cc_start: 0.7468 (t0) cc_final: 0.6860 (p0) REVERT: C 416 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6743 (tt) REVERT: C 467 GLU cc_start: 0.6290 (tm-30) cc_final: 0.5752 (tt0) outliers start: 33 outliers final: 23 residues processed: 127 average time/residue: 1.0320 time to fit residues: 149.8750 Evaluate side-chains 128 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 156 LEU 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 242 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 C residue 73 SER 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: 0.7980 chunk 101 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 20 optimal weight: 0.0770 chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 93 optimal weight: 0.0370 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 112 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 = 0.3823 r_free = 0.3823 target = 0.160860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121001 restraints weight = 12106.180| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.77 r_work: 0.3107 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11886 Z= 0.102 Angle : 0.581 11.715 16167 Z= 0.278 Chirality : 0.050 0.535 1914 Planarity : 0.003 0.040 2007 Dihedral : 9.452 106.121 2421 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.65 % Allowed : 19.60 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.30 (0.22), residues: 1425 helix: 2.60 (0.28), residues: 396 sheet: -1.03 (0.29), residues: 282 loop : -1.48 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 127 HIS 0.003 0.001 HIS B 69 PHE 0.011 0.001 PHE B 91 TYR 0.010 0.001 TYR C 504 ARG 0.002 0.000 ARG A 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00723 ( 18) link_NAG-ASN : angle 2.01379 ( 54) link_BETA1-2 : bond 0.00853 ( 3) link_BETA1-2 : angle 7.34825 ( 9) link_BETA1-4 : bond 0.00606 ( 9) link_BETA1-4 : angle 1.81727 ( 27) hydrogen bonds : bond 0.03550 ( 434) hydrogen bonds : angle 4.19959 ( 1263) link_BETA1-6 : bond 0.01181 ( 3) link_BETA1-6 : angle 0.87967 ( 9) SS BOND : bond 0.00144 ( 15) SS BOND : angle 0.44965 ( 30) glycosidic custom : bond 0.00162 ( 3) glycosidic custom : angle 0.56086 ( 9) link_BETA1-3 : bond 0.00309 ( 3) link_BETA1-3 : angle 4.93925 ( 9) covalent geometry : bond 0.00221 (11832) covalent geometry : angle 0.52546 (16020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8901.51 seconds wall clock time: 162 minutes 12.68 seconds (9732.68 seconds total)