Starting phenix.real_space_refine on Thu Aug 6 22:08:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zvh_74873/08_2026/9zvh_74873.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zvh_74873/08_2026/9zvh_74873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zvh_74873/08_2026/9zvh_74873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zvh_74873/08_2026/9zvh_74873.map" model { file = "/net/cci-nas-00/data/ceres_data/9zvh_74873/08_2026/9zvh_74873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zvh_74873/08_2026/9zvh_74873.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.036 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 96 5.16 5 C 10742 2.51 5 N 2901 2.21 5 O 3402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17141 Number of models: 1 Model: "" Number of chains: 15 Chain: "H" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 919 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 793 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain breaks: 1 Chain: "A" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3864 Classifications: {'peptide': 484} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 20, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3865 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 20, 'TRANS': 463} Chain breaks: 1 Chain: "C" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3865 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 20, 'TRANS': 463} Chain breaks: 1 Chain: "I" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 919 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "K" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 793 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain breaks: 1 Chain: "D" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 919 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 793 Classifications: {'peptide': 103} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 95} Chain breaks: 1 Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 95 Unusual residues: {'BMA': 1, 'GAL': 1, 'MAN': 1, 'NAG': 3, 'SIA': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.77, per 1000 atoms: 0.22 Number of scatterers: 17141 At special positions: 0 Unit cell: (152.625, 144.375, 143.55, 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 96 16.00 O 3402 8.00 N 2901 7.00 C 10742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 491 " distance=2.05 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 298 " distance=2.04 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 498 " - pdb=" SG CYS A 502 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 491 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 298 " distance=2.04 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 77 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 326 " distance=2.02 Simple disulfide: pdb=" SG CYS B 498 " - pdb=" SG CYS B 502 " distance=2.06 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 491 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 298 " distance=2.04 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.02 Simple disulfide: pdb=" SG CYS C 302 " - pdb=" SG CYS C 326 " distance=2.03 Simple disulfide: pdb=" SG CYS C 498 " - pdb=" SG CYS C 502 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 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=1, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " BETA1-2 " MAN E 4 " - " NAG E 5 " " MAN F 4 " - " NAG F 5 " " MAN J 4 " - " NAG J 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG E 5 " - " GAL E 6 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG F 5 " - " GAL F 6 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG J 5 " - " GAL J 6 " BETA2-3 " GAL E 6 " - " SIA E 7 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL F 6 " - " SIA F 7 " " GAL J 6 " - " SIA J 7 " NAG-ASN " NAG A 601 " - " ASN A 508 " " NAG A 602 " - " ASN A 310 " " NAG A 603 " - " ASN A 33 " " NAG B 601 " - " ASN B 310 " " NAG B 602 " - " ASN B 33 " " NAG C 601 " - " ASN C 310 " " NAG C 602 " - " ASN C 33 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 807.6 milliseconds 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3904 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 48 sheets defined 16.8% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.823A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.031A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 197 through 205 Processing helix chain 'A' and resid 400 through 413 removed outlier: 4.653A pdb=" N VAL A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 471 removed outlier: 3.634A pdb=" N GLU A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 460 " --> pdb=" O MET A 456 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N HIS A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ASP A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.624A pdb=" N ARG A 481 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASP A 482 " --> pdb=" O GLN A 479 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN A 483 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 484 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 484' Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 512 through 516 removed outlier: 3.687A pdb=" N GLN A 515 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 516 " --> pdb=" O TYR A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 512 through 516' Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 128 through 133 removed outlier: 4.059A pdb=" N TRP B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'B' and resid 391 through 414 removed outlier: 3.591A pdb=" N THR B 395 " --> pdb=" O ASP B 391 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR B 403 " --> pdb=" O ILE B 399 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 462 Processing helix chain 'B' and resid 464 through 478 Processing helix chain 'B' and resid 501 through 509 removed outlier: 6.373A pdb=" N ARG B 507 " --> pdb=" O MET B 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 128 through 133 removed outlier: 4.109A pdb=" N TRP C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 205 Processing helix chain 'C' and resid 391 through 413 removed outlier: 5.330A pdb=" N VAL C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN C 407 " --> pdb=" O THR C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 459 removed outlier: 3.511A pdb=" N ASP C 444 " --> pdb=" O ASP C 440 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 473 removed outlier: 4.929A pdb=" N LYS C 470 " --> pdb=" O ASP C 466 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN C 471 " --> pdb=" O SER C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 512 through 516 Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.107A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.060A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.518A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.747A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AA5, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AA6, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.934A pdb=" N GLY A 377 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 16 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A 14 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER A 381 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN A 12 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA8, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA9, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.605A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A 89 " --> pdb=" O MET A 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.542A pdb=" N SER A 104 " --> pdb=" O PHE A 242 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N TRP A 244 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU A 189 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A 266 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.542A pdb=" N SER A 104 " --> pdb=" O PHE A 242 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N TRP A 244 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU A 189 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AB4, first strand: chain 'A' and resid 143 through 148 removed outlier: 4.615A pdb=" N CYS A 146 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 174 through 176 Processing sheet with id=AB6, first strand: chain 'A' and resid 303 through 304 Processing sheet with id=AB7, first strand: chain 'B' and resid 385 through 388 removed outlier: 3.916A pdb=" N ASN B 382 " --> pdb=" O GLY B 385 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY B 377 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 16 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB9, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AC1, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AC2, first strand: chain 'B' and resid 60 through 61 removed outlier: 6.336A pdb=" N LEU B 60 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.513A pdb=" N SER B 104 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N TRP B 244 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU B 189 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR B 266 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.513A pdb=" N SER B 104 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N TRP B 244 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU B 189 " --> pdb=" O PRO B 264 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 118 through 120 removed outlier: 6.348A pdb=" N LYS B 282 " --> pdb=" O ASN B 119 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 136 through 137 Processing sheet with id=AC7, first strand: chain 'B' and resid 143 through 148 removed outlier: 4.620A pdb=" N CYS B 146 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 174 through 179 Processing sheet with id=AC9, first strand: chain 'B' and resid 307 through 309 removed outlier: 4.196A pdb=" N CYS B 302 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AD2, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AD3, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AD4, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AD5, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.594A pdb=" N LEU C 60 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.538A pdb=" N SER C 104 " --> pdb=" O PHE C 242 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N TRP C 244 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU C 189 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR C 266 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.538A pdb=" N SER C 104 " --> pdb=" O PHE C 242 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N TRP C 244 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU C 189 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AD9, first strand: chain 'C' and resid 143 through 148 removed outlier: 4.670A pdb=" N CYS C 146 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 174 through 179 Processing sheet with id=AE2, first strand: chain 'C' and resid 307 through 309 removed outlier: 3.959A pdb=" N CYS C 302 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.550A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.572A pdb=" N THR K 22 " --> pdb=" O SER K 7 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AE7, first strand: chain 'K' and resid 45 through 46 removed outlier: 3.532A pdb=" N THR K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.521A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.749A pdb=" N GLU G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AF3, first strand: chain 'G' and resid 45 through 46 569 hydrogen bonds defined for protein. 1491 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: 3.23 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5538 1.34 - 1.48: 4613 1.48 - 1.61: 7239 1.61 - 1.74: 0 1.74 - 1.87: 144 Bond restraints: 17534 Sorted by residual: bond pdb=" CA ASP A 27 " pdb=" CB ASP A 27 " ideal model delta sigma weight residual 1.526 1.572 -0.046 1.53e-02 4.27e+03 8.86e+00 bond pdb=" C2 NAG B 603 " pdb=" C3 NAG B 603 " ideal model delta sigma weight residual 1.526 1.582 -0.056 2.00e-02 2.50e+03 7.96e+00 bond pdb=" CA MET B 503 " pdb=" CB MET B 503 " ideal model delta sigma weight residual 1.530 1.570 -0.040 1.69e-02 3.50e+03 5.64e+00 bond pdb=" C CYS A 326 " pdb=" N PRO A 327 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.10e+00 bond pdb=" CB CYS A 491 " pdb=" SG CYS A 491 " ideal model delta sigma weight residual 1.808 1.874 -0.066 3.30e-02 9.18e+02 4.05e+00 ... (remaining 17529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 23645 3.95 - 7.90: 123 7.90 - 11.86: 17 11.86 - 15.81: 4 15.81 - 19.76: 2 Bond angle restraints: 23791 Sorted by residual: angle pdb=" CA MET B 503 " pdb=" CB MET B 503 " pdb=" CG MET B 503 " ideal model delta sigma weight residual 114.10 128.18 -14.08 2.00e+00 2.50e-01 4.95e+01 angle pdb=" C CYS B 502 " pdb=" N MET B 503 " pdb=" CA MET B 503 " ideal model delta sigma weight residual 121.54 134.79 -13.25 1.91e+00 2.74e-01 4.81e+01 angle pdb=" C2 NAG B 603 " pdb=" N2 NAG B 603 " pdb=" C7 NAG B 603 " ideal model delta sigma weight residual 124.56 144.32 -19.76 3.00e+00 1.11e-01 4.34e+01 angle pdb=" C ASN A 33 " pdb=" N VAL A 34 " pdb=" CA VAL A 34 " ideal model delta sigma weight residual 121.97 133.22 -11.25 1.80e+00 3.09e-01 3.90e+01 angle pdb=" C1 NAG B 603 " pdb=" C2 NAG B 603 " pdb=" N2 NAG B 603 " ideal model delta sigma weight residual 110.79 93.28 17.51 3.00e+00 1.11e-01 3.41e+01 ... (remaining 23786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9387 17.86 - 35.73: 1043 35.73 - 53.59: 301 53.59 - 71.46: 72 71.46 - 89.32: 25 Dihedral angle restraints: 10828 sinusoidal: 4719 harmonic: 6109 Sorted by residual: dihedral pdb=" CA PRO K 94 " pdb=" C PRO K 94 " pdb=" N PRO K 95 " pdb=" CA PRO K 95 " ideal model delta harmonic sigma weight residual -180.00 -106.39 -73.61 0 5.00e+00 4.00e-02 2.17e+02 dihedral pdb=" CA PRO L 94 " pdb=" C PRO L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual 180.00 -106.44 -73.56 0 5.00e+00 4.00e-02 2.16e+02 dihedral pdb=" CB CYS C 52 " pdb=" SG CYS C 52 " pdb=" SG CYS C 298 " pdb=" CB CYS C 298 " ideal model delta sinusoidal sigma weight residual 93.00 3.68 89.32 1 1.00e+01 1.00e-02 9.49e+01 ... (remaining 10825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 2547 0.118 - 0.235: 82 0.235 - 0.353: 6 0.353 - 0.471: 2 0.471 - 0.589: 3 Chirality restraints: 2640 Sorted by residual: chirality pdb=" C2 SIA F 7 " pdb=" O3 GAL F 6 " pdb=" C1 SIA F 7 " pdb=" O6 SIA F 7 " both_signs ideal model delta sigma weight residual False -2.50 -2.84 0.34 2.00e-02 2.50e+03 2.93e+02 chirality pdb=" C2 SIA E 7 " pdb=" O3 GAL E 6 " pdb=" C1 SIA E 7 " pdb=" O6 SIA E 7 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-02 2.50e+03 2.59e+02 chirality pdb=" C2 SIA J 7 " pdb=" O3 GAL J 6 " pdb=" C1 SIA J 7 " pdb=" O6 SIA J 7 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-02 2.50e+03 2.48e+02 ... (remaining 2637 not shown) Planarity restraints: 3058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 396 " -0.017 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C GLN A 396 " 0.061 2.00e-02 2.50e+03 pdb=" O GLN A 396 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS A 397 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 33 " 0.034 2.00e-02 2.50e+03 3.06e-02 1.17e+01 pdb=" CG ASN B 33 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 33 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 33 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG B 602 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO L 94 " -0.050 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO L 95 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.042 5.00e-02 4.00e+02 ... (remaining 3055 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 5127 2.84 - 3.35: 14174 3.35 - 3.87: 29289 3.87 - 4.38: 34226 4.38 - 4.90: 58858 Nonbonded interactions: 141674 Sorted by model distance: nonbonded pdb=" C MET B 503 " pdb=" N2 NAG B 603 " model vdw 2.323 2.680 nonbonded pdb=" O5 MAN F 4 " pdb=" O6 MAN F 4 " model vdw 2.412 2.432 nonbonded pdb=" N ILE A 29 " pdb=" O ILE A 29 " model vdw 2.470 2.496 nonbonded pdb=" N ILE C 29 " pdb=" N MET C 30 " model vdw 2.564 2.560 nonbonded pdb=" N ARG C 117 " pdb=" O ARG C 117 " model vdw 2.569 2.496 ... (remaining 141669 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' and (resid 11 through 251 or (resid 252 and (name N or name CA or nam \ e C or name O )) or resid 253 through 603)) selection = (chain 'C' and (resid 11 through 251 or (resid 252 and (name N or name CA or nam \ e C or name O )) or resid 253 through 603)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' 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: 3.700 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: 0.050 Set scattering table: 0.040 Process input model: 16.040 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 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 0.066 17581 Z= 0.191 Angle : 0.880 19.760 23908 Z= 0.456 Chirality : 0.055 0.589 2640 Planarity : 0.006 0.076 3051 Dihedral : 16.572 88.671 6861 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.14 % Favored : 93.57 % Rotamer: Outliers : 2.66 % Allowed : 21.81 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.17), residues: 2085 helix: -1.32 (0.28), residues: 305 sheet: -1.48 (0.20), residues: 621 loop : -2.11 (0.16), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 342 TYR 0.022 0.002 TYR B 473 PHE 0.024 0.002 PHE C 417 TRP 0.019 0.002 TRP B 375 HIS 0.009 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (17534) covalent geometry : angle 0.84882 / 0.45 (23791) SS BOND : bond 0.00887 / 0.59 ( 21) SS BOND : angle 2.34785 / 1.40 ( 42) hydrogen bonds : bond 0.21151 / 13.85 ( 539) hydrogen bonds : angle 9.00637 / 6.18 ( 1491) Misc. bond : bond 0.02647 / 1.39 ( 1) link_ALPHA1-3 : bond 0.00994 / 0.50 ( 3) link_ALPHA1-3 : angle 1.69672 / 1.08 ( 9) link_BETA1-2 : bond 0.00243 / 0.12 ( 3) link_BETA1-2 : angle 0.71862 / 0.54 ( 9) link_BETA1-4 : bond 0.00465 / 0.28 ( 9) link_BETA1-4 : angle 2.63750 / 1.62 ( 27) link_BETA2-3 : bond 0.00162 / 0.08 ( 3) link_BETA2-3 : angle 6.04958 / 3.56 ( 9) link_NAG-ASN : bond 0.00843 / 0.46 ( 7) link_NAG-ASN : angle 5.22579 / 3.76 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7043 (tt0) cc_final: 0.6435 (mt-10) REVERT: A 175 LYS cc_start: 0.7856 (mtmm) cc_final: 0.6197 (tptp) REVERT: A 223 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7051 (mt) REVERT: A 241 ASP cc_start: 0.5342 (OUTLIER) cc_final: 0.4885 (m-30) REVERT: A 285 ASP cc_start: 0.7517 (t0) cc_final: 0.7282 (t0) REVERT: A 300 THR cc_start: 0.6924 (p) cc_final: 0.6413 (t) REVERT: A 301 LYS cc_start: 0.7525 (mtpp) cc_final: 0.6404 (mtmt) REVERT: A 412 LYS cc_start: 0.6620 (mmtm) cc_final: 0.6156 (tptm) REVERT: A 426 ASN cc_start: 0.7550 (t0) cc_final: 0.6939 (t0) REVERT: A 429 ARG cc_start: 0.6759 (mmt90) cc_final: 0.6314 (mmm160) REVERT: A 431 ILE cc_start: 0.6671 (mt) cc_final: 0.6362 (mp) REVERT: A 440 ASP cc_start: 0.7190 (m-30) cc_final: 0.6969 (m-30) REVERT: A 497 LYS cc_start: 0.4831 (OUTLIER) cc_final: 0.3966 (mppt) REVERT: B 31 GLU cc_start: 0.6847 (tt0) cc_final: 0.6427 (mt-10) REVERT: B 64 ASP cc_start: 0.6768 (p0) cc_final: 0.5956 (m-30) REVERT: B 122 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: B 183 ARG cc_start: 0.5143 (OUTLIER) cc_final: 0.4400 (mmp-170) REVERT: B 218 THR cc_start: 0.8227 (t) cc_final: 0.7960 (p) REVERT: B 282 LYS cc_start: 0.6290 (tptt) cc_final: 0.5714 (ttmm) REVERT: B 283 LYS cc_start: 0.7617 (mtpt) cc_final: 0.6911 (mtmm) REVERT: B 300 THR cc_start: 0.6819 (p) cc_final: 0.6406 (t) REVERT: B 301 LYS cc_start: 0.7811 (mttt) cc_final: 0.6782 (mtmt) REVERT: B 328 LYS cc_start: 0.6762 (tttp) cc_final: 0.5260 (mptt) REVERT: B 368 TRP cc_start: 0.4699 (OUTLIER) cc_final: 0.4222 (m-10) REVERT: B 426 ASN cc_start: 0.7841 (t0) cc_final: 0.7257 (t0) REVERT: B 429 ARG cc_start: 0.6687 (mmt90) cc_final: 0.6047 (mmm160) REVERT: B 431 ILE cc_start: 0.6872 (mt) cc_final: 0.6600 (mp) REVERT: B 436 LYS cc_start: 0.7205 (tttp) cc_final: 0.6480 (ttpt) REVERT: B 440 ASP cc_start: 0.6974 (t0) cc_final: 0.6162 (m-30) REVERT: C 28 THR cc_start: 0.3233 (OUTLIER) cc_final: 0.2800 (p) REVERT: C 176 ILE cc_start: 0.7312 (tp) cc_final: 0.6859 (pt) REVERT: C 209 ILE cc_start: 0.7402 (mt) cc_final: 0.7032 (mm) REVERT: C 213 SER cc_start: 0.8225 (m) cc_final: 0.7754 (p) REVERT: C 300 THR cc_start: 0.6848 (p) cc_final: 0.6458 (t) REVERT: C 301 LYS cc_start: 0.7831 (mttm) cc_final: 0.6652 (mtmt) REVERT: C 325 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6242 (pt0) REVERT: C 411 ASP cc_start: 0.6801 (m-30) cc_final: 0.6298 (t0) REVERT: C 412 LYS cc_start: 0.5778 (mmtm) cc_final: 0.5126 (tptm) REVERT: C 413 MET cc_start: 0.5136 (mmm) cc_final: 0.4894 (mmm) REVERT: C 429 ARG cc_start: 0.6518 (mmt90) cc_final: 0.5830 (mmm160) REVERT: C 431 ILE cc_start: 0.6914 (mt) cc_final: 0.6669 (mp) REVERT: C 436 LYS cc_start: 0.7251 (ttpp) cc_final: 0.6482 (ttpt) REVERT: C 440 ASP cc_start: 0.7232 (m-30) cc_final: 0.6897 (m-30) REVERT: I 80 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7570 (ttp) outliers start: 49 outliers final: 30 residues processed: 250 average time/residue: 0.5058 time to fit residues: 141.8672 Evaluate side-chains 239 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 80 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 22 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 0.0170 chunk 122 optimal weight: 0.3980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN L 100 GLN A 94 ASN A 166 ASN A 425 ASN B 48 ASN B 94 ASN B 150 GLN B 179 ASN B 197 ASN C 25 GLN C 433 ASN K 100 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.185939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.137557 restraints weight = 17642.618| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.83 r_work: 0.3234 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17581 Z= 0.134 Angle : 0.635 13.267 23908 Z= 0.313 Chirality : 0.046 0.490 2640 Planarity : 0.005 0.072 3051 Dihedral : 9.102 83.288 3000 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.66 % Favored : 94.05 % Rotamer: Outliers : 4.84 % Allowed : 19.52 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.17), residues: 2085 helix: -0.03 (0.30), residues: 311 sheet: -1.12 (0.21), residues: 606 loop : -1.93 (0.16), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 342 TYR 0.013 0.001 TYR C 473 PHE 0.025 0.001 PHE C 417 TRP 0.015 0.001 TRP I 47 HIS 0.005 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (17534) covalent geometry : angle 0.60944 / 0.31 (23791) SS BOND : bond 0.00494 / 0.31 ( 21) SS BOND : angle 1.85730 / 1.12 ( 42) hydrogen bonds : bond 0.03852 / 2.55 ( 539) hydrogen bonds : angle 6.29086 / 4.32 ( 1491) Misc. bond : bond 0.01751 / 0.92 ( 1) link_ALPHA1-3 : bond 0.00953 / 0.48 ( 3) link_ALPHA1-3 : angle 1.83931 / 1.17 ( 9) link_BETA1-2 : bond 0.00285 / 0.14 ( 3) link_BETA1-2 : angle 0.67094 / 0.50 ( 9) link_BETA1-4 : bond 0.00406 / 0.24 ( 9) link_BETA1-4 : angle 2.60231 / 1.58 ( 27) link_BETA2-3 : bond 0.00703 / 0.35 ( 3) link_BETA2-3 : angle 4.31971 / 2.54 ( 9) link_NAG-ASN : bond 0.00690 / 0.37 ( 7) link_NAG-ASN : angle 3.66898 / 2.28 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 220 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 33 ASN cc_start: 0.6222 (OUTLIER) cc_final: 0.5920 (m110) REVERT: A 175 LYS cc_start: 0.8655 (mtmm) cc_final: 0.7888 (tptp) REVERT: A 185 ASP cc_start: 0.8807 (m-30) cc_final: 0.8540 (m-30) REVERT: A 301 LYS cc_start: 0.8353 (mtpp) cc_final: 0.7727 (mtmt) REVERT: A 412 LYS cc_start: 0.7217 (mmtm) cc_final: 0.6668 (tptm) REVERT: A 426 ASN cc_start: 0.8551 (t0) cc_final: 0.7979 (t0) REVERT: A 429 ARG cc_start: 0.8272 (mmt90) cc_final: 0.7972 (mmm160) REVERT: A 431 ILE cc_start: 0.8738 (mt) cc_final: 0.8515 (mp) REVERT: A 440 ASP cc_start: 0.8201 (m-30) cc_final: 0.7882 (m-30) REVERT: A 466 ASP cc_start: 0.3466 (OUTLIER) cc_final: 0.3074 (p0) REVERT: A 497 LYS cc_start: 0.4620 (OUTLIER) cc_final: 0.3795 (mppt) REVERT: B 31 GLU cc_start: 0.7608 (tt0) cc_final: 0.7226 (mt-10) REVERT: B 64 ASP cc_start: 0.7799 (p0) cc_final: 0.7157 (m-30) REVERT: B 82 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7392 (ptt-90) REVERT: B 183 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6846 (mmp-170) REVERT: B 282 LYS cc_start: 0.8109 (tptt) cc_final: 0.7748 (mtmm) REVERT: B 283 LYS cc_start: 0.8747 (mtpt) cc_final: 0.8539 (mtmm) REVERT: B 300 THR cc_start: 0.8058 (p) cc_final: 0.7452 (t) REVERT: B 301 LYS cc_start: 0.8454 (mttt) cc_final: 0.7914 (mtmt) REVERT: B 325 GLU cc_start: 0.7755 (pt0) cc_final: 0.7453 (pp20) REVERT: B 328 LYS cc_start: 0.7973 (tttp) cc_final: 0.6939 (mptt) REVERT: B 412 LYS cc_start: 0.6477 (tptm) cc_final: 0.6132 (tptp) REVERT: B 426 ASN cc_start: 0.8574 (t0) cc_final: 0.8111 (t0) REVERT: B 429 ARG cc_start: 0.8252 (mmt90) cc_final: 0.7876 (mmm160) REVERT: B 436 LYS cc_start: 0.8692 (tttp) cc_final: 0.8161 (ttpt) REVERT: B 440 ASP cc_start: 0.7908 (t0) cc_final: 0.7656 (m-30) REVERT: C 27 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6990 (t0) REVERT: C 176 ILE cc_start: 0.8218 (tp) cc_final: 0.7890 (pt) REVERT: C 300 THR cc_start: 0.7971 (p) cc_final: 0.7430 (t) REVERT: C 301 LYS cc_start: 0.8635 (mttm) cc_final: 0.8016 (mtmt) REVERT: C 325 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7590 (pt0) REVERT: C 411 ASP cc_start: 0.7042 (m-30) cc_final: 0.6644 (t0) REVERT: C 412 LYS cc_start: 0.6269 (OUTLIER) cc_final: 0.5697 (tptm) REVERT: C 413 MET cc_start: 0.6717 (mmm) cc_final: 0.6516 (mmm) REVERT: C 429 ARG cc_start: 0.8236 (mmt90) cc_final: 0.7828 (mmm160) REVERT: C 431 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8561 (mp) REVERT: C 436 LYS cc_start: 0.8630 (ttpp) cc_final: 0.8238 (ttpt) REVERT: C 440 ASP cc_start: 0.8139 (m-30) cc_final: 0.7861 (m-30) REVERT: I 81 GLU cc_start: 0.8321 (tt0) cc_final: 0.7777 (tt0) REVERT: D 81 GLU cc_start: 0.8325 (tt0) cc_final: 0.7754 (tt0) outliers start: 89 outliers final: 44 residues processed: 284 average time/residue: 0.5505 time to fit residues: 175.0054 Evaluate side-chains 255 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 71 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 100 GLN A 48 ASN A 94 ASN A 382 ASN A 425 ASN B 25 GLN B 48 ASN B 94 ASN B 150 GLN B 179 ASN B 197 ASN C 25 GLN C 197 ASN C 433 ASN K 100 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.182328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134399 restraints weight = 17805.885| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.07 r_work: 0.3173 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17581 Z= 0.207 Angle : 0.691 13.577 23908 Z= 0.338 Chirality : 0.048 0.457 2640 Planarity : 0.005 0.079 3051 Dihedral : 8.656 85.170 2968 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.43 % Favored : 93.29 % Rotamer: Outliers : 5.66 % Allowed : 19.20 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.17), residues: 2085 helix: 0.52 (0.31), residues: 297 sheet: -0.83 (0.21), residues: 589 loop : -1.91 (0.16), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 342 TYR 0.016 0.002 TYR G 96 PHE 0.029 0.002 PHE C 417 TRP 0.015 0.002 TRP I 47 HIS 0.006 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (17534) covalent geometry : angle 0.66270 / 0.33 (23791) SS BOND : bond 0.00643 / 0.38 ( 21) SS BOND : angle 2.41120 / 1.49 ( 42) hydrogen bonds : bond 0.03875 / 2.56 ( 539) hydrogen bonds : angle 5.98139 / 4.12 ( 1491) Misc. bond : bond 0.01848 / 0.97 ( 1) link_ALPHA1-3 : bond 0.01034 / 0.52 ( 3) link_ALPHA1-3 : angle 1.81779 / 1.17 ( 9) link_BETA1-2 : bond 0.00337 / 0.17 ( 3) link_BETA1-2 : angle 0.52220 / 0.40 ( 9) link_BETA1-4 : bond 0.00429 / 0.25 ( 9) link_BETA1-4 : angle 2.53719 / 1.53 ( 27) link_BETA2-3 : bond 0.00923 / 0.46 ( 3) link_BETA2-3 : angle 4.93094 / 2.89 ( 9) link_NAG-ASN : bond 0.00710 / 0.33 ( 7) link_NAG-ASN : angle 3.79594 / 2.44 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 192 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: H 81 GLU cc_start: 0.8316 (tt0) cc_final: 0.7870 (tt0) REVERT: A 99 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8242 (mp) REVERT: A 175 LYS cc_start: 0.8684 (mtmm) cc_final: 0.7942 (tptp) REVERT: A 185 ASP cc_start: 0.8785 (m-30) cc_final: 0.8548 (m-30) REVERT: A 250 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: A 283 LYS cc_start: 0.8479 (mtmm) cc_final: 0.7960 (mtmm) REVERT: A 300 THR cc_start: 0.8615 (p) cc_final: 0.7757 (t) REVERT: A 301 LYS cc_start: 0.8446 (mtpp) cc_final: 0.7655 (mtmt) REVERT: A 412 LYS cc_start: 0.7308 (mmtm) cc_final: 0.6705 (tptm) REVERT: A 426 ASN cc_start: 0.8548 (t0) cc_final: 0.7928 (t0) REVERT: A 429 ARG cc_start: 0.8310 (mmt90) cc_final: 0.7982 (mmm160) REVERT: A 431 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8576 (mp) REVERT: A 456 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8151 (ttm) REVERT: A 497 LYS cc_start: 0.4558 (OUTLIER) cc_final: 0.3818 (mppt) REVERT: B 25 GLN cc_start: 0.8219 (mt0) cc_final: 0.7924 (mt0) REVERT: B 31 GLU cc_start: 0.7755 (tt0) cc_final: 0.7290 (mt-10) REVERT: B 64 ASP cc_start: 0.7809 (p0) cc_final: 0.7151 (m-30) REVERT: B 82 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7485 (ptt-90) REVERT: B 114 MET cc_start: 0.8277 (mmp) cc_final: 0.7909 (ttp) REVERT: B 183 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7185 (mmp-170) REVERT: B 282 LYS cc_start: 0.8152 (tptt) cc_final: 0.7803 (mtmm) REVERT: B 283 LYS cc_start: 0.8800 (mtpt) cc_final: 0.8581 (mtmm) REVERT: B 301 LYS cc_start: 0.8555 (mttt) cc_final: 0.8044 (mtmt) REVERT: B 325 GLU cc_start: 0.7817 (pt0) cc_final: 0.7569 (pp20) REVERT: B 328 LYS cc_start: 0.8095 (tttp) cc_final: 0.7051 (mptt) REVERT: B 426 ASN cc_start: 0.8553 (t0) cc_final: 0.8111 (t0) REVERT: B 429 ARG cc_start: 0.8335 (mmt90) cc_final: 0.7889 (mmm160) REVERT: B 436 LYS cc_start: 0.8702 (tttp) cc_final: 0.8079 (ttpt) REVERT: B 440 ASP cc_start: 0.7937 (t0) cc_final: 0.7679 (m-30) REVERT: C 176 ILE cc_start: 0.8218 (tp) cc_final: 0.7841 (pt) REVERT: C 300 THR cc_start: 0.8297 (p) cc_final: 0.7627 (t) REVERT: C 301 LYS cc_start: 0.8686 (mttm) cc_final: 0.8083 (mtmt) REVERT: C 325 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7702 (pt0) REVERT: C 411 ASP cc_start: 0.7037 (m-30) cc_final: 0.6678 (t0) REVERT: C 412 LYS cc_start: 0.6437 (OUTLIER) cc_final: 0.5866 (tptm) REVERT: C 429 ARG cc_start: 0.8260 (mmt90) cc_final: 0.7775 (mmm160) REVERT: C 436 LYS cc_start: 0.8644 (ttpp) cc_final: 0.8394 (ttpt) REVERT: C 440 ASP cc_start: 0.8214 (m-30) cc_final: 0.7990 (m-30) REVERT: I 81 GLU cc_start: 0.8322 (tt0) cc_final: 0.7799 (tt0) REVERT: K 70 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7420 (mm-30) REVERT: D 81 GLU cc_start: 0.8325 (tt0) cc_final: 0.7763 (tt0) outliers start: 104 outliers final: 61 residues processed: 267 average time/residue: 0.5247 time to fit residues: 157.5199 Evaluate side-chains 252 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 182 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 45 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 160 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 129 optimal weight: 0.0670 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 100 GLN A 94 ASN A 333 ASN A 382 ASN B 48 ASN B 94 ASN B 179 ASN B 343 ASN C 25 GLN C 94 ASN C 197 ASN C 433 ASN K 100 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.183881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.135426 restraints weight = 17688.661| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.64 r_work: 0.3196 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17581 Z= 0.144 Angle : 0.640 13.053 23908 Z= 0.312 Chirality : 0.046 0.443 2640 Planarity : 0.004 0.073 3051 Dihedral : 8.386 84.324 2963 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.80 % Favored : 93.91 % Rotamer: Outliers : 5.17 % Allowed : 20.01 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.18), residues: 2085 helix: 0.84 (0.32), residues: 296 sheet: -0.65 (0.21), residues: 587 loop : -1.82 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 342 TYR 0.013 0.001 TYR C 473 PHE 0.026 0.001 PHE C 417 TRP 0.013 0.001 TRP I 47 HIS 0.004 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (17534) covalent geometry : angle 0.61003 / 0.30 (23791) SS BOND : bond 0.00563 / 0.35 ( 21) SS BOND : angle 2.15057 / 1.32 ( 42) hydrogen bonds : bond 0.03309 / 2.19 ( 539) hydrogen bonds : angle 5.64800 / 3.89 ( 1491) Misc. bond : bond 0.01870 / 0.98 ( 1) link_ALPHA1-3 : bond 0.00930 / 0.47 ( 3) link_ALPHA1-3 : angle 1.68610 / 1.08 ( 9) link_BETA1-2 : bond 0.00343 / 0.17 ( 3) link_BETA1-2 : angle 0.55730 / 0.43 ( 9) link_BETA1-4 : bond 0.00419 / 0.24 ( 9) link_BETA1-4 : angle 2.47138 / 1.49 ( 27) link_BETA2-3 : bond 0.00702 / 0.35 ( 3) link_BETA2-3 : angle 4.59072 / 2.69 ( 9) link_NAG-ASN : bond 0.01230 / 0.60 ( 7) link_NAG-ASN : angle 4.15419 / 2.81 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 198 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 68 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8474 (m) REVERT: A 27 ASP cc_start: 0.8425 (m-30) cc_final: 0.7901 (m-30) REVERT: A 146 CYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8240 (m) REVERT: A 185 ASP cc_start: 0.8711 (m-30) cc_final: 0.8496 (m-30) REVERT: A 250 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: A 283 LYS cc_start: 0.8407 (mtmm) cc_final: 0.7920 (mtmm) REVERT: A 301 LYS cc_start: 0.8417 (mtpp) cc_final: 0.7823 (mtmt) REVERT: A 412 LYS cc_start: 0.7304 (mmtm) cc_final: 0.6791 (tptm) REVERT: A 426 ASN cc_start: 0.8570 (t0) cc_final: 0.8004 (t0) REVERT: A 429 ARG cc_start: 0.8295 (mmt90) cc_final: 0.7995 (mmm160) REVERT: A 431 ILE cc_start: 0.8769 (mt) cc_final: 0.8550 (mp) REVERT: A 456 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8105 (ttm) REVERT: A 497 LYS cc_start: 0.4540 (OUTLIER) cc_final: 0.3796 (mppt) REVERT: B 25 GLN cc_start: 0.8296 (mt0) cc_final: 0.8053 (mt0) REVERT: B 64 ASP cc_start: 0.7812 (p0) cc_final: 0.7166 (m-30) REVERT: B 82 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7466 (ptt-90) REVERT: B 114 MET cc_start: 0.8263 (mmp) cc_final: 0.7898 (ttp) REVERT: B 146 CYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8197 (m) REVERT: B 183 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7145 (mmp-170) REVERT: B 218 THR cc_start: 0.9062 (t) cc_final: 0.8834 (p) REVERT: B 282 LYS cc_start: 0.8118 (tptt) cc_final: 0.7795 (mtmm) REVERT: B 300 THR cc_start: 0.8449 (p) cc_final: 0.7749 (t) REVERT: B 301 LYS cc_start: 0.8521 (mttt) cc_final: 0.7904 (mtmt) REVERT: B 325 GLU cc_start: 0.7740 (pt0) cc_final: 0.7516 (pp20) REVERT: B 328 LYS cc_start: 0.8065 (tttp) cc_final: 0.7034 (mptt) REVERT: B 426 ASN cc_start: 0.8541 (t0) cc_final: 0.8137 (t0) REVERT: B 429 ARG cc_start: 0.8277 (mmt90) cc_final: 0.7868 (mmm160) REVERT: B 436 LYS cc_start: 0.8659 (tttp) cc_final: 0.8114 (ttpt) REVERT: B 440 ASP cc_start: 0.7889 (t0) cc_final: 0.7665 (m-30) REVERT: C 176 ILE cc_start: 0.8194 (tp) cc_final: 0.7845 (pt) REVERT: C 185 ASP cc_start: 0.8904 (m-30) cc_final: 0.8575 (m-30) REVERT: C 300 THR cc_start: 0.8173 (p) cc_final: 0.7538 (t) REVERT: C 301 LYS cc_start: 0.8678 (mttm) cc_final: 0.8106 (mtmt) REVERT: C 325 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7662 (pt0) REVERT: C 411 ASP cc_start: 0.7025 (m-30) cc_final: 0.6679 (t0) REVERT: C 412 LYS cc_start: 0.6392 (OUTLIER) cc_final: 0.5868 (tptm) REVERT: C 429 ARG cc_start: 0.8208 (mmt90) cc_final: 0.7750 (mmm160) REVERT: C 436 LYS cc_start: 0.8685 (ttpp) cc_final: 0.8400 (ttpt) REVERT: C 440 ASP cc_start: 0.8262 (m-30) cc_final: 0.8043 (m-30) REVERT: I 81 GLU cc_start: 0.8313 (tt0) cc_final: 0.7801 (tt0) REVERT: G 70 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7370 (mm-30) outliers start: 95 outliers final: 52 residues processed: 264 average time/residue: 0.4941 time to fit residues: 146.6483 Evaluate side-chains 249 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 187 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 70 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 12 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 152 optimal weight: 20.0000 chunk 170 optimal weight: 0.1980 chunk 97 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 100 GLN A 18 HIS A 48 ASN A 94 ASN A 425 ASN B 94 ASN B 379 HIS C 18 HIS C 25 GLN C 94 ASN C 197 ASN C 433 ASN K 100 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.181336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132634 restraints weight = 17609.558| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.63 r_work: 0.3167 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17581 Z= 0.210 Angle : 0.694 12.965 23908 Z= 0.339 Chirality : 0.048 0.437 2640 Planarity : 0.005 0.079 3051 Dihedral : 8.507 87.159 2963 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.86 % Favored : 92.85 % Rotamer: Outliers : 6.14 % Allowed : 19.25 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.18), residues: 2085 helix: 0.76 (0.32), residues: 300 sheet: -0.73 (0.21), residues: 610 loop : -1.77 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 342 TYR 0.013 0.002 TYR G 96 PHE 0.030 0.002 PHE C 417 TRP 0.014 0.002 TRP I 47 HIS 0.006 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (17534) covalent geometry : angle 0.66212 / 0.33 (23791) SS BOND : bond 0.00691 / 0.39 ( 21) SS BOND : angle 2.48859 / 1.53 ( 42) hydrogen bonds : bond 0.03641 / 2.41 ( 539) hydrogen bonds : angle 5.66102 / 3.91 ( 1491) Misc. bond : bond 0.01794 / 0.94 ( 1) link_ALPHA1-3 : bond 0.00907 / 0.46 ( 3) link_ALPHA1-3 : angle 1.65532 / 1.08 ( 9) link_BETA1-2 : bond 0.00346 / 0.17 ( 3) link_BETA1-2 : angle 0.49606 / 0.38 ( 9) link_BETA1-4 : bond 0.00455 / 0.26 ( 9) link_BETA1-4 : angle 2.52581 / 1.51 ( 27) link_BETA2-3 : bond 0.00867 / 0.43 ( 3) link_BETA2-3 : angle 5.09342 / 2.98 ( 9) link_NAG-ASN : bond 0.01057 / 0.50 ( 7) link_NAG-ASN : angle 4.28423 / 3.00 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 186 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8398 (m-30) cc_final: 0.7981 (m-30) REVERT: A 99 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8332 (mp) REVERT: A 146 CYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8284 (m) REVERT: A 250 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: A 283 LYS cc_start: 0.8467 (mtmm) cc_final: 0.7971 (mtmm) REVERT: A 300 THR cc_start: 0.8701 (p) cc_final: 0.7801 (t) REVERT: A 301 LYS cc_start: 0.8564 (mtpp) cc_final: 0.7724 (mtmt) REVERT: A 368 TRP cc_start: 0.5353 (OUTLIER) cc_final: 0.3627 (p-90) REVERT: A 412 LYS cc_start: 0.7371 (mmtm) cc_final: 0.6810 (tptm) REVERT: A 426 ASN cc_start: 0.8585 (t0) cc_final: 0.8044 (t0) REVERT: A 429 ARG cc_start: 0.8308 (mmt90) cc_final: 0.7933 (mmm160) REVERT: A 431 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8577 (mp) REVERT: A 456 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8171 (ttm) REVERT: A 497 LYS cc_start: 0.4388 (OUTLIER) cc_final: 0.3670 (mppt) REVERT: A 498 CYS cc_start: 0.0367 (OUTLIER) cc_final: -0.1527 (m) REVERT: B 64 ASP cc_start: 0.7832 (p0) cc_final: 0.7175 (m-30) REVERT: B 114 MET cc_start: 0.8283 (mmp) cc_final: 0.7918 (ttp) REVERT: B 146 CYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8247 (m) REVERT: B 218 THR cc_start: 0.9011 (t) cc_final: 0.8799 (p) REVERT: B 282 LYS cc_start: 0.8133 (tptt) cc_final: 0.7839 (mtmm) REVERT: B 301 LYS cc_start: 0.8544 (mttt) cc_final: 0.8027 (mtmt) REVERT: B 328 LYS cc_start: 0.8055 (tttp) cc_final: 0.7027 (mptt) REVERT: B 426 ASN cc_start: 0.8580 (t0) cc_final: 0.8220 (t0) REVERT: B 429 ARG cc_start: 0.8312 (mmt90) cc_final: 0.7895 (mmm160) REVERT: B 436 LYS cc_start: 0.8651 (tttp) cc_final: 0.8125 (ttpt) REVERT: B 440 ASP cc_start: 0.7908 (t0) cc_final: 0.7687 (m-30) REVERT: C 185 ASP cc_start: 0.8909 (m-30) cc_final: 0.8555 (m-30) REVERT: C 300 THR cc_start: 0.8498 (p) cc_final: 0.7822 (t) REVERT: C 301 LYS cc_start: 0.8697 (mttm) cc_final: 0.8093 (mtmt) REVERT: C 411 ASP cc_start: 0.7048 (m-30) cc_final: 0.6760 (t0) REVERT: C 412 LYS cc_start: 0.6677 (OUTLIER) cc_final: 0.6061 (tptm) REVERT: C 429 ARG cc_start: 0.8271 (mmt90) cc_final: 0.7764 (mmm160) REVERT: C 436 LYS cc_start: 0.8684 (ttpp) cc_final: 0.8482 (ttpt) REVERT: G 70 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7373 (mm-30) outliers start: 113 outliers final: 73 residues processed: 273 average time/residue: 0.4873 time to fit residues: 149.9965 Evaluate side-chains 260 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 176 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 191 optimal weight: 1.9990 chunk 68 optimal weight: 30.0000 chunk 76 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 164 optimal weight: 20.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 100 GLN A 48 ASN A 94 ASN B 25 GLN B 48 ASN B 94 ASN C 25 GLN C 38 HIS C 94 ASN ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.181235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132985 restraints weight = 17627.161| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.56 r_work: 0.3153 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17581 Z= 0.205 Angle : 0.691 12.601 23908 Z= 0.337 Chirality : 0.048 0.430 2640 Planarity : 0.005 0.079 3051 Dihedral : 8.483 88.564 2963 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.14 % Favored : 93.57 % Rotamer: Outliers : 6.09 % Allowed : 19.68 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.18), residues: 2085 helix: 0.64 (0.31), residues: 309 sheet: -0.74 (0.21), residues: 616 loop : -1.74 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 342 TYR 0.019 0.002 TYR B 17 PHE 0.031 0.002 PHE C 417 TRP 0.013 0.002 TRP I 47 HIS 0.007 0.001 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.20 (17534) covalent geometry : angle 0.66009 / 0.33 (23791) SS BOND : bond 0.00901 / 0.55 ( 21) SS BOND : angle 2.41832 / 1.51 ( 42) hydrogen bonds : bond 0.03545 / 2.35 ( 539) hydrogen bonds : angle 5.58420 / 3.86 ( 1491) Misc. bond : bond 0.01783 / 0.94 ( 1) link_ALPHA1-3 : bond 0.00807 / 0.40 ( 3) link_ALPHA1-3 : angle 1.57644 / 1.02 ( 9) link_BETA1-2 : bond 0.00348 / 0.17 ( 3) link_BETA1-2 : angle 0.48940 / 0.37 ( 9) link_BETA1-4 : bond 0.00459 / 0.26 ( 9) link_BETA1-4 : angle 2.52239 / 1.51 ( 27) link_BETA2-3 : bond 0.00954 / 0.48 ( 3) link_BETA2-3 : angle 5.14520 / 3.01 ( 9) link_NAG-ASN : bond 0.01046 / 0.51 ( 7) link_NAG-ASN : angle 4.21279 / 2.97 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 186 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 68 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8540 (m) REVERT: A 37 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7536 (p) REVERT: A 99 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8316 (mp) REVERT: A 146 CYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8275 (m) REVERT: A 185 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8223 (m-30) REVERT: A 250 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7326 (m-30) REVERT: A 283 LYS cc_start: 0.8577 (mtmm) cc_final: 0.7900 (mtmm) REVERT: A 300 THR cc_start: 0.8757 (p) cc_final: 0.7890 (t) REVERT: A 301 LYS cc_start: 0.8553 (mtpp) cc_final: 0.7732 (mtmt) REVERT: A 368 TRP cc_start: 0.5310 (OUTLIER) cc_final: 0.3504 (p-90) REVERT: A 411 ASP cc_start: 0.7222 (m-30) cc_final: 0.6835 (t0) REVERT: A 412 LYS cc_start: 0.7359 (mmtm) cc_final: 0.6728 (tptm) REVERT: A 426 ASN cc_start: 0.8589 (t0) cc_final: 0.8026 (t0) REVERT: A 429 ARG cc_start: 0.8294 (mmt90) cc_final: 0.7915 (mmm160) REVERT: A 431 ILE cc_start: 0.8809 (mt) cc_final: 0.8597 (mp) REVERT: A 456 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8158 (ttm) REVERT: A 497 LYS cc_start: 0.4393 (OUTLIER) cc_final: 0.3732 (mppt) REVERT: B 64 ASP cc_start: 0.7867 (p0) cc_final: 0.7192 (m-30) REVERT: B 114 MET cc_start: 0.8303 (mmp) cc_final: 0.7936 (ttp) REVERT: B 146 CYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8265 (m) REVERT: B 218 THR cc_start: 0.9035 (t) cc_final: 0.8824 (p) REVERT: B 282 LYS cc_start: 0.8153 (tptt) cc_final: 0.7830 (mtmm) REVERT: B 301 LYS cc_start: 0.8552 (mttt) cc_final: 0.8019 (mtmt) REVERT: B 328 LYS cc_start: 0.8042 (tttp) cc_final: 0.7019 (mptt) REVERT: B 426 ASN cc_start: 0.8592 (t0) cc_final: 0.8253 (t0) REVERT: B 429 ARG cc_start: 0.8319 (mmt90) cc_final: 0.7906 (mmm160) REVERT: B 436 LYS cc_start: 0.8654 (tttp) cc_final: 0.8132 (ttpt) REVERT: B 440 ASP cc_start: 0.7919 (t0) cc_final: 0.7674 (m-30) REVERT: C 185 ASP cc_start: 0.8897 (m-30) cc_final: 0.8552 (m-30) REVERT: C 300 THR cc_start: 0.8476 (p) cc_final: 0.7875 (t) REVERT: C 301 LYS cc_start: 0.8602 (mttm) cc_final: 0.7946 (mtmt) REVERT: C 321 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8641 (mp) REVERT: C 325 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7490 (tp30) REVERT: C 411 ASP cc_start: 0.7007 (m-30) cc_final: 0.6750 (t0) REVERT: C 412 LYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6123 (tptm) REVERT: C 429 ARG cc_start: 0.8287 (mmt90) cc_final: 0.7777 (mmm160) REVERT: C 498 CYS cc_start: 0.0916 (OUTLIER) cc_final: 0.0289 (p) outliers start: 112 outliers final: 66 residues processed: 272 average time/residue: 0.4789 time to fit residues: 147.3904 Evaluate side-chains 261 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 181 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 498 CYS Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 89 optimal weight: 1.9990 chunk 66 optimal weight: 30.0000 chunk 93 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 140 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 88 optimal weight: 0.1980 chunk 75 optimal weight: 0.0770 chunk 132 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 162 optimal weight: 30.0000 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 100 GLN A 48 ASN A 94 ASN B 25 GLN B 94 ASN B 179 ASN C 25 GLN C 38 HIS C 94 ASN C 150 GLN C 433 ASN K 100 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.182825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134531 restraints weight = 17606.528| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.62 r_work: 0.3188 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17581 Z= 0.146 Angle : 0.644 12.695 23908 Z= 0.313 Chirality : 0.047 0.431 2640 Planarity : 0.004 0.073 3051 Dihedral : 8.264 86.464 2963 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.85 % Favored : 93.86 % Rotamer: Outliers : 5.38 % Allowed : 20.72 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.18), residues: 2085 helix: 0.67 (0.31), residues: 314 sheet: -0.68 (0.21), residues: 611 loop : -1.69 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 342 TYR 0.014 0.001 TYR B 17 PHE 0.028 0.001 PHE C 417 TRP 0.012 0.001 TRP C 446 HIS 0.004 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (17534) covalent geometry : angle 0.61410 / 0.31 (23791) SS BOND : bond 0.00555 / 0.34 ( 21) SS BOND : angle 1.94447 / 1.21 ( 42) hydrogen bonds : bond 0.03234 / 2.14 ( 539) hydrogen bonds : angle 5.39836 / 3.73 ( 1491) Misc. bond : bond 0.01768 / 0.93 ( 1) link_ALPHA1-3 : bond 0.00815 / 0.41 ( 3) link_ALPHA1-3 : angle 1.53081 / 0.99 ( 9) link_BETA1-2 : bond 0.00348 / 0.17 ( 3) link_BETA1-2 : angle 0.51345 / 0.38 ( 9) link_BETA1-4 : bond 0.00437 / 0.25 ( 9) link_BETA1-4 : angle 2.41694 / 1.45 ( 27) link_BETA2-3 : bond 0.00739 / 0.37 ( 3) link_BETA2-3 : angle 4.75862 / 2.79 ( 9) link_NAG-ASN : bond 0.01056 / 0.52 ( 7) link_NAG-ASN : angle 4.29374 / 3.10 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 187 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 68 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8517 (m) REVERT: L 7 SER cc_start: 0.8782 (m) cc_final: 0.8553 (p) REVERT: L 70 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: A 14 CYS cc_start: 0.4976 (OUTLIER) cc_final: 0.3696 (m) REVERT: A 37 THR cc_start: 0.7959 (OUTLIER) cc_final: 0.7547 (p) REVERT: A 146 CYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8230 (m) REVERT: A 250 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7254 (m-30) REVERT: A 283 LYS cc_start: 0.8503 (mtmm) cc_final: 0.7935 (mtmm) REVERT: A 300 THR cc_start: 0.8612 (p) cc_final: 0.7773 (t) REVERT: A 301 LYS cc_start: 0.8478 (mtpp) cc_final: 0.7710 (mtmt) REVERT: A 368 TRP cc_start: 0.5227 (OUTLIER) cc_final: 0.3520 (p-90) REVERT: A 412 LYS cc_start: 0.7264 (mmtm) cc_final: 0.6788 (tptm) REVERT: A 413 MET cc_start: 0.7736 (mmm) cc_final: 0.7529 (mmm) REVERT: A 429 ARG cc_start: 0.8276 (mmt90) cc_final: 0.7999 (mmm160) REVERT: A 431 ILE cc_start: 0.8787 (mt) cc_final: 0.8557 (mp) REVERT: A 456 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8149 (ttm) REVERT: A 497 LYS cc_start: 0.4357 (OUTLIER) cc_final: 0.3675 (mppt) REVERT: A 498 CYS cc_start: 0.0524 (OUTLIER) cc_final: -0.1334 (m) REVERT: B 64 ASP cc_start: 0.7832 (p0) cc_final: 0.7196 (m-30) REVERT: B 146 CYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8204 (m) REVERT: B 218 THR cc_start: 0.9014 (t) cc_final: 0.8808 (p) REVERT: B 282 LYS cc_start: 0.8119 (tptt) cc_final: 0.7812 (mtmm) REVERT: B 300 THR cc_start: 0.8580 (p) cc_final: 0.7902 (t) REVERT: B 301 LYS cc_start: 0.8562 (mttt) cc_final: 0.7927 (mtmt) REVERT: B 328 LYS cc_start: 0.7965 (tttp) cc_final: 0.6966 (mptt) REVERT: B 426 ASN cc_start: 0.8560 (t0) cc_final: 0.8223 (t0) REVERT: B 429 ARG cc_start: 0.8275 (mmt90) cc_final: 0.7883 (mmm160) REVERT: B 436 LYS cc_start: 0.8608 (tttp) cc_final: 0.8125 (ttpt) REVERT: B 440 ASP cc_start: 0.7849 (t0) cc_final: 0.7637 (m-30) REVERT: C 176 ILE cc_start: 0.8305 (tp) cc_final: 0.7903 (pt) REVERT: C 185 ASP cc_start: 0.8882 (m-30) cc_final: 0.8529 (m-30) REVERT: C 300 THR cc_start: 0.8261 (p) cc_final: 0.7629 (t) REVERT: C 301 LYS cc_start: 0.8566 (mttm) cc_final: 0.7904 (mtmt) REVERT: C 325 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7303 (tp30) REVERT: C 411 ASP cc_start: 0.7022 (m-30) cc_final: 0.6736 (t0) REVERT: C 412 LYS cc_start: 0.6649 (OUTLIER) cc_final: 0.6070 (tptm) REVERT: C 429 ARG cc_start: 0.8218 (mmt90) cc_final: 0.7710 (mmm160) REVERT: G 70 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7286 (mm-30) outliers start: 99 outliers final: 62 residues processed: 265 average time/residue: 0.4676 time to fit residues: 140.0466 Evaluate side-chains 259 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 183 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 70 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 189 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 112 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 129 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 100 GLN A 48 ASN A 94 ASN B 48 ASN B 94 ASN B 179 ASN C 25 GLN C 38 HIS C 94 ASN C 150 GLN C 433 ASN C 435 ASN K 100 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.182731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.134388 restraints weight = 17707.012| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.64 r_work: 0.3194 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17581 Z= 0.155 Angle : 0.647 12.688 23908 Z= 0.315 Chirality : 0.047 0.428 2640 Planarity : 0.004 0.072 3051 Dihedral : 8.160 85.654 2963 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.66 % Favored : 94.05 % Rotamer: Outliers : 5.17 % Allowed : 21.10 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.18), residues: 2085 helix: 0.83 (0.31), residues: 309 sheet: -0.74 (0.21), residues: 618 loop : -1.63 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 342 TYR 0.015 0.001 TYR A 473 PHE 0.026 0.001 PHE C 417 TRP 0.012 0.001 TRP I 47 HIS 0.005 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (17534) covalent geometry : angle 0.61693 / 0.31 (23791) SS BOND : bond 0.00568 / 0.33 ( 21) SS BOND : angle 2.05115 / 1.28 ( 42) hydrogen bonds : bond 0.03218 / 2.13 ( 539) hydrogen bonds : angle 5.34600 / 3.69 ( 1491) Misc. bond : bond 0.01756 / 0.92 ( 1) link_ALPHA1-3 : bond 0.00786 / 0.40 ( 3) link_ALPHA1-3 : angle 1.51160 / 0.98 ( 9) link_BETA1-2 : bond 0.00353 / 0.18 ( 3) link_BETA1-2 : angle 0.49749 / 0.36 ( 9) link_BETA1-4 : bond 0.00440 / 0.25 ( 9) link_BETA1-4 : angle 2.38328 / 1.43 ( 27) link_BETA2-3 : bond 0.00744 / 0.37 ( 3) link_BETA2-3 : angle 4.71110 / 2.76 ( 9) link_NAG-ASN : bond 0.00975 / 0.48 ( 7) link_NAG-ASN : angle 4.28709 / 3.11 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 191 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 68 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8501 (m) REVERT: A 14 CYS cc_start: 0.4935 (OUTLIER) cc_final: 0.3640 (m) REVERT: A 37 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7540 (p) REVERT: A 146 CYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8218 (m) REVERT: A 283 LYS cc_start: 0.8542 (mtmm) cc_final: 0.7962 (mtmm) REVERT: A 300 THR cc_start: 0.8589 (p) cc_final: 0.7721 (t) REVERT: A 301 LYS cc_start: 0.8483 (mtpp) cc_final: 0.7699 (mtmt) REVERT: A 368 TRP cc_start: 0.5199 (OUTLIER) cc_final: 0.3567 (p-90) REVERT: A 412 LYS cc_start: 0.7215 (mmtm) cc_final: 0.6753 (tptm) REVERT: A 413 MET cc_start: 0.7719 (mmm) cc_final: 0.7463 (mmm) REVERT: A 429 ARG cc_start: 0.8258 (mmt90) cc_final: 0.7919 (mmm160) REVERT: A 431 ILE cc_start: 0.8765 (mt) cc_final: 0.8540 (mp) REVERT: A 456 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8131 (ttm) REVERT: A 497 LYS cc_start: 0.4354 (OUTLIER) cc_final: 0.3713 (mppt) REVERT: B 64 ASP cc_start: 0.7848 (p0) cc_final: 0.7198 (m-30) REVERT: B 146 CYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8196 (m) REVERT: B 218 THR cc_start: 0.9019 (t) cc_final: 0.8801 (p) REVERT: B 282 LYS cc_start: 0.8160 (tptt) cc_final: 0.7833 (mtmm) REVERT: B 300 THR cc_start: 0.8550 (p) cc_final: 0.7876 (t) REVERT: B 301 LYS cc_start: 0.8565 (mttt) cc_final: 0.7924 (mtmt) REVERT: B 311 SER cc_start: 0.8574 (t) cc_final: 0.8367 (p) REVERT: B 325 GLU cc_start: 0.7970 (pp20) cc_final: 0.7056 (tp30) REVERT: B 328 LYS cc_start: 0.7989 (tttp) cc_final: 0.6973 (mptt) REVERT: B 429 ARG cc_start: 0.8261 (mmt90) cc_final: 0.7867 (mmm160) REVERT: B 436 LYS cc_start: 0.8598 (tttp) cc_final: 0.8118 (ttpt) REVERT: B 440 ASP cc_start: 0.7829 (t0) cc_final: 0.7626 (m-30) REVERT: C 176 ILE cc_start: 0.8284 (tp) cc_final: 0.7884 (pt) REVERT: C 185 ASP cc_start: 0.8877 (m-30) cc_final: 0.8524 (m-30) REVERT: C 300 THR cc_start: 0.8262 (p) cc_final: 0.7575 (t) REVERT: C 301 LYS cc_start: 0.8569 (mttm) cc_final: 0.7878 (mtmt) REVERT: C 325 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7220 (tp30) REVERT: C 411 ASP cc_start: 0.7035 (m-30) cc_final: 0.6717 (t0) REVERT: C 412 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.6049 (tptm) REVERT: C 429 ARG cc_start: 0.8206 (mmt90) cc_final: 0.7680 (mmm160) REVERT: C 503 MET cc_start: 0.0083 (tmt) cc_final: -0.0804 (mmm) REVERT: G 70 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7271 (mm-30) outliers start: 95 outliers final: 66 residues processed: 265 average time/residue: 0.4686 time to fit residues: 140.7001 Evaluate side-chains 267 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 190 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 70 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 175 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 94 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 100 GLN A 94 ASN B 94 ASN C 25 GLN C 38 HIS C 94 ASN C 433 ASN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.180548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132574 restraints weight = 17722.874| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.60 r_work: 0.3138 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17581 Z= 0.226 Angle : 0.702 12.712 23908 Z= 0.342 Chirality : 0.049 0.418 2640 Planarity : 0.005 0.079 3051 Dihedral : 8.368 88.695 2963 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.86 % Favored : 92.85 % Rotamer: Outliers : 5.22 % Allowed : 20.99 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.18), residues: 2085 helix: 0.69 (0.31), residues: 309 sheet: -0.69 (0.21), residues: 614 loop : -1.69 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 342 TYR 0.014 0.002 TYR A 473 PHE 0.031 0.002 PHE C 417 TRP 0.014 0.002 TRP I 47 HIS 0.007 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (17534) covalent geometry : angle 0.67220 / 0.33 (23791) SS BOND : bond 0.00721 / 0.40 ( 21) SS BOND : angle 2.38878 / 1.50 ( 42) hydrogen bonds : bond 0.03589 / 2.37 ( 539) hydrogen bonds : angle 5.52865 / 3.82 ( 1491) Misc. bond : bond 0.01743 / 0.92 ( 1) link_ALPHA1-3 : bond 0.00774 / 0.39 ( 3) link_ALPHA1-3 : angle 1.50022 / 1.00 ( 9) link_BETA1-2 : bond 0.00354 / 0.18 ( 3) link_BETA1-2 : angle 0.42931 / 0.30 ( 9) link_BETA1-4 : bond 0.00460 / 0.26 ( 9) link_BETA1-4 : angle 2.50154 / 1.50 ( 27) link_BETA2-3 : bond 0.00878 / 0.44 ( 3) link_BETA2-3 : angle 5.20982 / 3.04 ( 9) link_NAG-ASN : bond 0.00991 / 0.49 ( 7) link_NAG-ASN : angle 4.15691 / 2.98 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 186 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 68 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8564 (m) REVERT: H 105 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8275 (pt0) REVERT: A 14 CYS cc_start: 0.5004 (OUTLIER) cc_final: 0.3661 (m) REVERT: A 37 THR cc_start: 0.7921 (OUTLIER) cc_final: 0.7499 (p) REVERT: A 146 CYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8303 (m) REVERT: A 185 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8241 (m-30) REVERT: A 283 LYS cc_start: 0.8608 (mtmm) cc_final: 0.7911 (mtmm) REVERT: A 300 THR cc_start: 0.8846 (p) cc_final: 0.7996 (t) REVERT: A 301 LYS cc_start: 0.8554 (mtpp) cc_final: 0.7722 (mtmt) REVERT: A 368 TRP cc_start: 0.5410 (OUTLIER) cc_final: 0.3572 (p-90) REVERT: A 411 ASP cc_start: 0.7248 (m-30) cc_final: 0.6860 (t0) REVERT: A 412 LYS cc_start: 0.7193 (mmtm) cc_final: 0.6657 (tptm) REVERT: A 429 ARG cc_start: 0.8287 (mmt90) cc_final: 0.7939 (mmm160) REVERT: A 431 ILE cc_start: 0.8826 (mt) cc_final: 0.8594 (mp) REVERT: A 456 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8159 (ttm) REVERT: A 497 LYS cc_start: 0.4355 (OUTLIER) cc_final: 0.3719 (mppt) REVERT: B 64 ASP cc_start: 0.7872 (p0) cc_final: 0.7188 (m-30) REVERT: B 146 CYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8237 (m) REVERT: B 282 LYS cc_start: 0.8198 (tptt) cc_final: 0.7845 (mtmm) REVERT: B 301 LYS cc_start: 0.8565 (mttt) cc_final: 0.8013 (mtmt) REVERT: B 328 LYS cc_start: 0.8066 (tttp) cc_final: 0.7060 (mptt) REVERT: B 426 ASN cc_start: 0.8605 (t0) cc_final: 0.8268 (t0) REVERT: B 429 ARG cc_start: 0.8336 (mmt90) cc_final: 0.7909 (mmm160) REVERT: B 436 LYS cc_start: 0.8653 (tttp) cc_final: 0.8151 (ttpt) REVERT: B 440 ASP cc_start: 0.7956 (t0) cc_final: 0.7694 (m-30) REVERT: C 185 ASP cc_start: 0.8895 (m-30) cc_final: 0.8559 (m-30) REVERT: C 300 THR cc_start: 0.8612 (p) cc_final: 0.7903 (t) REVERT: C 301 LYS cc_start: 0.8613 (mttm) cc_final: 0.7890 (mtmt) REVERT: C 325 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7248 (tp30) REVERT: C 411 ASP cc_start: 0.7019 (m-30) cc_final: 0.6741 (t0) REVERT: C 412 LYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6127 (tptm) REVERT: C 429 ARG cc_start: 0.8289 (mmt90) cc_final: 0.7761 (mmm160) REVERT: G 70 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7357 (mm-30) outliers start: 96 outliers final: 69 residues processed: 261 average time/residue: 0.4592 time to fit residues: 135.5726 Evaluate side-chains 264 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 182 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 70 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 90 optimal weight: 0.0470 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 100 GLN A 48 ASN A 94 ASN B 48 ASN B 94 ASN B 179 ASN B 197 ASN C 25 GLN C 38 HIS C 94 ASN C 433 ASN I 52 ASN K 100 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.183678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.135551 restraints weight = 17574.589| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.56 r_work: 0.3204 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17581 Z= 0.130 Angle : 0.637 12.694 23908 Z= 0.309 Chirality : 0.046 0.414 2640 Planarity : 0.004 0.070 3051 Dihedral : 8.129 85.204 2963 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.42 % Favored : 94.29 % Rotamer: Outliers : 4.89 % Allowed : 21.59 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.18), residues: 2085 helix: 0.86 (0.32), residues: 308 sheet: -0.70 (0.21), residues: 616 loop : -1.61 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 342 TYR 0.013 0.001 TYR C 473 PHE 0.025 0.001 PHE C 417 TRP 0.015 0.001 TRP B 446 HIS 0.004 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (17534) covalent geometry : angle 0.60615 / 0.30 (23791) SS BOND : bond 0.00500 / 0.30 ( 21) SS BOND : angle 1.91032 / 1.17 ( 42) hydrogen bonds : bond 0.03071 / 2.02 ( 539) hydrogen bonds : angle 5.28997 / 3.65 ( 1491) Misc. bond : bond 0.01759 / 0.93 ( 1) link_ALPHA1-3 : bond 0.00748 / 0.38 ( 3) link_ALPHA1-3 : angle 1.45940 / 0.93 ( 9) link_BETA1-2 : bond 0.00357 / 0.18 ( 3) link_BETA1-2 : angle 0.48858 / 0.34 ( 9) link_BETA1-4 : bond 0.00431 / 0.25 ( 9) link_BETA1-4 : angle 2.34441 / 1.42 ( 27) link_BETA2-3 : bond 0.00645 / 0.32 ( 3) link_BETA2-3 : angle 4.56442 / 2.68 ( 9) link_NAG-ASN : bond 0.01186 / 0.54 ( 7) link_NAG-ASN : angle 4.65483 / 3.43 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 190 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 68 THR cc_start: 0.8809 (t) cc_final: 0.8530 (m) REVERT: A 14 CYS cc_start: 0.4937 (OUTLIER) cc_final: 0.3640 (m) REVERT: A 37 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7528 (p) REVERT: A 114 MET cc_start: 0.8268 (mmp) cc_final: 0.7907 (ttp) REVERT: A 146 CYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8270 (m) REVERT: A 185 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8328 (m-30) REVERT: A 283 LYS cc_start: 0.8490 (mtmm) cc_final: 0.7838 (mtmm) REVERT: A 300 THR cc_start: 0.8551 (p) cc_final: 0.7684 (t) REVERT: A 301 LYS cc_start: 0.8422 (mtpp) cc_final: 0.7680 (mtmt) REVERT: A 368 TRP cc_start: 0.5276 (OUTLIER) cc_final: 0.3647 (p-90) REVERT: A 412 LYS cc_start: 0.7044 (mmtm) cc_final: 0.6746 (tptm) REVERT: A 413 MET cc_start: 0.7628 (mmm) cc_final: 0.7331 (mmm) REVERT: A 429 ARG cc_start: 0.8237 (mmt90) cc_final: 0.7930 (mmm160) REVERT: A 431 ILE cc_start: 0.8779 (mt) cc_final: 0.8559 (mp) REVERT: A 456 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8114 (ttp) REVERT: A 497 LYS cc_start: 0.4317 (OUTLIER) cc_final: 0.3687 (mppt) REVERT: B 64 ASP cc_start: 0.7841 (p0) cc_final: 0.7196 (m-30) REVERT: B 114 MET cc_start: 0.8271 (mmp) cc_final: 0.7927 (ttp) REVERT: B 146 CYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8198 (m) REVERT: B 197 ASN cc_start: 0.8679 (p0) cc_final: 0.8427 (p0) REVERT: B 218 THR cc_start: 0.9040 (t) cc_final: 0.8834 (p) REVERT: B 282 LYS cc_start: 0.8123 (tptt) cc_final: 0.7812 (mtmm) REVERT: B 300 THR cc_start: 0.8471 (p) cc_final: 0.7821 (t) REVERT: B 301 LYS cc_start: 0.8522 (mttt) cc_final: 0.7956 (mtmt) REVERT: B 328 LYS cc_start: 0.8010 (tttp) cc_final: 0.7004 (mptt) REVERT: B 426 ASN cc_start: 0.8572 (t0) cc_final: 0.8249 (t0) REVERT: B 429 ARG cc_start: 0.8250 (mmt90) cc_final: 0.7869 (mmm160) REVERT: B 436 LYS cc_start: 0.8609 (tttp) cc_final: 0.8113 (ttpt) REVERT: C 176 ILE cc_start: 0.8279 (tp) cc_final: 0.7911 (pt) REVERT: C 185 ASP cc_start: 0.8878 (m-30) cc_final: 0.8496 (m-30) REVERT: C 300 THR cc_start: 0.8227 (p) cc_final: 0.7553 (t) REVERT: C 301 LYS cc_start: 0.8559 (mttm) cc_final: 0.7856 (mtmt) REVERT: C 325 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7086 (tp30) REVERT: C 411 ASP cc_start: 0.7002 (m-30) cc_final: 0.6737 (t0) REVERT: C 412 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.6046 (tptm) REVERT: C 422 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.6229 (ttt-90) REVERT: C 429 ARG cc_start: 0.8197 (mmt90) cc_final: 0.7685 (mmm160) REVERT: C 503 MET cc_start: -0.0016 (tmt) cc_final: -0.0836 (mmm) REVERT: G 70 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7343 (mm-30) outliers start: 90 outliers final: 64 residues processed: 260 average time/residue: 0.4551 time to fit residues: 133.7023 Evaluate side-chains 265 residues out of total 1839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 189 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 98 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 70 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 100 GLN A 94 ASN A 425 ASN B 94 ASN C 25 GLN C 94 ASN C 433 ASN I 52 ASN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.183658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.135402 restraints weight = 17657.314| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.63 r_work: 0.3205 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17581 Z= 0.137 Angle : 0.635 12.689 23908 Z= 0.307 Chirality : 0.046 0.408 2640 Planarity : 0.004 0.069 3051 Dihedral : 7.972 83.373 2963 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.90 % Favored : 93.86 % Rotamer: Outliers : 4.19 % Allowed : 22.35 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.18), residues: 2085 helix: 0.94 (0.31), residues: 308 sheet: -0.70 (0.21), residues: 606 loop : -1.58 (0.17), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 342 TYR 0.013 0.001 TYR A 473 PHE 0.024 0.001 PHE C 417 TRP 0.013 0.001 TRP B 446 HIS 0.005 0.001 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (17534) covalent geometry : angle 0.60368 / 0.30 (23791) SS BOND : bond 0.00523 / 0.29 ( 21) SS BOND : angle 1.91832 / 1.17 ( 42) hydrogen bonds : bond 0.03055 / 2.01 ( 539) hydrogen bonds : angle 5.21210 / 3.60 ( 1491) Misc. bond : bond 0.01750 / 0.92 ( 1) link_ALPHA1-3 : bond 0.00729 / 0.37 ( 3) link_ALPHA1-3 : angle 1.41553 / 0.91 ( 9) link_BETA1-2 : bond 0.00360 / 0.18 ( 3) link_BETA1-2 : angle 0.46684 / 0.32 ( 9) link_BETA1-4 : bond 0.00439 / 0.25 ( 9) link_BETA1-4 : angle 2.30861 / 1.39 ( 27) link_BETA2-3 : bond 0.00618 / 0.31 ( 3) link_BETA2-3 : angle 4.44674 / 2.61 ( 9) link_NAG-ASN : bond 0.01109 / 0.51 ( 7) link_NAG-ASN : angle 4.67796 / 3.42 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5767.93 seconds wall clock time: 98 minutes 55.16 seconds (5935.16 seconds total)