Starting phenix.real_space_refine on Sun May 18 02:09:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j34_61105/05_2025/9j34_61105.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j34_61105/05_2025/9j34_61105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j34_61105/05_2025/9j34_61105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j34_61105/05_2025/9j34_61105.map" model { file = "/net/cci-nas-00/data/ceres_data/9j34_61105/05_2025/9j34_61105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j34_61105/05_2025/9j34_61105.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.108 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: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 104 5.16 5 C 10700 2.51 5 N 2712 2.21 5 O 2908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 150 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16427 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 4104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4104 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 23, 'TRANS': 478} Chain breaks: 4 Chain: "A" Number of atoms: 4104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4104 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 23, 'TRANS': 478} Chain breaks: 4 Chain: "B" Number of atoms: 4104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4104 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 23, 'TRANS': 478} Chain breaks: 4 Chain: "C" Number of atoms: 4104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4104 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 23, 'TRANS': 478} Chain breaks: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 10.01, per 1000 atoms: 0.61 Number of scatterers: 16427 At special positions: 0 Unit cell: (116.5, 116.5, 128.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 104 16.00 O 2908 8.00 N 2712 7.00 C 10700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 307 " distance=1.80 Simple disulfide: pdb=" SG CYS D 288 " - pdb=" SG CYS D 322 " distance=2.03 Simple disulfide: pdb=" SG CYS D 293 " - pdb=" SG CYS D 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 307 " distance=2.15 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 322 " distance=2.03 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 300 " distance=1.90 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 307 " distance=1.80 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 322 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 307 " distance=2.22 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 322 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 300 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.8 seconds 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3848 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 12 sheets defined 61.5% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'D' and resid 89 through 96 removed outlier: 3.671A pdb=" N ARG D 94 " --> pdb=" O PRO D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 106 removed outlier: 3.629A pdb=" N ILE D 104 " --> pdb=" O VAL D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 Processing helix chain 'D' and resid 129 through 145 removed outlier: 3.584A pdb=" N THR D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'D' and resid 178 through 187 removed outlier: 3.526A pdb=" N ARG D 182 " --> pdb=" O GLU D 178 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR D 183 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 194 Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'D' and resid 213 through 229 removed outlier: 3.593A pdb=" N VAL D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 245 removed outlier: 3.921A pdb=" N LEU D 240 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 295 removed outlier: 3.525A pdb=" N ARG D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 322 removed outlier: 3.503A pdb=" N SER D 321 " --> pdb=" O PHE D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 350 through 368 Processing helix chain 'D' and resid 378 through 410 removed outlier: 3.583A pdb=" N THR D 410 " --> pdb=" O TYR D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 425 Processing helix chain 'D' and resid 434 through 453 removed outlier: 3.726A pdb=" N ARG D 440 " --> pdb=" O ASN D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 463 removed outlier: 3.547A pdb=" N ASN D 463 " --> pdb=" O ASN D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 477 Processing helix chain 'D' and resid 477 through 482 Processing helix chain 'D' and resid 486 through 490 removed outlier: 3.667A pdb=" N MET D 490 " --> pdb=" O PHE D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 501 removed outlier: 3.527A pdb=" N ARG D 501 " --> pdb=" O ALA D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 removed outlier: 4.641A pdb=" N THR D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP D 562 " --> pdb=" O GLU D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 601 removed outlier: 3.585A pdb=" N VAL D 598 " --> pdb=" O ASP D 594 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER D 600 " --> pdb=" O LYS D 596 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN D 601 " --> pdb=" O PHE D 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 96 removed outlier: 3.672A pdb=" N ARG A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.630A pdb=" N ILE A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 129 through 145 removed outlier: 3.584A pdb=" N THR A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 Processing helix chain 'A' and resid 178 through 187 removed outlier: 3.525A pdb=" N ARG A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 197 through 205 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 213 through 229 removed outlier: 3.593A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 245 removed outlier: 3.921A pdb=" N LEU A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 295 removed outlier: 3.525A pdb=" N ARG A 295 " --> pdb=" O GLN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 322 removed outlier: 3.503A pdb=" N SER A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 350 through 368 Processing helix chain 'A' and resid 378 through 410 removed outlier: 3.525A pdb=" N SER A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 425 Processing helix chain 'A' and resid 434 through 453 removed outlier: 3.726A pdb=" N ARG A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 463 removed outlier: 3.548A pdb=" N ASN A 463 " --> pdb=" O ASN A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 486 through 490 removed outlier: 3.667A pdb=" N MET A 490 " --> pdb=" O PHE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 removed outlier: 3.527A pdb=" N ARG A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 4.642A pdb=" N THR A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 601 removed outlier: 3.584A pdb=" N VAL A 598 " --> pdb=" O ASP A 594 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 96 removed outlier: 3.671A pdb=" N ARG B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 106 removed outlier: 3.629A pdb=" N ILE B 104 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 129 through 145 removed outlier: 3.585A pdb=" N THR B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 178 through 187 removed outlier: 3.526A pdb=" N ARG B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 194 Processing helix chain 'B' and resid 197 through 205 Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 213 through 229 removed outlier: 3.594A pdb=" N VAL B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.921A pdb=" N LEU B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 295 removed outlier: 3.525A pdb=" N ARG B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 322 removed outlier: 3.503A pdb=" N SER B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 350 through 368 Processing helix chain 'B' and resid 378 through 410 removed outlier: 3.619A pdb=" N THR B 410 " --> pdb=" O TYR B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 425 Processing helix chain 'B' and resid 434 through 453 removed outlier: 3.726A pdb=" N ARG B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 463 removed outlier: 3.547A pdb=" N ASN B 463 " --> pdb=" O ASN B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 486 through 490 removed outlier: 3.667A pdb=" N MET B 490 " --> pdb=" O PHE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 501 removed outlier: 3.527A pdb=" N ARG B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 4.641A pdb=" N THR B 561 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 601 removed outlier: 3.585A pdb=" N VAL B 598 " --> pdb=" O ASP B 594 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER B 600 " --> pdb=" O LYS B 596 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN B 601 " --> pdb=" O PHE B 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 96 removed outlier: 3.671A pdb=" N ARG C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 106 removed outlier: 3.630A pdb=" N ILE C 104 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 129 through 145 removed outlier: 3.585A pdb=" N THR C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 152 Processing helix chain 'C' and resid 178 through 187 removed outlier: 3.526A pdb=" N ARG C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 183 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 194 Processing helix chain 'C' and resid 197 through 205 Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 213 through 229 removed outlier: 3.593A pdb=" N VAL C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 245 removed outlier: 3.921A pdb=" N LEU C 240 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 295 removed outlier: 3.525A pdb=" N ARG C 295 " --> pdb=" O GLN C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.793A pdb=" N LEU C 305 " --> pdb=" O SER C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 322 removed outlier: 3.503A pdb=" N SER C 321 " --> pdb=" O PHE C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 350 through 368 Processing helix chain 'C' and resid 378 through 410 removed outlier: 3.624A pdb=" N SER C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 410 " --> pdb=" O TYR C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 434 through 453 removed outlier: 3.727A pdb=" N ARG C 440 " --> pdb=" O ASN C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 463 removed outlier: 3.548A pdb=" N ASN C 463 " --> pdb=" O ASN C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 477 Processing helix chain 'C' and resid 477 through 482 Processing helix chain 'C' and resid 486 through 490 removed outlier: 3.668A pdb=" N MET C 490 " --> pdb=" O PHE C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 501 removed outlier: 3.527A pdb=" N ARG C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 removed outlier: 4.641A pdb=" N THR C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 601 removed outlier: 3.584A pdb=" N VAL C 598 " --> pdb=" O ASP C 594 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C 600 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN C 601 " --> pdb=" O PHE C 597 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 117 through 120 Processing sheet with id=AA2, first strand: chain 'D' and resid 503 through 507 removed outlier: 6.243A pdb=" N GLU D 586 " --> pdb=" O MET D 527 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 512 through 514 removed outlier: 6.578A pdb=" N VAL D 579 " --> pdb=" O ILE D 513 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 120 Processing sheet with id=AA5, first strand: chain 'A' and resid 503 through 507 removed outlier: 6.243A pdb=" N GLU A 586 " --> pdb=" O MET A 527 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.579A pdb=" N VAL A 579 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 117 through 120 Processing sheet with id=AA8, first strand: chain 'B' and resid 503 through 507 removed outlier: 6.242A pdb=" N GLU B 586 " --> pdb=" O MET B 527 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 512 through 514 removed outlier: 6.578A pdb=" N VAL B 579 " --> pdb=" O ILE B 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 117 through 120 Processing sheet with id=AB2, first strand: chain 'C' and resid 503 through 507 removed outlier: 6.243A pdb=" N GLU C 586 " --> pdb=" O MET C 527 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 512 through 514 removed outlier: 6.578A pdb=" N VAL C 579 " --> pdb=" O ILE C 513 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.55 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.29: 2661 1.29 - 1.44: 4691 1.44 - 1.59: 9296 1.59 - 1.75: 0 1.75 - 1.90: 160 Bond restraints: 16808 Sorted by residual: bond pdb=" C ASP A 308 " pdb=" N PRO A 309 " ideal model delta sigma weight residual 1.335 1.591 -0.256 1.19e-02 7.06e+03 4.63e+02 bond pdb=" C LEU C 304 " pdb=" N LEU C 305 " ideal model delta sigma weight residual 1.334 1.536 -0.201 1.38e-02 5.25e+03 2.13e+02 bond pdb=" N GLN B 404 " pdb=" CA GLN B 404 " ideal model delta sigma weight residual 1.457 1.314 0.142 1.33e-02 5.65e+03 1.15e+02 bond pdb=" C ALA C 424 " pdb=" N GLU C 425 " ideal model delta sigma weight residual 1.329 1.462 -0.133 1.36e-02 5.41e+03 9.50e+01 bond pdb=" CA GLN B 404 " pdb=" CB GLN B 404 " ideal model delta sigma weight residual 1.530 1.374 0.156 1.68e-02 3.54e+03 8.60e+01 ... (remaining 16803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.77: 22457 4.77 - 9.55: 263 9.55 - 14.32: 21 14.32 - 19.09: 9 19.09 - 23.87: 6 Bond angle restraints: 22756 Sorted by residual: angle pdb=" O THR A 311 " pdb=" C THR A 311 " pdb=" N ALA A 312 " ideal model delta sigma weight residual 123.22 146.85 -23.63 1.14e+00 7.69e-01 4.30e+02 angle pdb=" CA THR A 311 " pdb=" C THR A 311 " pdb=" N ALA A 312 " ideal model delta sigma weight residual 116.20 92.33 23.87 1.25e+00 6.40e-01 3.65e+02 angle pdb=" C THR A 311 " pdb=" N ALA A 312 " pdb=" CA ALA A 312 " ideal model delta sigma weight residual 123.00 101.37 21.63 1.38e+00 5.25e-01 2.46e+02 angle pdb=" C CYS D 307 " pdb=" N ASP D 308 " pdb=" CA ASP D 308 " ideal model delta sigma weight residual 121.83 142.22 -20.39 1.56e+00 4.11e-01 1.71e+02 angle pdb=" C CYS B 307 " pdb=" N ASP B 308 " pdb=" CA ASP B 308 " ideal model delta sigma weight residual 121.83 142.21 -20.38 1.56e+00 4.11e-01 1.71e+02 ... (remaining 22751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8901 17.98 - 35.95: 994 35.95 - 53.93: 144 53.93 - 71.91: 33 71.91 - 89.88: 12 Dihedral angle restraints: 10084 sinusoidal: 4180 harmonic: 5904 Sorted by residual: dihedral pdb=" CA ASP B 144 " pdb=" C ASP B 144 " pdb=" N VAL B 145 " pdb=" CA VAL B 145 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA TYR B 306 " pdb=" C TYR B 306 " pdb=" N CYS B 307 " pdb=" CA CYS B 307 " ideal model delta harmonic sigma weight residual -180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA TYR D 306 " pdb=" C TYR D 306 " pdb=" N CYS D 307 " pdb=" CA CYS D 307 " ideal model delta harmonic sigma weight residual 180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 10081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2227 0.090 - 0.179: 245 0.179 - 0.269: 16 0.269 - 0.359: 32 0.359 - 0.448: 28 Chirality restraints: 2548 Sorted by residual: chirality pdb=" CA LEU C 395 " pdb=" N LEU C 395 " pdb=" C LEU C 395 " pdb=" CB LEU C 395 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CA LEU B 399 " pdb=" N LEU B 399 " pdb=" C LEU B 399 " pdb=" CB LEU B 399 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CA LEU C 399 " pdb=" N LEU C 399 " pdb=" C LEU C 399 " pdb=" CB LEU C 399 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.89e+00 ... (remaining 2545 not shown) Planarity restraints: 2860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 424 " 0.032 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C ALA C 424 " -0.110 2.00e-02 2.50e+03 pdb=" O ALA C 424 " 0.043 2.00e-02 2.50e+03 pdb=" N GLU C 425 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 308 " 0.034 2.00e-02 2.50e+03 6.25e-02 3.90e+01 pdb=" C ASP A 308 " -0.108 2.00e-02 2.50e+03 pdb=" O ASP A 308 " 0.042 2.00e-02 2.50e+03 pdb=" N PRO A 309 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 297 " 0.093 5.00e-02 4.00e+02 1.44e-01 3.33e+01 pdb=" N PRO A 298 " -0.250 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " 0.081 5.00e-02 4.00e+02 ... (remaining 2857 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2069 2.75 - 3.29: 15364 3.29 - 3.83: 27713 3.83 - 4.36: 34547 4.36 - 4.90: 56058 Nonbonded interactions: 135751 Sorted by model distance: nonbonded pdb=" CG2 ILE B 160 " pdb=" CD2 LEU B 172 " model vdw 2.217 3.880 nonbonded pdb=" CG2 ILE C 160 " pdb=" CD2 LEU C 172 " model vdw 2.218 3.880 nonbonded pdb=" CG2 ILE D 160 " pdb=" CD2 LEU D 172 " model vdw 2.218 3.880 nonbonded pdb=" CG2 ILE A 160 " pdb=" CD2 LEU A 172 " model vdw 2.218 3.880 nonbonded pdb=" NH2 ARG A 422 " pdb=" O SER B 409 " model vdw 2.245 3.120 ... (remaining 135746 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' and resid 84 through 603) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.150 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: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 35.100 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 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 : 0.013 0.256 16820 Z= 0.842 Angle : 1.429 55.165 22780 Z= 0.827 Chirality : 0.077 0.448 2548 Planarity : 0.008 0.144 2860 Dihedral : 15.196 89.882 6200 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.44 % Allowed : 6.75 % Favored : 92.81 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.13 (0.13), residues: 1968 helix: -3.98 (0.08), residues: 1256 sheet: -0.87 (0.41), residues: 92 loop : -1.89 (0.21), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 427 HIS 0.012 0.002 HIS C 187 PHE 0.021 0.002 PHE C 396 TYR 0.022 0.002 TYR A 306 ARG 0.010 0.001 ARG C 94 Details of bonding type rmsd hydrogen bonds : bond 0.24688 ( 848) hydrogen bonds : angle 9.36978 ( 2382) SS BOND : bond 0.12075 ( 12) SS BOND : angle 16.93831 ( 24) covalent geometry : bond 0.01234 (16808) covalent geometry : angle 1.31948 (22756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 322 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 416 GLU cc_start: 0.7399 (tt0) cc_final: 0.6939 (tt0) REVERT: D 445 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7266 (mm-30) REVERT: D 471 ASP cc_start: 0.7938 (m-30) cc_final: 0.7697 (m-30) REVERT: D 501 ARG cc_start: 0.7579 (mtt90) cc_final: 0.7301 (mtt-85) REVERT: D 518 ASP cc_start: 0.8041 (m-30) cc_final: 0.7744 (m-30) REVERT: D 530 LYS cc_start: 0.8252 (tttt) cc_final: 0.8042 (tttm) REVERT: A 156 ARG cc_start: 0.6346 (ptt180) cc_final: 0.6124 (ptm160) REVERT: A 446 GLN cc_start: 0.7398 (tp40) cc_final: 0.7142 (tm130) REVERT: A 458 GLU cc_start: 0.7336 (tm-30) cc_final: 0.7125 (tm-30) REVERT: A 474 ARG cc_start: 0.7630 (mtp-110) cc_final: 0.7374 (ttp-170) REVERT: B 319 ASN cc_start: 0.7395 (p0) cc_final: 0.7153 (p0) REVERT: B 416 GLU cc_start: 0.7822 (tt0) cc_final: 0.7379 (tt0) REVERT: B 446 GLN cc_start: 0.7486 (tp40) cc_final: 0.7278 (tm130) REVERT: B 471 ASP cc_start: 0.7959 (m-30) cc_final: 0.7713 (m-30) REVERT: B 530 LYS cc_start: 0.8389 (tttt) cc_final: 0.8086 (tttm) REVERT: B 549 LEU cc_start: 0.8186 (mt) cc_final: 0.7848 (mp) REVERT: C 139 LEU cc_start: 0.8685 (mt) cc_final: 0.8484 (mt) REVERT: C 156 ARG cc_start: 0.6684 (ptt180) cc_final: 0.6190 (ptm-80) REVERT: C 319 ASN cc_start: 0.7709 (p0) cc_final: 0.7494 (p0) REVERT: C 408 GLN cc_start: 0.8131 (mt0) cc_final: 0.7666 (mt0) REVERT: C 416 GLU cc_start: 0.8024 (tt0) cc_final: 0.7703 (tt0) REVERT: C 471 ASP cc_start: 0.8087 (m-30) cc_final: 0.7822 (m-30) REVERT: C 490 MET cc_start: 0.7115 (mtt) cc_final: 0.6838 (mtt) REVERT: C 501 ARG cc_start: 0.7797 (mtt90) cc_final: 0.7496 (mtp85) REVERT: C 511 SER cc_start: 0.7737 (t) cc_final: 0.7485 (t) REVERT: C 523 MET cc_start: 0.8310 (ttt) cc_final: 0.8090 (ttp) outliers start: 8 outliers final: 0 residues processed: 325 average time/residue: 1.4401 time to fit residues: 514.1526 Evaluate side-chains 243 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.5980 chunk 151 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 156 optimal weight: 0.1980 chunk 60 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 chunk 181 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 262 ASN ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 537 ASN A 262 ASN A 271 HIS A 446 GLN A 537 ASN B 262 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN B 537 ASN C 262 ASN C 537 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.199619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.162309 restraints weight = 14882.140| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.57 r_work: 0.3112 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16820 Z= 0.136 Angle : 0.653 7.052 22780 Z= 0.339 Chirality : 0.042 0.146 2548 Planarity : 0.005 0.066 2860 Dihedral : 6.000 28.483 2180 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.55 % Allowed : 11.73 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.17), residues: 1968 helix: -1.66 (0.13), residues: 1256 sheet: -0.28 (0.42), residues: 92 loop : -1.06 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 277 HIS 0.002 0.001 HIS C 430 PHE 0.012 0.001 PHE C 351 TYR 0.014 0.002 TYR C 306 ARG 0.003 0.000 ARG B 422 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 848) hydrogen bonds : angle 4.95364 ( 2382) SS BOND : bond 0.00341 ( 12) SS BOND : angle 1.20935 ( 24) covalent geometry : bond 0.00302 (16808) covalent geometry : angle 0.65223 (22756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 1.707 Fit side-chains revert: symmetry clash REVERT: D 415 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7803 (mm-30) REVERT: D 416 GLU cc_start: 0.8545 (tt0) cc_final: 0.8051 (tt0) REVERT: D 420 LYS cc_start: 0.8628 (mttt) cc_final: 0.8370 (mtpp) REVERT: D 471 ASP cc_start: 0.8337 (m-30) cc_final: 0.8121 (m-30) REVERT: D 474 ARG cc_start: 0.8323 (mtp-110) cc_final: 0.7963 (mtt90) REVERT: D 501 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7758 (mtt-85) REVERT: D 522 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7672 (mt-10) REVERT: D 530 LYS cc_start: 0.8593 (tttt) cc_final: 0.8351 (tttm) REVERT: D 557 GLU cc_start: 0.7955 (pm20) cc_final: 0.7638 (pm20) REVERT: D 580 ARG cc_start: 0.7937 (ttp-170) cc_final: 0.7576 (ttt180) REVERT: A 121 ASP cc_start: 0.8144 (t70) cc_final: 0.7919 (t0) REVERT: A 156 ARG cc_start: 0.6599 (ptt180) cc_final: 0.6293 (ptm160) REVERT: A 408 GLN cc_start: 0.8105 (mt0) cc_final: 0.7743 (mm-40) REVERT: A 413 ARG cc_start: 0.8701 (mmt-90) cc_final: 0.8160 (tpt170) REVERT: A 417 MET cc_start: 0.9050 (tmm) cc_final: 0.8826 (tmm) REVERT: A 474 ARG cc_start: 0.7977 (mtp-110) cc_final: 0.7715 (ttp-170) REVERT: A 532 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8329 (tp) REVERT: A 557 GLU cc_start: 0.8000 (pm20) cc_final: 0.7779 (pm20) REVERT: A 580 ARG cc_start: 0.7886 (ttp-170) cc_final: 0.7530 (ttt180) REVERT: B 415 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7850 (mm-30) REVERT: B 416 GLU cc_start: 0.8512 (tt0) cc_final: 0.8070 (tt0) REVERT: B 471 ASP cc_start: 0.8384 (m-30) cc_final: 0.8152 (m-30) REVERT: B 474 ARG cc_start: 0.8489 (mtp-110) cc_final: 0.8052 (mtt90) REVERT: B 530 LYS cc_start: 0.8657 (tttt) cc_final: 0.8361 (tttm) REVERT: B 577 ARG cc_start: 0.7374 (mtm180) cc_final: 0.7108 (mtp-110) REVERT: B 580 ARG cc_start: 0.8078 (ttt-90) cc_final: 0.7767 (mtp180) REVERT: B 583 MET cc_start: 0.8417 (ptm) cc_final: 0.8158 (ptt) REVERT: C 132 MET cc_start: 0.8836 (tpt) cc_final: 0.7558 (tpt) REVERT: C 156 ARG cc_start: 0.6813 (ptt180) cc_final: 0.6275 (ptm-80) REVERT: C 408 GLN cc_start: 0.8216 (mt0) cc_final: 0.7819 (mt0) REVERT: C 415 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7875 (mm-30) REVERT: C 416 GLU cc_start: 0.8644 (tt0) cc_final: 0.8256 (tt0) REVERT: C 420 LYS cc_start: 0.8691 (mttt) cc_final: 0.8428 (mtpp) REVERT: C 471 ASP cc_start: 0.8331 (m-30) cc_final: 0.8117 (m-30) REVERT: C 501 ARG cc_start: 0.8167 (mtt90) cc_final: 0.7942 (mtt-85) REVERT: C 511 SER cc_start: 0.8346 (t) cc_final: 0.7958 (t) REVERT: C 583 MET cc_start: 0.8268 (ptm) cc_final: 0.7982 (ptt) outliers start: 28 outliers final: 9 residues processed: 278 average time/residue: 1.4745 time to fit residues: 449.1030 Evaluate side-chains 252 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 239 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 533 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 125 optimal weight: 0.0470 chunk 0 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 0.0570 chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN B 262 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.199678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.161967 restraints weight = 14785.752| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.57 r_work: 0.3101 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16820 Z= 0.120 Angle : 0.582 6.664 22780 Z= 0.304 Chirality : 0.041 0.216 2548 Planarity : 0.004 0.052 2860 Dihedral : 5.470 30.031 2180 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.94 % Allowed : 12.72 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.19), residues: 1968 helix: -0.58 (0.15), residues: 1300 sheet: 0.28 (0.47), residues: 92 loop : -0.73 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 277 HIS 0.001 0.000 HIS D 475 PHE 0.009 0.001 PHE B 264 TYR 0.012 0.001 TYR C 306 ARG 0.004 0.000 ARG C 422 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 848) hydrogen bonds : angle 4.40224 ( 2382) SS BOND : bond 0.00211 ( 12) SS BOND : angle 1.49680 ( 24) covalent geometry : bond 0.00272 (16808) covalent geometry : angle 0.57998 (22756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 2.050 Fit side-chains revert: symmetry clash REVERT: D 415 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7794 (mm-30) REVERT: D 416 GLU cc_start: 0.8601 (tt0) cc_final: 0.8091 (tt0) REVERT: D 420 LYS cc_start: 0.8706 (mttt) cc_final: 0.8447 (mtpp) REVERT: D 446 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7765 (tm130) REVERT: D 471 ASP cc_start: 0.8390 (m-30) cc_final: 0.8189 (m-30) REVERT: D 474 ARG cc_start: 0.8367 (mtp-110) cc_final: 0.7957 (mtt90) REVERT: D 501 ARG cc_start: 0.8127 (mtt90) cc_final: 0.7821 (mtt-85) REVERT: D 518 ASP cc_start: 0.7774 (m-30) cc_final: 0.7444 (m-30) REVERT: D 522 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7566 (mt-10) REVERT: D 530 LYS cc_start: 0.8591 (tttt) cc_final: 0.8293 (tttm) REVERT: D 532 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8234 (tp) REVERT: D 558 GLU cc_start: 0.7813 (mp0) cc_final: 0.7487 (mt-10) REVERT: D 577 ARG cc_start: 0.7325 (mtm110) cc_final: 0.7095 (mtp-110) REVERT: D 580 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.7701 (ttm-80) REVERT: A 413 ARG cc_start: 0.8746 (mmt-90) cc_final: 0.8313 (tpt170) REVERT: A 417 MET cc_start: 0.9025 (tmm) cc_final: 0.8778 (tmm) REVERT: A 474 ARG cc_start: 0.8133 (mtp-110) cc_final: 0.7863 (ttm-80) REVERT: A 518 ASP cc_start: 0.7735 (m-30) cc_final: 0.7298 (m-30) REVERT: A 532 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8328 (tp) REVERT: A 557 GLU cc_start: 0.7941 (pm20) cc_final: 0.7557 (pm20) REVERT: A 580 ARG cc_start: 0.7941 (ttp-170) cc_final: 0.7588 (ttt180) REVERT: B 201 MET cc_start: 0.7030 (mmt) cc_final: 0.6808 (mmp) REVERT: B 415 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7839 (mm-30) REVERT: B 416 GLU cc_start: 0.8556 (tt0) cc_final: 0.8054 (tt0) REVERT: B 420 LYS cc_start: 0.8737 (mttt) cc_final: 0.8496 (mtpp) REVERT: B 467 ASP cc_start: 0.7499 (p0) cc_final: 0.7179 (p0) REVERT: B 474 ARG cc_start: 0.8459 (mtp-110) cc_final: 0.8004 (mtt90) REVERT: B 518 ASP cc_start: 0.7747 (m-30) cc_final: 0.7255 (m-30) REVERT: B 530 LYS cc_start: 0.8599 (tttt) cc_final: 0.8324 (tttm) REVERT: B 580 ARG cc_start: 0.8043 (ttt-90) cc_final: 0.7762 (mtp180) REVERT: B 583 MET cc_start: 0.8314 (ptm) cc_final: 0.8077 (ptt) REVERT: C 209 HIS cc_start: 0.7149 (m90) cc_final: 0.6904 (m-70) REVERT: C 415 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7929 (mm-30) REVERT: C 416 GLU cc_start: 0.8590 (tt0) cc_final: 0.8092 (tt0) REVERT: C 420 LYS cc_start: 0.8812 (mttt) cc_final: 0.8581 (mtpp) REVERT: C 446 GLN cc_start: 0.8266 (tt0) cc_final: 0.7693 (tm130) REVERT: C 466 LYS cc_start: 0.8587 (tttm) cc_final: 0.8287 (ttpp) REVERT: C 501 ARG cc_start: 0.8145 (mtt90) cc_final: 0.7883 (mtt-85) REVERT: C 530 LYS cc_start: 0.8477 (tttt) cc_final: 0.8081 (tttm) REVERT: C 583 MET cc_start: 0.8303 (ptm) cc_final: 0.8051 (ptt) outliers start: 35 outliers final: 8 residues processed: 268 average time/residue: 1.4660 time to fit residues: 430.0948 Evaluate side-chains 250 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 446 GLN Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 533 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 149 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 193 optimal weight: 7.9990 chunk 161 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 262 ASN ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.194291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.149816 restraints weight = 14592.623| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.67 r_work: 0.2975 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16820 Z= 0.240 Angle : 0.683 8.480 22780 Z= 0.359 Chirality : 0.048 0.210 2548 Planarity : 0.004 0.046 2860 Dihedral : 5.715 27.971 2180 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.32 % Allowed : 12.61 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.19), residues: 1968 helix: -0.48 (0.15), residues: 1296 sheet: 0.40 (0.48), residues: 92 loop : -0.66 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 427 HIS 0.003 0.001 HIS C 271 PHE 0.020 0.002 PHE D 351 TYR 0.018 0.002 TYR A 230 ARG 0.005 0.001 ARG C 431 Details of bonding type rmsd hydrogen bonds : bond 0.04777 ( 848) hydrogen bonds : angle 4.52485 ( 2382) SS BOND : bond 0.00350 ( 12) SS BOND : angle 2.15546 ( 24) covalent geometry : bond 0.00579 (16808) covalent geometry : angle 0.67978 (22756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 234 time to evaluate : 1.772 Fit side-chains revert: symmetry clash REVERT: D 415 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7881 (mm-30) REVERT: D 416 GLU cc_start: 0.8617 (tt0) cc_final: 0.8123 (tt0) REVERT: D 439 LYS cc_start: 0.8437 (pptt) cc_final: 0.7909 (mmpt) REVERT: D 445 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8119 (mp0) REVERT: D 446 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7755 (tm130) REVERT: D 490 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.7079 (mtp) REVERT: D 501 ARG cc_start: 0.8080 (mtt90) cc_final: 0.7796 (mtt-85) REVERT: D 522 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7339 (pt0) REVERT: D 530 LYS cc_start: 0.8638 (tttt) cc_final: 0.8267 (tttm) REVERT: D 532 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8073 (tp) REVERT: D 557 GLU cc_start: 0.7789 (pm20) cc_final: 0.7362 (pm20) REVERT: D 558 GLU cc_start: 0.7917 (mp0) cc_final: 0.7520 (mt-10) REVERT: D 580 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7490 (ttm-80) REVERT: A 96 ASN cc_start: 0.7266 (t0) cc_final: 0.7057 (t0) REVERT: A 415 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: A 439 LYS cc_start: 0.8326 (pptt) cc_final: 0.7779 (mmpt) REVERT: A 445 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8085 (mp0) REVERT: A 446 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7847 (tm130) REVERT: A 532 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8076 (tp) REVERT: A 557 GLU cc_start: 0.7766 (pm20) cc_final: 0.7500 (pm20) REVERT: A 580 ARG cc_start: 0.7961 (ttp-170) cc_final: 0.7395 (ttt-90) REVERT: B 240 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7502 (tt) REVERT: B 369 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8709 (mt) REVERT: B 415 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7910 (mm-30) REVERT: B 416 GLU cc_start: 0.8632 (tt0) cc_final: 0.8197 (tt0) REVERT: B 439 LYS cc_start: 0.8373 (pptt) cc_final: 0.7817 (mmpt) REVERT: B 446 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7622 (tm130) REVERT: B 474 ARG cc_start: 0.8522 (mtp-110) cc_final: 0.7973 (mtt90) REVERT: B 530 LYS cc_start: 0.8632 (tttt) cc_final: 0.8290 (tttm) REVERT: B 583 MET cc_start: 0.8209 (ptm) cc_final: 0.7981 (ptt) REVERT: C 131 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7491 (pptt) REVERT: C 209 HIS cc_start: 0.7103 (m90) cc_final: 0.6641 (m-70) REVERT: C 369 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8774 (mt) REVERT: C 415 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7922 (mm-30) REVERT: C 416 GLU cc_start: 0.8619 (tt0) cc_final: 0.8103 (tt0) REVERT: C 439 LYS cc_start: 0.8338 (pptt) cc_final: 0.7801 (mmpt) REVERT: C 446 GLN cc_start: 0.8373 (tt0) cc_final: 0.7692 (tm130) REVERT: C 501 ARG cc_start: 0.8106 (mtt90) cc_final: 0.7773 (mtt-85) REVERT: C 530 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8143 (tttm) REVERT: C 583 MET cc_start: 0.8407 (ptm) cc_final: 0.8140 (ptt) outliers start: 60 outliers final: 24 residues processed: 269 average time/residue: 1.4104 time to fit residues: 417.3836 Evaluate side-chains 268 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 229 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 446 GLN Chi-restraints excluded: chain D residue 490 MET Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 446 GLN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 518 ASP Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 533 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 49 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 GLN B 262 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.196600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.158371 restraints weight = 14707.338| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.56 r_work: 0.3055 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16820 Z= 0.149 Angle : 0.594 9.031 22780 Z= 0.311 Chirality : 0.043 0.241 2548 Planarity : 0.004 0.043 2860 Dihedral : 5.484 31.612 2180 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.15 % Allowed : 13.16 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.19), residues: 1968 helix: -0.17 (0.15), residues: 1288 sheet: 0.63 (0.50), residues: 92 loop : -0.60 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 427 HIS 0.002 0.000 HIS C 475 PHE 0.012 0.001 PHE D 351 TYR 0.013 0.001 TYR A 306 ARG 0.007 0.000 ARG D 474 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 848) hydrogen bonds : angle 4.30709 ( 2382) SS BOND : bond 0.00321 ( 12) SS BOND : angle 1.83498 ( 24) covalent geometry : bond 0.00354 (16808) covalent geometry : angle 0.59083 (22756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 229 time to evaluate : 1.705 Fit side-chains revert: symmetry clash REVERT: D 320 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7756 (mm-30) REVERT: D 369 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8688 (mt) REVERT: D 415 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: D 416 GLU cc_start: 0.8616 (tt0) cc_final: 0.8127 (tt0) REVERT: D 439 LYS cc_start: 0.8391 (pptt) cc_final: 0.8018 (mmpt) REVERT: D 445 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8161 (mp0) REVERT: D 446 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7875 (tm130) REVERT: D 466 LYS cc_start: 0.8684 (tttm) cc_final: 0.8363 (ttpt) REVERT: D 474 ARG cc_start: 0.8479 (mtp-110) cc_final: 0.8251 (mtp85) REVERT: D 501 ARG cc_start: 0.8109 (mtt90) cc_final: 0.7861 (mtt-85) REVERT: D 522 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7435 (pt0) REVERT: D 530 LYS cc_start: 0.8646 (tttt) cc_final: 0.8312 (tttm) REVERT: D 532 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8203 (tp) REVERT: D 558 GLU cc_start: 0.7892 (mp0) cc_final: 0.7533 (mt-10) REVERT: A 369 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8695 (mt) REVERT: A 439 LYS cc_start: 0.8357 (pptt) cc_final: 0.7911 (mmpt) REVERT: A 445 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8114 (mp0) REVERT: A 446 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7880 (tm130) REVERT: A 518 ASP cc_start: 0.7762 (m-30) cc_final: 0.7257 (m-30) REVERT: A 580 ARG cc_start: 0.7928 (ttp-170) cc_final: 0.7619 (ttt180) REVERT: B 415 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7936 (mm-30) REVERT: B 416 GLU cc_start: 0.8615 (tt0) cc_final: 0.8123 (tt0) REVERT: B 439 LYS cc_start: 0.8338 (pptt) cc_final: 0.7921 (mmpt) REVERT: B 446 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7759 (tm130) REVERT: B 467 ASP cc_start: 0.7555 (p0) cc_final: 0.7206 (p0) REVERT: B 474 ARG cc_start: 0.8435 (mtp-110) cc_final: 0.8016 (mtt90) REVERT: B 518 ASP cc_start: 0.7926 (m-30) cc_final: 0.7528 (m-30) REVERT: B 530 LYS cc_start: 0.8636 (tttt) cc_final: 0.8336 (tttm) REVERT: B 580 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7865 (mtp180) REVERT: B 583 MET cc_start: 0.8249 (ptm) cc_final: 0.7994 (ptt) REVERT: C 209 HIS cc_start: 0.7276 (m90) cc_final: 0.6813 (m-70) REVERT: C 369 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8668 (mt) REVERT: C 415 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7934 (mm-30) REVERT: C 416 GLU cc_start: 0.8590 (tt0) cc_final: 0.8104 (tt0) REVERT: C 439 LYS cc_start: 0.8388 (pptt) cc_final: 0.7920 (mmpt) REVERT: C 446 GLN cc_start: 0.8311 (tt0) cc_final: 0.7751 (tm130) REVERT: C 501 ARG cc_start: 0.8142 (mtt90) cc_final: 0.7846 (mtt-85) REVERT: C 530 LYS cc_start: 0.8593 (tttt) cc_final: 0.8234 (tttm) REVERT: C 583 MET cc_start: 0.8333 (ptm) cc_final: 0.8100 (ptt) outliers start: 57 outliers final: 27 residues processed: 259 average time/residue: 1.3989 time to fit residues: 398.2332 Evaluate side-chains 258 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 446 GLN Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 446 GLN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 533 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 145 optimal weight: 7.9990 chunk 183 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN A 436 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN C 436 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.196412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.156223 restraints weight = 14658.360| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.64 r_work: 0.3023 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16820 Z= 0.158 Angle : 0.602 9.765 22780 Z= 0.314 Chirality : 0.043 0.238 2548 Planarity : 0.004 0.042 2860 Dihedral : 5.489 37.076 2180 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.21 % Allowed : 13.50 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 1968 helix: -0.09 (0.15), residues: 1296 sheet: 0.78 (0.50), residues: 92 loop : -0.40 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 427 HIS 0.002 0.001 HIS C 475 PHE 0.013 0.001 PHE B 351 TYR 0.011 0.001 TYR A 306 ARG 0.005 0.000 ARG D 474 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 848) hydrogen bonds : angle 4.23764 ( 2382) SS BOND : bond 0.00580 ( 12) SS BOND : angle 2.44884 ( 24) covalent geometry : bond 0.00378 (16808) covalent geometry : angle 0.59674 (22756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 226 time to evaluate : 1.910 Fit side-chains REVERT: D 320 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7656 (mm-30) REVERT: D 369 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8708 (mt) REVERT: D 415 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7770 (mm-30) REVERT: D 416 GLU cc_start: 0.8601 (tt0) cc_final: 0.8074 (tt0) REVERT: D 439 LYS cc_start: 0.8346 (pptt) cc_final: 0.7884 (mmmt) REVERT: D 445 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8120 (mp0) REVERT: D 446 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7793 (tm130) REVERT: D 466 LYS cc_start: 0.8670 (tttm) cc_final: 0.8308 (ttpt) REVERT: D 467 ASP cc_start: 0.7425 (p0) cc_final: 0.7099 (p0) REVERT: D 474 ARG cc_start: 0.8478 (mtp-110) cc_final: 0.8276 (mtp85) REVERT: D 501 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7872 (mtt-85) REVERT: D 518 ASP cc_start: 0.7818 (m-30) cc_final: 0.7479 (m-30) REVERT: D 522 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7399 (pt0) REVERT: D 530 LYS cc_start: 0.8613 (tttt) cc_final: 0.8340 (tttt) REVERT: D 532 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8132 (tp) REVERT: D 558 GLU cc_start: 0.7891 (mp0) cc_final: 0.7512 (mt-10) REVERT: D 580 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7659 (ttt-90) REVERT: A 369 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8710 (mt) REVERT: A 439 LYS cc_start: 0.8328 (pptt) cc_final: 0.7822 (mmpt) REVERT: A 445 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8111 (mp0) REVERT: A 446 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7819 (tm130) REVERT: A 518 ASP cc_start: 0.7702 (m-30) cc_final: 0.7263 (m-30) REVERT: A 580 ARG cc_start: 0.7827 (ttp-170) cc_final: 0.7478 (ttt180) REVERT: B 320 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 369 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8707 (mt) REVERT: B 415 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7888 (mm-30) REVERT: B 416 GLU cc_start: 0.8595 (tt0) cc_final: 0.8057 (tt0) REVERT: B 445 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8120 (mm-30) REVERT: B 446 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7727 (tm130) REVERT: B 466 LYS cc_start: 0.8633 (tttm) cc_final: 0.8287 (ttpt) REVERT: B 467 ASP cc_start: 0.7497 (p0) cc_final: 0.7154 (p0) REVERT: B 474 ARG cc_start: 0.8408 (mtp-110) cc_final: 0.7963 (mtt90) REVERT: B 518 ASP cc_start: 0.7865 (m-30) cc_final: 0.7502 (m-30) REVERT: B 530 LYS cc_start: 0.8620 (tttt) cc_final: 0.8287 (tttm) REVERT: B 580 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7734 (mtp180) REVERT: B 583 MET cc_start: 0.8209 (ptm) cc_final: 0.7959 (ptt) REVERT: C 201 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6711 (mmp) REVERT: C 209 HIS cc_start: 0.7214 (m90) cc_final: 0.6805 (m-70) REVERT: C 320 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7576 (mm-30) REVERT: C 369 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8684 (mt) REVERT: C 415 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7867 (mm-30) REVERT: C 416 GLU cc_start: 0.8580 (tt0) cc_final: 0.8053 (tt0) REVERT: C 439 LYS cc_start: 0.8325 (pptt) cc_final: 0.7850 (mmpt) REVERT: C 446 GLN cc_start: 0.8286 (tt0) cc_final: 0.7718 (tm130) REVERT: C 466 LYS cc_start: 0.8644 (tttm) cc_final: 0.8292 (ttpt) REVERT: C 467 ASP cc_start: 0.7450 (p0) cc_final: 0.7124 (p0) REVERT: C 501 ARG cc_start: 0.8096 (mtt90) cc_final: 0.7780 (mtt-85) REVERT: C 530 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8162 (tttm) REVERT: C 557 GLU cc_start: 0.7522 (pm20) cc_final: 0.7194 (pm20) REVERT: C 580 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7545 (ttm-80) REVERT: C 583 MET cc_start: 0.8249 (ptm) cc_final: 0.7998 (ptt) outliers start: 58 outliers final: 27 residues processed: 259 average time/residue: 1.3622 time to fit residues: 389.4381 Evaluate side-chains 260 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 446 GLN Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 446 GLN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 533 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 181 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 262 ASN ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 ASN B 262 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.197235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.158530 restraints weight = 14603.049| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.59 r_work: 0.3059 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16820 Z= 0.139 Angle : 0.591 11.450 22780 Z= 0.307 Chirality : 0.043 0.248 2548 Planarity : 0.004 0.041 2860 Dihedral : 5.333 34.956 2180 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.04 % Allowed : 14.10 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.19), residues: 1968 helix: 0.03 (0.15), residues: 1296 sheet: 0.90 (0.51), residues: 92 loop : -0.37 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 427 HIS 0.001 0.000 HIS D 475 PHE 0.011 0.001 PHE A 351 TYR 0.012 0.001 TYR A 306 ARG 0.004 0.000 ARG D 474 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 848) hydrogen bonds : angle 4.17260 ( 2382) SS BOND : bond 0.00205 ( 12) SS BOND : angle 1.97717 ( 24) covalent geometry : bond 0.00328 (16808) covalent geometry : angle 0.58776 (22756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 1.736 Fit side-chains REVERT: D 227 PHE cc_start: 0.7573 (m-10) cc_final: 0.7369 (m-10) REVERT: D 266 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.7262 (t80) REVERT: D 320 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7634 (mm-30) REVERT: D 369 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8697 (mt) REVERT: D 415 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7794 (mm-30) REVERT: D 416 GLU cc_start: 0.8608 (tt0) cc_final: 0.8075 (tt0) REVERT: D 439 LYS cc_start: 0.8341 (pptt) cc_final: 0.7914 (mmmt) REVERT: D 445 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8097 (mp0) REVERT: D 446 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7798 (tm130) REVERT: D 466 LYS cc_start: 0.8644 (tttm) cc_final: 0.8299 (ttpt) REVERT: D 467 ASP cc_start: 0.7443 (p0) cc_final: 0.7093 (p0) REVERT: D 501 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7879 (mtt-85) REVERT: D 518 ASP cc_start: 0.7792 (m-30) cc_final: 0.7449 (m-30) REVERT: D 522 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7429 (pt0) REVERT: D 530 LYS cc_start: 0.8614 (tttt) cc_final: 0.8305 (tttm) REVERT: D 532 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8170 (tp) REVERT: D 580 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7782 (ttt-90) REVERT: A 266 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.7181 (t80) REVERT: A 369 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8695 (mt) REVERT: A 439 LYS cc_start: 0.8351 (pptt) cc_final: 0.7897 (mmpt) REVERT: A 445 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8127 (mp0) REVERT: A 446 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7840 (tm130) REVERT: A 518 ASP cc_start: 0.7747 (m-30) cc_final: 0.7360 (m-30) REVERT: A 532 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8125 (tp) REVERT: A 580 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7632 (ttm-80) REVERT: B 266 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.7261 (t80) REVERT: B 320 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7600 (mm-30) REVERT: B 415 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7907 (mm-30) REVERT: B 416 GLU cc_start: 0.8587 (tt0) cc_final: 0.8046 (tt0) REVERT: B 439 LYS cc_start: 0.8285 (pptt) cc_final: 0.7837 (mmmt) REVERT: B 446 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7825 (tm130) REVERT: B 466 LYS cc_start: 0.8663 (tttm) cc_final: 0.8333 (ttpt) REVERT: B 467 ASP cc_start: 0.7506 (p0) cc_final: 0.7195 (p0) REVERT: B 474 ARG cc_start: 0.8413 (mtp-110) cc_final: 0.7951 (mtt90) REVERT: B 518 ASP cc_start: 0.7818 (m-30) cc_final: 0.7500 (m-30) REVERT: B 530 LYS cc_start: 0.8597 (tttt) cc_final: 0.8261 (tttm) REVERT: B 580 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7775 (mtp180) REVERT: B 583 MET cc_start: 0.8186 (ptm) cc_final: 0.7935 (ptt) REVERT: C 209 HIS cc_start: 0.7269 (m90) cc_final: 0.6853 (m-70) REVERT: C 266 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.7213 (t80) REVERT: C 320 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7586 (mm-30) REVERT: C 369 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8729 (mt) REVERT: C 415 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7868 (mm-30) REVERT: C 416 GLU cc_start: 0.8572 (tt0) cc_final: 0.8045 (tt0) REVERT: C 439 LYS cc_start: 0.8329 (pptt) cc_final: 0.7822 (mmmt) REVERT: C 446 GLN cc_start: 0.8296 (tt0) cc_final: 0.7797 (tm130) REVERT: C 466 LYS cc_start: 0.8684 (tttm) cc_final: 0.8340 (ttpt) REVERT: C 467 ASP cc_start: 0.7440 (p0) cc_final: 0.7102 (p0) REVERT: C 501 ARG cc_start: 0.8116 (mtt90) cc_final: 0.7770 (mtt-85) REVERT: C 530 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8149 (tttm) REVERT: C 580 ARG cc_start: 0.7844 (ttp-170) cc_final: 0.7643 (ttm-80) REVERT: C 583 MET cc_start: 0.8270 (ptm) cc_final: 0.8033 (ptt) outliers start: 55 outliers final: 24 residues processed: 262 average time/residue: 1.4124 time to fit residues: 406.3151 Evaluate side-chains 258 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 218 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 446 GLN Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 446 GLN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 533 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.196706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.152027 restraints weight = 14666.283| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.68 r_work: 0.3044 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16820 Z= 0.138 Angle : 0.590 11.378 22780 Z= 0.306 Chirality : 0.043 0.249 2548 Planarity : 0.004 0.040 2860 Dihedral : 5.267 38.045 2180 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.99 % Allowed : 14.60 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.19), residues: 1968 helix: 0.08 (0.15), residues: 1300 sheet: 0.99 (0.51), residues: 92 loop : -0.40 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 427 HIS 0.002 0.001 HIS C 475 PHE 0.013 0.001 PHE A 264 TYR 0.013 0.001 TYR B 306 ARG 0.003 0.000 ARG C 422 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 848) hydrogen bonds : angle 4.14217 ( 2382) SS BOND : bond 0.00193 ( 12) SS BOND : angle 2.05958 ( 24) covalent geometry : bond 0.00327 (16808) covalent geometry : angle 0.58668 (22756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 218 time to evaluate : 1.929 Fit side-chains REVERT: D 266 TYR cc_start: 0.9010 (OUTLIER) cc_final: 0.7260 (t80) REVERT: D 320 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7537 (mm-30) REVERT: D 369 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8708 (mt) REVERT: D 415 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7801 (mm-30) REVERT: D 416 GLU cc_start: 0.8570 (tt0) cc_final: 0.8017 (tt0) REVERT: D 439 LYS cc_start: 0.8335 (pptt) cc_final: 0.7904 (mmmt) REVERT: D 445 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8088 (mp0) REVERT: D 446 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7802 (tm130) REVERT: D 466 LYS cc_start: 0.8622 (tttm) cc_final: 0.8271 (ttpt) REVERT: D 467 ASP cc_start: 0.7412 (p0) cc_final: 0.7066 (p0) REVERT: D 501 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7822 (mtt-85) REVERT: D 518 ASP cc_start: 0.7768 (m-30) cc_final: 0.7443 (m-30) REVERT: D 522 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7222 (pt0) REVERT: D 530 LYS cc_start: 0.8564 (tttt) cc_final: 0.8200 (tttt) REVERT: D 532 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8098 (tp) REVERT: D 577 ARG cc_start: 0.7267 (mtm110) cc_final: 0.6975 (mtp-110) REVERT: D 580 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7677 (ttt-90) REVERT: A 266 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.7197 (t80) REVERT: A 369 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8703 (mt) REVERT: A 439 LYS cc_start: 0.8318 (pptt) cc_final: 0.7857 (mmpt) REVERT: A 445 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8110 (mp0) REVERT: A 446 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7833 (tm130) REVERT: A 518 ASP cc_start: 0.7785 (m-30) cc_final: 0.7374 (m-30) REVERT: A 532 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8088 (tp) REVERT: A 580 ARG cc_start: 0.7768 (ttp-170) cc_final: 0.7544 (ttm-80) REVERT: B 266 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.7250 (t80) REVERT: B 320 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7525 (mm-30) REVERT: B 369 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8700 (mt) REVERT: B 415 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7893 (mm-30) REVERT: B 416 GLU cc_start: 0.8547 (tt0) cc_final: 0.7990 (tt0) REVERT: B 439 LYS cc_start: 0.8297 (pptt) cc_final: 0.7875 (mmmt) REVERT: B 445 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8061 (mp0) REVERT: B 446 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7776 (tm130) REVERT: B 466 LYS cc_start: 0.8631 (tttm) cc_final: 0.8297 (ttpt) REVERT: B 467 ASP cc_start: 0.7503 (p0) cc_final: 0.7150 (p0) REVERT: B 474 ARG cc_start: 0.8393 (mtp-110) cc_final: 0.7902 (mtt90) REVERT: B 518 ASP cc_start: 0.7810 (m-30) cc_final: 0.7459 (m-30) REVERT: B 521 ASP cc_start: 0.7812 (p0) cc_final: 0.7556 (p0) REVERT: B 530 LYS cc_start: 0.8556 (tttt) cc_final: 0.8237 (tttm) REVERT: B 580 ARG cc_start: 0.8103 (ttm-80) cc_final: 0.7697 (mtp180) REVERT: B 583 MET cc_start: 0.8155 (ptm) cc_final: 0.7901 (ptt) REVERT: C 131 LYS cc_start: 0.8292 (ttpt) cc_final: 0.7476 (tmtt) REVERT: C 209 HIS cc_start: 0.7180 (m90) cc_final: 0.6789 (m-70) REVERT: C 266 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.7220 (t80) REVERT: C 320 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7511 (mm-30) REVERT: C 369 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8725 (mt) REVERT: C 415 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7783 (mm-30) REVERT: C 416 GLU cc_start: 0.8569 (tt0) cc_final: 0.8025 (tt0) REVERT: C 439 LYS cc_start: 0.8322 (pptt) cc_final: 0.7832 (mmmt) REVERT: C 446 GLN cc_start: 0.8271 (tt0) cc_final: 0.7798 (tm130) REVERT: C 466 LYS cc_start: 0.8643 (tttm) cc_final: 0.8288 (ttpt) REVERT: C 467 ASP cc_start: 0.7422 (p0) cc_final: 0.7070 (p0) REVERT: C 501 ARG cc_start: 0.8073 (mtt90) cc_final: 0.7713 (mtt-85) REVERT: C 521 ASP cc_start: 0.7923 (p0) cc_final: 0.7694 (p0) REVERT: C 530 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8121 (tttm) REVERT: C 580 ARG cc_start: 0.7801 (ttp-170) cc_final: 0.7530 (ttm-80) REVERT: C 583 MET cc_start: 0.8245 (ptm) cc_final: 0.8000 (ptt) outliers start: 54 outliers final: 26 residues processed: 254 average time/residue: 1.4647 time to fit residues: 409.1639 Evaluate side-chains 259 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 446 GLN Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 446 GLN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 533 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 122 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 198 optimal weight: 0.0040 chunk 64 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.198140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.153229 restraints weight = 14659.693| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.68 r_work: 0.3048 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16820 Z= 0.123 Angle : 0.573 12.031 22780 Z= 0.296 Chirality : 0.041 0.166 2548 Planarity : 0.004 0.040 2860 Dihedral : 5.154 37.009 2180 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.99 % Allowed : 14.99 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.19), residues: 1968 helix: 0.20 (0.15), residues: 1296 sheet: 1.07 (0.52), residues: 92 loop : -0.33 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 427 HIS 0.002 0.000 HIS C 475 PHE 0.028 0.001 PHE C 227 TYR 0.011 0.001 TYR A 306 ARG 0.009 0.000 ARG D 474 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 848) hydrogen bonds : angle 4.10006 ( 2382) SS BOND : bond 0.00193 ( 12) SS BOND : angle 1.85729 ( 24) covalent geometry : bond 0.00289 (16808) covalent geometry : angle 0.56981 (22756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 224 time to evaluate : 1.927 Fit side-chains REVERT: D 266 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.7270 (t80) REVERT: D 320 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7568 (mm-30) REVERT: D 369 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8735 (mt) REVERT: D 415 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7747 (mm-30) REVERT: D 416 GLU cc_start: 0.8607 (tt0) cc_final: 0.8045 (tt0) REVERT: D 439 LYS cc_start: 0.8355 (pptt) cc_final: 0.7892 (mmmt) REVERT: D 445 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8070 (mp0) REVERT: D 446 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7779 (tm130) REVERT: D 466 LYS cc_start: 0.8655 (tttm) cc_final: 0.8280 (ttpt) REVERT: D 467 ASP cc_start: 0.7386 (p0) cc_final: 0.7042 (p0) REVERT: D 474 ARG cc_start: 0.8370 (mtp-110) cc_final: 0.8152 (mtp85) REVERT: D 501 ARG cc_start: 0.8048 (mtt90) cc_final: 0.7798 (mtt-85) REVERT: D 518 ASP cc_start: 0.7772 (m-30) cc_final: 0.7484 (m-30) REVERT: D 522 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7265 (pt0) REVERT: D 530 LYS cc_start: 0.8555 (tttt) cc_final: 0.8257 (tttt) REVERT: D 532 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8063 (tp) REVERT: D 580 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7838 (ttm-80) REVERT: A 266 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.7207 (t80) REVERT: A 369 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8749 (mt) REVERT: A 415 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8010 (tm-30) REVERT: A 439 LYS cc_start: 0.8304 (pptt) cc_final: 0.7830 (mmpt) REVERT: A 445 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8101 (mp0) REVERT: A 446 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7842 (tm130) REVERT: A 467 ASP cc_start: 0.8231 (t70) cc_final: 0.7101 (p0) REVERT: A 518 ASP cc_start: 0.7768 (m-30) cc_final: 0.7385 (m-30) REVERT: A 532 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8034 (tp) REVERT: A 580 ARG cc_start: 0.7776 (ttp-170) cc_final: 0.7534 (ttm-80) REVERT: B 266 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.7315 (t80) REVERT: B 320 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7547 (mm-30) REVERT: B 415 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: B 416 GLU cc_start: 0.8577 (tt0) cc_final: 0.8015 (tt0) REVERT: B 439 LYS cc_start: 0.8298 (pptt) cc_final: 0.7840 (mmmt) REVERT: B 445 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8108 (mp0) REVERT: B 446 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7850 (tm130) REVERT: B 466 LYS cc_start: 0.8654 (tttm) cc_final: 0.8293 (ttpt) REVERT: B 467 ASP cc_start: 0.7472 (p0) cc_final: 0.7116 (p0) REVERT: B 474 ARG cc_start: 0.8410 (mtp-110) cc_final: 0.7903 (mtt90) REVERT: B 518 ASP cc_start: 0.7752 (m-30) cc_final: 0.7436 (m-30) REVERT: B 521 ASP cc_start: 0.7900 (p0) cc_final: 0.7681 (p0) REVERT: B 530 LYS cc_start: 0.8514 (tttt) cc_final: 0.8244 (tttt) REVERT: B 583 MET cc_start: 0.8169 (ptm) cc_final: 0.7928 (ptt) REVERT: C 131 LYS cc_start: 0.8272 (ttpt) cc_final: 0.7460 (tmtt) REVERT: C 209 HIS cc_start: 0.7148 (m90) cc_final: 0.6753 (m-70) REVERT: C 230 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7276 (t80) REVERT: C 266 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.7225 (t80) REVERT: C 320 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7504 (mm-30) REVERT: C 369 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8771 (mt) REVERT: C 415 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7759 (mm-30) REVERT: C 416 GLU cc_start: 0.8608 (tt0) cc_final: 0.8045 (tt0) REVERT: C 439 LYS cc_start: 0.8311 (pptt) cc_final: 0.7800 (mmmt) REVERT: C 446 GLN cc_start: 0.8316 (tt0) cc_final: 0.7845 (tm130) REVERT: C 466 LYS cc_start: 0.8645 (tttm) cc_final: 0.8277 (ttpt) REVERT: C 467 ASP cc_start: 0.7389 (p0) cc_final: 0.7020 (p0) REVERT: C 501 ARG cc_start: 0.8035 (mtt90) cc_final: 0.7667 (mtt-85) REVERT: C 530 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8063 (tttm) REVERT: C 580 ARG cc_start: 0.7798 (ttp-170) cc_final: 0.7472 (ttm-80) REVERT: C 583 MET cc_start: 0.8226 (ptm) cc_final: 0.7980 (ptt) outliers start: 54 outliers final: 28 residues processed: 255 average time/residue: 1.4818 time to fit residues: 414.6261 Evaluate side-chains 267 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 221 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 446 GLN Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 446 GLN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 230 TYR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 408 GLN Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 533 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 173 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 178 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 chunk 8 optimal weight: 0.0970 chunk 124 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 GLN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.198735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.148958 restraints weight = 14724.819| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.79 r_work: 0.3034 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16820 Z= 0.116 Angle : 0.569 12.467 22780 Z= 0.293 Chirality : 0.041 0.235 2548 Planarity : 0.004 0.039 2860 Dihedral : 5.056 36.178 2180 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.49 % Allowed : 15.76 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.19), residues: 1968 helix: 0.30 (0.15), residues: 1296 sheet: 1.15 (0.52), residues: 92 loop : -0.27 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 277 HIS 0.002 0.000 HIS C 475 PHE 0.029 0.001 PHE B 227 TYR 0.011 0.001 TYR A 306 ARG 0.008 0.000 ARG D 474 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 848) hydrogen bonds : angle 4.04376 ( 2382) SS BOND : bond 0.00129 ( 12) SS BOND : angle 1.73074 ( 24) covalent geometry : bond 0.00267 (16808) covalent geometry : angle 0.56626 (22756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 1.691 Fit side-chains REVERT: D 227 PHE cc_start: 0.7420 (m-10) cc_final: 0.7200 (m-10) REVERT: D 266 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.7351 (t80) REVERT: D 320 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7498 (mm-30) REVERT: D 415 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7709 (mm-30) REVERT: D 416 GLU cc_start: 0.8574 (tt0) cc_final: 0.7980 (tt0) REVERT: D 439 LYS cc_start: 0.8327 (pptt) cc_final: 0.7804 (mmmt) REVERT: D 445 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8071 (mp0) REVERT: D 446 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7777 (tm130) REVERT: D 466 LYS cc_start: 0.8612 (tttm) cc_final: 0.8214 (ttpt) REVERT: D 467 ASP cc_start: 0.7324 (p0) cc_final: 0.6955 (p0) REVERT: D 474 ARG cc_start: 0.8360 (mtp-110) cc_final: 0.8118 (mtp85) REVERT: D 501 ARG cc_start: 0.7976 (mtt90) cc_final: 0.7698 (mtt-85) REVERT: D 518 ASP cc_start: 0.7639 (m-30) cc_final: 0.7389 (m-30) REVERT: D 522 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7209 (pt0) REVERT: D 530 LYS cc_start: 0.8503 (tttt) cc_final: 0.8170 (tttt) REVERT: D 532 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7997 (tp) REVERT: D 580 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7729 (ttm-80) REVERT: A 266 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.7256 (t80) REVERT: A 415 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: A 439 LYS cc_start: 0.8269 (pptt) cc_final: 0.7737 (mmpt) REVERT: A 445 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8050 (mp0) REVERT: A 446 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7791 (tm130) REVERT: A 467 ASP cc_start: 0.8203 (t70) cc_final: 0.7057 (p0) REVERT: A 518 ASP cc_start: 0.7666 (m-30) cc_final: 0.7329 (m-30) REVERT: A 532 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7913 (tp) REVERT: A 577 ARG cc_start: 0.7268 (mtm110) cc_final: 0.6791 (mtp-110) REVERT: A 580 ARG cc_start: 0.7673 (ttp-170) cc_final: 0.7364 (ttm-80) REVERT: B 266 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.7369 (t80) REVERT: B 320 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7516 (mm-30) REVERT: B 415 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7809 (mm-30) REVERT: B 416 GLU cc_start: 0.8567 (tt0) cc_final: 0.7956 (tt0) REVERT: B 439 LYS cc_start: 0.8273 (pptt) cc_final: 0.7761 (mmmt) REVERT: B 445 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8082 (mp0) REVERT: B 446 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7804 (tm130) REVERT: B 466 LYS cc_start: 0.8576 (tttm) cc_final: 0.8179 (ttpt) REVERT: B 467 ASP cc_start: 0.7401 (p0) cc_final: 0.7026 (p0) REVERT: B 474 ARG cc_start: 0.8360 (mtp-110) cc_final: 0.7829 (mtt90) REVERT: B 511 SER cc_start: 0.8793 (t) cc_final: 0.8554 (t) REVERT: B 518 ASP cc_start: 0.7677 (m-30) cc_final: 0.7360 (m-30) REVERT: B 530 LYS cc_start: 0.8428 (tttt) cc_final: 0.8133 (tttt) REVERT: B 577 ARG cc_start: 0.7206 (mtm110) cc_final: 0.6901 (mtp-110) REVERT: B 583 MET cc_start: 0.8136 (ptm) cc_final: 0.7889 (ptt) REVERT: C 131 LYS cc_start: 0.8293 (ttpt) cc_final: 0.7465 (tmtt) REVERT: C 209 HIS cc_start: 0.7090 (m90) cc_final: 0.6695 (m-70) REVERT: C 230 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7034 (t80) REVERT: C 266 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.7285 (t80) REVERT: C 320 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7464 (mm-30) REVERT: C 369 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8794 (mt) REVERT: C 415 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7746 (mm-30) REVERT: C 416 GLU cc_start: 0.8586 (tt0) cc_final: 0.7983 (tt0) REVERT: C 439 LYS cc_start: 0.8245 (pptt) cc_final: 0.7693 (mmmt) REVERT: C 446 GLN cc_start: 0.8310 (tt0) cc_final: 0.7803 (tm130) REVERT: C 466 LYS cc_start: 0.8610 (tttm) cc_final: 0.8198 (ttpt) REVERT: C 467 ASP cc_start: 0.7311 (p0) cc_final: 0.6923 (p0) REVERT: C 474 ARG cc_start: 0.8403 (mtp-110) cc_final: 0.7834 (mtt90) REVERT: C 501 ARG cc_start: 0.7967 (mtt90) cc_final: 0.7673 (mtt-85) REVERT: C 518 ASP cc_start: 0.7131 (m-30) cc_final: 0.6867 (m-30) REVERT: C 521 ASP cc_start: 0.8260 (p0) cc_final: 0.8059 (p0) REVERT: C 530 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8003 (tttm) REVERT: C 580 ARG cc_start: 0.7716 (ttp-170) cc_final: 0.7336 (ttm-80) REVERT: C 583 MET cc_start: 0.8191 (ptm) cc_final: 0.7944 (ptt) outliers start: 45 outliers final: 26 residues processed: 254 average time/residue: 1.4834 time to fit residues: 411.8320 Evaluate side-chains 260 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 446 GLN Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 446 GLN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 230 TYR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 533 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 41 optimal weight: 0.0020 chunk 116 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.198928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.153354 restraints weight = 14646.611| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.70 r_work: 0.3054 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16820 Z= 0.122 Angle : 0.577 12.570 22780 Z= 0.296 Chirality : 0.042 0.169 2548 Planarity : 0.004 0.039 2860 Dihedral : 5.038 35.784 2180 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.32 % Allowed : 15.71 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 1968 helix: 0.30 (0.15), residues: 1296 sheet: 1.31 (0.53), residues: 92 loop : -0.21 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 277 HIS 0.002 0.000 HIS C 475 PHE 0.032 0.001 PHE A 227 TYR 0.012 0.001 TYR A 306 ARG 0.008 0.000 ARG D 474 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 848) hydrogen bonds : angle 4.03149 ( 2382) SS BOND : bond 0.00150 ( 12) SS BOND : angle 1.71705 ( 24) covalent geometry : bond 0.00287 (16808) covalent geometry : angle 0.57447 (22756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11958.23 seconds wall clock time: 205 minutes 55.86 seconds (12355.86 seconds total)