Starting phenix.real_space_refine on Thu Sep 18 11:30:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j34_61105/09_2025/9j34_61105.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j34_61105/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9j34_61105/09_2025/9j34_61105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j34_61105/09_2025/9j34_61105.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j34_61105/09_2025/9j34_61105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j34_61105/09_2025/9j34_61105.map" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.38, per 1000 atoms: 0.27 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: 1.35 Conformation dependent library (CDL) restraints added in 736.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.40 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: 2.31 Time building geometry restraints manager: 1.85 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: 4.420 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.930 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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: 0.020 Load rotamer database and sin/cos tables:10.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.580 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.010 0.001 ARG C 94 TYR 0.022 0.002 TYR A 306 PHE 0.021 0.002 PHE C 396 TRP 0.012 0.002 TRP A 427 HIS 0.012 0.002 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.01234 (16808) covalent geometry : angle 1.31948 (22756) SS BOND : bond 0.12075 ( 12) SS BOND : angle 16.93831 ( 24) hydrogen bonds : bond 0.24688 ( 848) hydrogen bonds : angle 9.36978 ( 2382) *********************** 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 : 0.641 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: 0.6351 time to fit residues: 225.9662 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 : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 ASN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.199513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.161771 restraints weight = 14837.413| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.58 r_work: 0.3094 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2203 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= 0.140 Angle : 0.655 6.649 22780 Z= 0.340 Chirality : 0.042 0.144 2548 Planarity : 0.005 0.065 2860 Dihedral : 5.932 28.736 2180 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.77 % Allowed : 11.56 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.17), residues: 1968 helix: -1.70 (0.13), residues: 1260 sheet: -0.24 (0.42), residues: 92 loop : -0.99 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 413 TYR 0.014 0.001 TYR B 306 PHE 0.013 0.001 PHE A 355 TRP 0.011 0.002 TRP B 277 HIS 0.002 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00316 (16808) covalent geometry : angle 0.65370 (22756) SS BOND : bond 0.00235 ( 12) SS BOND : angle 1.25112 ( 24) hydrogen bonds : bond 0.04239 ( 848) hydrogen bonds : angle 4.94436 ( 2382) *********************** 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 301 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 269 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 415 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7838 (mm-30) REVERT: D 416 GLU cc_start: 0.8587 (tt0) cc_final: 0.8091 (tt0) REVERT: D 420 LYS cc_start: 0.8649 (mttt) cc_final: 0.8390 (mtpp) REVERT: D 471 ASP cc_start: 0.8358 (m-30) cc_final: 0.8114 (m-30) REVERT: D 474 ARG cc_start: 0.8367 (mtp-110) cc_final: 0.7982 (mtt90) REVERT: D 501 ARG cc_start: 0.8057 (mtt90) cc_final: 0.7778 (mtt-85) REVERT: D 530 LYS cc_start: 0.8606 (tttt) cc_final: 0.8360 (tttm) REVERT: D 557 GLU cc_start: 0.7949 (pm20) cc_final: 0.7642 (pm20) REVERT: D 583 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7962 (ptt) REVERT: A 121 ASP cc_start: 0.8152 (t70) cc_final: 0.7921 (t0) REVERT: A 156 ARG cc_start: 0.6558 (ptt180) cc_final: 0.6255 (ptm160) REVERT: A 408 GLN cc_start: 0.8112 (mt0) cc_final: 0.7684 (mm-40) REVERT: A 413 ARG cc_start: 0.8711 (mmt-90) cc_final: 0.8162 (tpt170) REVERT: A 417 MET cc_start: 0.9041 (tmm) cc_final: 0.8833 (tmm) REVERT: A 474 ARG cc_start: 0.8016 (mtp-110) cc_final: 0.7734 (ttp-170) REVERT: A 532 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8333 (tp) REVERT: A 580 ARG cc_start: 0.7901 (ttp-170) cc_final: 0.7543 (ttt180) REVERT: B 408 GLN cc_start: 0.8167 (mt0) cc_final: 0.7814 (mm-40) REVERT: B 415 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7836 (mm-30) REVERT: B 416 GLU cc_start: 0.8530 (tt0) cc_final: 0.8082 (tt0) REVERT: B 471 ASP cc_start: 0.8398 (m-30) cc_final: 0.8164 (m-30) REVERT: B 530 LYS cc_start: 0.8661 (tttt) cc_final: 0.8352 (tttm) REVERT: B 557 GLU cc_start: 0.7732 (pm20) cc_final: 0.7497 (pm20) REVERT: B 580 ARG cc_start: 0.8087 (ttt-90) cc_final: 0.7796 (mtp180) REVERT: B 583 MET cc_start: 0.8336 (ptm) cc_final: 0.8090 (ptt) REVERT: C 132 MET cc_start: 0.8843 (tpt) cc_final: 0.7623 (tpt) REVERT: C 156 ARG cc_start: 0.6810 (ptt180) cc_final: 0.6245 (ptm-80) REVERT: C 408 GLN cc_start: 0.8221 (mt0) cc_final: 0.7864 (mt0) REVERT: C 415 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7902 (mm-30) REVERT: C 416 GLU cc_start: 0.8658 (tt0) cc_final: 0.8272 (tt0) REVERT: C 420 LYS cc_start: 0.8720 (mttt) cc_final: 0.8451 (mtpp) REVERT: C 471 ASP cc_start: 0.8333 (m-30) cc_final: 0.8112 (m-30) REVERT: C 501 ARG cc_start: 0.8150 (mtt90) cc_final: 0.7830 (mtt-85) REVERT: C 511 SER cc_start: 0.8430 (t) cc_final: 0.8030 (t) REVERT: C 530 LYS cc_start: 0.8352 (tttt) cc_final: 0.7942 (tttm) REVERT: C 583 MET cc_start: 0.8324 (ptm) cc_final: 0.8083 (ptt) outliers start: 32 outliers final: 9 residues processed: 284 average time/residue: 0.6375 time to fit residues: 198.4607 Evaluate side-chains 260 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 246 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 156 ARG 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 583 MET 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 533 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 161 optimal weight: 0.0370 chunk 93 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- 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 262 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 ASN ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.193761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.155048 restraints weight = 14780.604| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.55 r_work: 0.3013 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 16820 Z= 0.268 Angle : 0.725 9.360 22780 Z= 0.381 Chirality : 0.049 0.225 2548 Planarity : 0.005 0.051 2860 Dihedral : 6.002 32.065 2180 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.82 % Allowed : 12.33 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.18), residues: 1968 helix: -0.91 (0.14), residues: 1296 sheet: -0.02 (0.45), residues: 92 loop : -0.84 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 177 TYR 0.019 0.002 TYR C 306 PHE 0.021 0.003 PHE D 351 TRP 0.015 0.003 TRP C 427 HIS 0.003 0.001 HIS C 271 Details of bonding type rmsd covalent geometry : bond 0.00642 (16808) covalent geometry : angle 0.72306 (22756) SS BOND : bond 0.00332 ( 12) SS BOND : angle 1.79228 ( 24) hydrogen bonds : bond 0.05098 ( 848) hydrogen bonds : angle 4.74651 ( 2382) *********************** 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 295 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 244 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: D 240 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7781 (tt) REVERT: D 415 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7954 (mm-30) REVERT: D 439 LYS cc_start: 0.8447 (pptt) cc_final: 0.8005 (mmpt) REVERT: D 466 LYS cc_start: 0.8722 (tttm) cc_final: 0.8371 (ttpt) REVERT: D 501 ARG cc_start: 0.8160 (mtt90) cc_final: 0.7910 (mtt-85) REVERT: D 530 LYS cc_start: 0.8662 (tttt) cc_final: 0.8347 (tttm) REVERT: D 532 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8233 (tp) REVERT: D 557 GLU cc_start: 0.7946 (pm20) cc_final: 0.7628 (pm20) REVERT: D 558 GLU cc_start: 0.7959 (mp0) cc_final: 0.7642 (mt-10) REVERT: D 583 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7922 (ptt) REVERT: A 413 ARG cc_start: 0.8764 (mmt-90) cc_final: 0.8354 (tpt170) REVERT: A 445 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8078 (mp0) REVERT: A 446 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7796 (tm130) REVERT: A 474 ARG cc_start: 0.8333 (mtp-110) cc_final: 0.7962 (ttm-80) REVERT: A 557 GLU cc_start: 0.7999 (pm20) cc_final: 0.7765 (pm20) REVERT: A 580 ARG cc_start: 0.8019 (ttp-170) cc_final: 0.7671 (ttm-80) REVERT: B 131 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7556 (tmtt) REVERT: B 240 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7823 (tt) REVERT: B 415 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7965 (mm-30) REVERT: B 416 GLU cc_start: 0.8622 (tt0) cc_final: 0.8161 (tt0) REVERT: B 446 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7712 (tm130) REVERT: B 530 LYS cc_start: 0.8658 (tttt) cc_final: 0.8458 (tttt) REVERT: B 557 GLU cc_start: 0.7816 (pm20) cc_final: 0.7509 (pm20) REVERT: C 131 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7593 (pptt) REVERT: C 209 HIS cc_start: 0.7228 (m90) cc_final: 0.7001 (m-70) REVERT: C 369 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8789 (mt) REVERT: C 415 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8004 (mm-30) REVERT: C 416 GLU cc_start: 0.8652 (tt0) cc_final: 0.8165 (tt0) REVERT: C 439 LYS cc_start: 0.8507 (pptt) cc_final: 0.7964 (mmpt) REVERT: C 466 LYS cc_start: 0.8697 (tttm) cc_final: 0.8353 (ttpt) REVERT: C 530 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8202 (tttm) REVERT: C 583 MET cc_start: 0.8457 (ptm) cc_final: 0.8201 (ptt) outliers start: 51 outliers final: 19 residues processed: 278 average time/residue: 0.6173 time to fit residues: 188.0179 Evaluate side-chains 264 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 240 LEU Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 583 MET Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 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 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 530 LYS 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 82 optimal weight: 0.5980 chunk 20 optimal weight: 0.0570 chunk 139 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 196 optimal weight: 0.6980 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.4136 r_free = 0.4136 target = 0.198446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.154747 restraints weight = 14789.462| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.71 r_work: 0.3048 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3229 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= 0.114 Angle : 0.569 6.806 22780 Z= 0.299 Chirality : 0.041 0.229 2548 Planarity : 0.004 0.046 2860 Dihedral : 5.422 33.683 2180 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.43 % Allowed : 12.94 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.19), residues: 1968 helix: -0.23 (0.15), residues: 1288 sheet: 0.45 (0.49), residues: 92 loop : -0.71 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 474 TYR 0.013 0.001 TYR C 306 PHE 0.015 0.001 PHE A 227 TRP 0.010 0.001 TRP A 277 HIS 0.002 0.001 HIS A 430 Details of bonding type rmsd covalent geometry : bond 0.00257 (16808) covalent geometry : angle 0.56710 (22756) SS BOND : bond 0.00295 ( 12) SS BOND : angle 1.68726 ( 24) hydrogen bonds : bond 0.03570 ( 848) hydrogen bonds : angle 4.30197 ( 2382) *********************** 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 291 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 247 time to evaluate : 0.451 Fit side-chains REVERT: D 104 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6748 (pp) REVERT: D 227 PHE cc_start: 0.7349 (m-10) cc_final: 0.7147 (m-10) REVERT: D 369 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8721 (mt) REVERT: D 415 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7776 (mm-30) REVERT: D 439 LYS cc_start: 0.8370 (pptt) cc_final: 0.7856 (mmpt) REVERT: D 445 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7981 (tp30) REVERT: D 446 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7711 (tm130) REVERT: D 501 ARG cc_start: 0.8087 (mtt90) cc_final: 0.7766 (mtt-85) REVERT: D 518 ASP cc_start: 0.7771 (m-30) cc_final: 0.7511 (m-30) REVERT: D 530 LYS cc_start: 0.8609 (tttt) cc_final: 0.8280 (tttm) REVERT: D 532 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8079 (tp) REVERT: D 557 GLU cc_start: 0.7823 (pm20) cc_final: 0.7323 (pm20) REVERT: D 558 GLU cc_start: 0.7843 (mp0) cc_final: 0.7459 (mt-10) REVERT: D 583 MET cc_start: 0.8193 (ptm) cc_final: 0.7971 (ptt) REVERT: A 445 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8102 (mp0) REVERT: A 446 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7781 (tm130) REVERT: A 474 ARG cc_start: 0.8259 (mtp-110) cc_final: 0.7816 (mtt90) REVERT: A 518 ASP cc_start: 0.7681 (m-30) cc_final: 0.7198 (m-30) REVERT: A 580 ARG cc_start: 0.7770 (ttp-170) cc_final: 0.7467 (ttm-80) REVERT: B 201 MET cc_start: 0.6958 (mmt) cc_final: 0.6700 (mmp) REVERT: B 408 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7872 (mt0) REVERT: B 415 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7824 (mm-30) REVERT: B 416 GLU cc_start: 0.8549 (tt0) cc_final: 0.8054 (tt0) REVERT: B 439 LYS cc_start: 0.8363 (pptt) cc_final: 0.7807 (mmpt) REVERT: B 445 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8069 (tp30) REVERT: B 446 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7665 (tm130) REVERT: B 518 ASP cc_start: 0.7755 (m-30) cc_final: 0.7400 (m-30) REVERT: B 530 LYS cc_start: 0.8631 (tttt) cc_final: 0.8269 (tttm) REVERT: C 209 HIS cc_start: 0.7139 (m90) cc_final: 0.6883 (m-70) REVERT: C 408 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7735 (mm-40) REVERT: C 415 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7890 (mm-30) REVERT: C 439 LYS cc_start: 0.8320 (pptt) cc_final: 0.7807 (mmpt) REVERT: C 446 GLN cc_start: 0.8275 (tt0) cc_final: 0.7666 (tm130) REVERT: C 530 LYS cc_start: 0.8514 (tttt) cc_final: 0.8133 (tttm) REVERT: C 557 GLU cc_start: 0.7451 (pm20) cc_final: 0.7249 (pm20) REVERT: C 580 ARG cc_start: 0.7835 (ttp-170) cc_final: 0.7529 (ttm-80) REVERT: C 583 MET cc_start: 0.8349 (ptm) cc_final: 0.8077 (ptt) outliers start: 44 outliers final: 16 residues processed: 268 average time/residue: 0.6546 time to fit residues: 192.0357 Evaluate side-chains 258 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 104 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 195 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 408 GLN 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 139 LEU Chi-restraints excluded: chain C residue 195 VAL 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 408 GLN Chi-restraints excluded: chain C residue 415 GLU 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 97 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 175 optimal weight: 0.0670 chunk 56 optimal weight: 5.9990 chunk 161 optimal weight: 0.1980 chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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** D 436 ASN A 262 ASN B 262 ASN ** B 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 = 0.4142 r_free = 0.4142 target = 0.198813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.157309 restraints weight = 14754.421| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.68 r_work: 0.3058 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16820 Z= 0.116 Angle : 0.565 8.744 22780 Z= 0.294 Chirality : 0.041 0.235 2548 Planarity : 0.004 0.043 2860 Dihedral : 5.248 31.136 2180 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.93 % Allowed : 13.61 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.19), residues: 1968 helix: 0.03 (0.15), residues: 1292 sheet: 0.74 (0.50), residues: 92 loop : -0.54 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 422 TYR 0.011 0.001 TYR B 306 PHE 0.018 0.001 PHE B 227 TRP 0.009 0.001 TRP D 277 HIS 0.001 0.000 HIS D 475 Details of bonding type rmsd covalent geometry : bond 0.00267 (16808) covalent geometry : angle 0.56088 (22756) SS BOND : bond 0.00358 ( 12) SS BOND : angle 2.06710 ( 24) hydrogen bonds : bond 0.03540 ( 848) hydrogen bonds : angle 4.13903 ( 2382) *********************** 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 290 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: D 320 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7636 (mm-30) REVERT: D 415 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7766 (mm-30) REVERT: D 439 LYS cc_start: 0.8349 (pptt) cc_final: 0.7898 (mmpt) REVERT: D 445 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8101 (tp30) REVERT: D 446 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7774 (tm130) REVERT: D 466 LYS cc_start: 0.8673 (tttm) cc_final: 0.8296 (ttpt) REVERT: D 467 ASP cc_start: 0.7420 (p0) cc_final: 0.7104 (p0) REVERT: D 501 ARG cc_start: 0.8104 (mtt90) cc_final: 0.7796 (mtt-85) REVERT: D 518 ASP cc_start: 0.7727 (m-30) cc_final: 0.7461 (m-30) REVERT: D 530 LYS cc_start: 0.8606 (tttt) cc_final: 0.8315 (tttm) REVERT: D 532 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8103 (tp) REVERT: D 558 GLU cc_start: 0.7837 (mp0) cc_final: 0.7482 (mt-10) REVERT: D 580 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7645 (mtp180) REVERT: A 369 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8688 (mt) REVERT: A 408 GLN cc_start: 0.8082 (mt0) cc_final: 0.7737 (mt0) REVERT: A 445 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8098 (mp0) REVERT: A 446 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7818 (tm130) REVERT: A 474 ARG cc_start: 0.8282 (mtp-110) cc_final: 0.7895 (mtt90) REVERT: A 518 ASP cc_start: 0.7637 (m-30) cc_final: 0.7169 (m-30) REVERT: A 580 ARG cc_start: 0.7780 (ttp-170) cc_final: 0.7524 (ttm-80) REVERT: B 408 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7859 (mt0) REVERT: B 415 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: B 416 GLU cc_start: 0.8569 (tt0) cc_final: 0.8060 (tt0) REVERT: B 439 LYS cc_start: 0.8348 (pptt) cc_final: 0.7849 (mmpt) REVERT: B 445 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8093 (tp30) REVERT: B 446 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7748 (tm130) REVERT: B 467 ASP cc_start: 0.7411 (p0) cc_final: 0.7084 (p0) REVERT: B 518 ASP cc_start: 0.7808 (m-30) cc_final: 0.7486 (m-30) REVERT: B 530 LYS cc_start: 0.8646 (tttt) cc_final: 0.8282 (tttm) REVERT: B 557 GLU cc_start: 0.7409 (pm20) cc_final: 0.7035 (pm20) REVERT: C 209 HIS cc_start: 0.7204 (m90) cc_final: 0.6922 (m-70) REVERT: C 369 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8764 (mt) REVERT: C 408 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7835 (mt0) REVERT: C 415 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7793 (mm-30) REVERT: C 416 GLU cc_start: 0.8621 (tt0) cc_final: 0.8094 (tt0) REVERT: C 439 LYS cc_start: 0.8360 (pptt) cc_final: 0.7847 (mmmt) REVERT: C 446 GLN cc_start: 0.8333 (tt0) cc_final: 0.7741 (tm130) REVERT: C 466 LYS cc_start: 0.8657 (tttm) cc_final: 0.8289 (ttpt) REVERT: C 467 ASP cc_start: 0.7431 (p0) cc_final: 0.7095 (p0) REVERT: C 530 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8145 (tttm) REVERT: C 583 MET cc_start: 0.8262 (ptm) cc_final: 0.8010 (ptt) outliers start: 53 outliers final: 19 residues processed: 267 average time/residue: 0.6016 time to fit residues: 176.9874 Evaluate side-chains 259 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 300 CYS 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 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 202 VAL Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 408 GLN 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 139 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 202 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 122 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 170 optimal weight: 0.2980 chunk 130 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN C 262 ASN C 436 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.197655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.159847 restraints weight = 14714.314| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.55 r_work: 0.3064 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16820 Z= 0.138 Angle : 0.585 10.668 22780 Z= 0.305 Chirality : 0.043 0.243 2548 Planarity : 0.004 0.041 2860 Dihedral : 5.322 36.488 2180 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.26 % Allowed : 13.61 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.19), residues: 1968 helix: 0.07 (0.15), residues: 1292 sheet: 0.85 (0.51), residues: 92 loop : -0.45 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 422 TYR 0.012 0.001 TYR D 306 PHE 0.012 0.001 PHE A 351 TRP 0.010 0.001 TRP C 427 HIS 0.002 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00324 (16808) covalent geometry : angle 0.58098 (22756) SS BOND : bond 0.00223 ( 12) SS BOND : angle 2.17305 ( 24) hydrogen bonds : bond 0.03792 ( 848) hydrogen bonds : angle 4.13856 ( 2382) *********************** 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 291 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 232 time to evaluate : 0.503 Fit side-chains REVERT: D 266 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.7282 (t80) REVERT: D 320 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7705 (mm-30) REVERT: D 415 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7821 (mm-30) REVERT: D 439 LYS cc_start: 0.8379 (pptt) cc_final: 0.7967 (mmmt) REVERT: D 445 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8102 (tp30) REVERT: D 446 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7809 (tm130) REVERT: D 466 LYS cc_start: 0.8702 (tttm) cc_final: 0.8364 (ttpt) REVERT: D 467 ASP cc_start: 0.7474 (p0) cc_final: 0.7145 (p0) REVERT: D 501 ARG cc_start: 0.8110 (mtt90) cc_final: 0.7797 (mtt-85) REVERT: D 518 ASP cc_start: 0.7698 (m-30) cc_final: 0.7442 (m-30) REVERT: D 530 LYS cc_start: 0.8633 (tttt) cc_final: 0.8328 (tttm) REVERT: D 532 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8178 (tp) REVERT: D 558 GLU cc_start: 0.7881 (mp0) cc_final: 0.7508 (mt-10) REVERT: D 580 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.7731 (mtp180) REVERT: A 266 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.7187 (t80) REVERT: A 369 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8706 (mt) REVERT: A 439 LYS cc_start: 0.8473 (pptt) cc_final: 0.7930 (mmpt) REVERT: A 445 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8085 (mp0) REVERT: A 446 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7852 (tm130) REVERT: A 474 ARG cc_start: 0.8297 (mtp-110) cc_final: 0.7945 (mtt90) REVERT: A 518 ASP cc_start: 0.7687 (m-30) cc_final: 0.7240 (m-30) REVERT: A 532 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8154 (tp) REVERT: B 266 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.7270 (t80) REVERT: B 320 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7701 (mm-30) REVERT: B 369 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8708 (mt) REVERT: B 408 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: B 415 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7822 (mm-30) REVERT: B 416 GLU cc_start: 0.8601 (tt0) cc_final: 0.8089 (tt0) REVERT: B 439 LYS cc_start: 0.8381 (pptt) cc_final: 0.7997 (mmpt) REVERT: B 445 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8103 (tp30) REVERT: B 446 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7824 (tm130) REVERT: B 466 LYS cc_start: 0.8686 (tttm) cc_final: 0.8377 (ttpt) REVERT: B 467 ASP cc_start: 0.7480 (p0) cc_final: 0.7130 (p0) REVERT: B 518 ASP cc_start: 0.7789 (m-30) cc_final: 0.7465 (m-30) REVERT: B 530 LYS cc_start: 0.8639 (tttt) cc_final: 0.8371 (tttt) REVERT: B 557 GLU cc_start: 0.7441 (pm20) cc_final: 0.7079 (pm20) REVERT: C 209 HIS cc_start: 0.7231 (m90) cc_final: 0.6839 (m-70) REVERT: C 266 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.7243 (t80) REVERT: C 369 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8663 (mt) REVERT: C 415 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: C 416 GLU cc_start: 0.8629 (tt0) cc_final: 0.8109 (tt0) REVERT: C 439 LYS cc_start: 0.8364 (pptt) cc_final: 0.7926 (mmmt) REVERT: C 446 GLN cc_start: 0.8346 (tt0) cc_final: 0.7802 (tm130) REVERT: C 466 LYS cc_start: 0.8689 (tttm) cc_final: 0.8351 (ttpt) REVERT: C 467 ASP cc_start: 0.7465 (p0) cc_final: 0.7149 (p0) REVERT: C 523 MET cc_start: 0.8633 (ttt) cc_final: 0.8429 (ttt) REVERT: C 530 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8209 (tttm) REVERT: C 577 ARG cc_start: 0.7129 (mtm180) cc_final: 0.6926 (mtm110) REVERT: C 583 MET cc_start: 0.8240 (ptm) cc_final: 0.8018 (ptt) outliers start: 59 outliers final: 25 residues processed: 266 average time/residue: 0.5837 time to fit residues: 171.1274 Evaluate side-chains 267 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 225 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 300 CYS 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 266 TYR 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 369 LEU Chi-restraints excluded: chain B residue 408 GLN 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 185 SER 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 511 SER 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 30 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 191 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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 436 ASN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN ** B 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 = 0.4113 r_free = 0.4113 target = 0.195691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.151014 restraints weight = 14555.997| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.63 r_work: 0.3007 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3533 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= 0.185 Angle : 0.632 11.711 22780 Z= 0.329 Chirality : 0.045 0.238 2548 Planarity : 0.004 0.040 2860 Dihedral : 5.475 36.393 2180 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.15 % Allowed : 14.21 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.19), residues: 1968 helix: 0.01 (0.15), residues: 1292 sheet: 0.82 (0.50), residues: 92 loop : -0.40 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 422 TYR 0.014 0.002 TYR C 306 PHE 0.017 0.002 PHE A 351 TRP 0.015 0.002 TRP D 427 HIS 0.002 0.001 HIS D 271 Details of bonding type rmsd covalent geometry : bond 0.00444 (16808) covalent geometry : angle 0.62821 (22756) SS BOND : bond 0.00322 ( 12) SS BOND : angle 2.14014 ( 24) hydrogen bonds : bond 0.04228 ( 848) hydrogen bonds : angle 4.23424 ( 2382) *********************** 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 289 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.619 Fit side-chains REVERT: D 320 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7604 (mm-30) REVERT: D 369 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8722 (mt) REVERT: D 415 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7737 (mm-30) REVERT: D 439 LYS cc_start: 0.8319 (pptt) cc_final: 0.7910 (mmpt) REVERT: D 446 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7688 (tm130) REVERT: D 466 LYS cc_start: 0.8655 (tttm) cc_final: 0.8286 (ttpt) REVERT: D 467 ASP cc_start: 0.7443 (p0) cc_final: 0.7049 (p0) REVERT: D 501 ARG cc_start: 0.8065 (mtt90) cc_final: 0.7817 (mtt-85) REVERT: D 530 LYS cc_start: 0.8594 (tttt) cc_final: 0.8309 (tttt) REVERT: D 532 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8059 (tp) REVERT: A 369 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8711 (mt) REVERT: A 439 LYS cc_start: 0.8409 (pptt) cc_final: 0.7847 (mmpt) REVERT: A 446 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7773 (tm130) REVERT: A 474 ARG cc_start: 0.8225 (mtp-110) cc_final: 0.7811 (mtt90) REVERT: A 518 ASP cc_start: 0.7764 (m-30) cc_final: 0.7352 (m-30) REVERT: A 532 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8048 (tp) REVERT: B 320 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7581 (mm-30) REVERT: B 369 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8719 (mt) REVERT: B 415 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7909 (mm-30) REVERT: B 416 GLU cc_start: 0.8595 (tt0) cc_final: 0.8054 (tt0) REVERT: B 439 LYS cc_start: 0.8342 (pptt) cc_final: 0.7882 (mmmt) REVERT: B 446 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7729 (tm130) REVERT: B 466 LYS cc_start: 0.8643 (tttm) cc_final: 0.8291 (ttpt) REVERT: B 467 ASP cc_start: 0.7436 (p0) cc_final: 0.7046 (p0) REVERT: B 518 ASP cc_start: 0.7839 (m-30) cc_final: 0.7560 (m-30) REVERT: B 530 LYS cc_start: 0.8603 (tttt) cc_final: 0.8313 (tttt) REVERT: B 557 GLU cc_start: 0.7523 (pm20) cc_final: 0.7138 (pm20) REVERT: C 209 HIS cc_start: 0.7198 (m90) cc_final: 0.6779 (m-70) REVERT: C 369 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8648 (mt) REVERT: C 415 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7875 (mm-30) REVERT: C 439 LYS cc_start: 0.8326 (pptt) cc_final: 0.7899 (mmpt) REVERT: C 446 GLN cc_start: 0.8307 (tt0) cc_final: 0.7716 (tm130) REVERT: C 466 LYS cc_start: 0.8643 (tttm) cc_final: 0.8279 (ttpt) REVERT: C 467 ASP cc_start: 0.7456 (p0) cc_final: 0.7084 (p0) REVERT: C 530 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8159 (tttm) REVERT: C 577 ARG cc_start: 0.6971 (mtm180) cc_final: 0.6764 (mtm110) REVERT: C 583 MET cc_start: 0.8225 (ptm) cc_final: 0.7964 (ptt) outliers start: 57 outliers final: 26 residues processed: 265 average time/residue: 0.6113 time to fit residues: 177.9725 Evaluate side-chains 269 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 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 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 185 SER Chi-restraints excluded: chain C residue 195 VAL 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 511 SER 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 42 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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** A 503 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 = 0.4135 r_free = 0.4135 target = 0.197943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.153943 restraints weight = 14674.399| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.72 r_work: 0.3039 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3667 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= 0.128 Angle : 0.587 11.443 22780 Z= 0.304 Chirality : 0.042 0.259 2548 Planarity : 0.004 0.040 2860 Dihedral : 5.273 38.442 2180 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.88 % Allowed : 15.27 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.19), residues: 1968 helix: 0.16 (0.15), residues: 1296 sheet: 0.97 (0.51), residues: 92 loop : -0.32 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 474 TYR 0.013 0.001 TYR A 306 PHE 0.009 0.001 PHE A 351 TRP 0.010 0.001 TRP B 427 HIS 0.002 0.000 HIS C 475 Details of bonding type rmsd covalent geometry : bond 0.00302 (16808) covalent geometry : angle 0.58289 (22756) SS BOND : bond 0.00213 ( 12) SS BOND : angle 2.26794 ( 24) hydrogen bonds : bond 0.03690 ( 848) hydrogen bonds : angle 4.11863 ( 2382) *********************** 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 281 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 229 time to evaluate : 0.619 Fit side-chains REVERT: D 266 TYR cc_start: 0.9036 (OUTLIER) cc_final: 0.7294 (t80) REVERT: D 320 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7556 (mm-30) REVERT: D 369 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8692 (mt) REVERT: D 415 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7732 (mm-30) REVERT: D 439 LYS cc_start: 0.8344 (pptt) cc_final: 0.7893 (mmmt) REVERT: D 445 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8102 (mp0) REVERT: D 446 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7768 (tm130) REVERT: D 466 LYS cc_start: 0.8622 (tttm) cc_final: 0.8254 (ttpt) REVERT: D 467 ASP cc_start: 0.7453 (p0) cc_final: 0.7072 (p0) REVERT: D 474 ARG cc_start: 0.8386 (mtp-110) cc_final: 0.8183 (mtp85) REVERT: D 501 ARG cc_start: 0.8057 (mtt90) cc_final: 0.7807 (mtt-85) REVERT: D 518 ASP cc_start: 0.7647 (m-30) cc_final: 0.7378 (m-30) REVERT: D 530 LYS cc_start: 0.8589 (tttt) cc_final: 0.8261 (tttm) REVERT: D 532 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8052 (tp) REVERT: A 266 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.7210 (t80) REVERT: A 369 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8709 (mt) REVERT: A 439 LYS cc_start: 0.8377 (pptt) cc_final: 0.7843 (mmpt) REVERT: A 445 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8069 (mp0) REVERT: A 446 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7838 (tm130) REVERT: A 467 ASP cc_start: 0.8285 (t70) cc_final: 0.7182 (p0) REVERT: A 474 ARG cc_start: 0.8236 (mtp-110) cc_final: 0.7856 (mtt90) REVERT: A 518 ASP cc_start: 0.7760 (m-30) cc_final: 0.7362 (m-30) REVERT: A 532 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8037 (tp) REVERT: B 266 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.7291 (t80) REVERT: B 320 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7520 (mm-30) REVERT: B 369 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8709 (mt) REVERT: B 415 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7847 (mm-30) REVERT: B 416 GLU cc_start: 0.8546 (tt0) cc_final: 0.7979 (tt0) REVERT: B 439 LYS cc_start: 0.8330 (pptt) cc_final: 0.7859 (mmmt) REVERT: B 445 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8086 (tp30) REVERT: B 446 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7783 (tm130) REVERT: B 466 LYS cc_start: 0.8649 (tttm) cc_final: 0.8294 (ttpt) REVERT: B 467 ASP cc_start: 0.7410 (p0) cc_final: 0.7027 (p0) REVERT: B 518 ASP cc_start: 0.7853 (m-30) cc_final: 0.7504 (m-30) REVERT: B 530 LYS cc_start: 0.8601 (tttt) cc_final: 0.8308 (tttt) REVERT: B 557 GLU cc_start: 0.7507 (pm20) cc_final: 0.7184 (pm20) REVERT: C 209 HIS cc_start: 0.7172 (m90) cc_final: 0.6775 (m-70) REVERT: C 230 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.7243 (t80) REVERT: C 266 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.7259 (t80) REVERT: C 369 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8742 (mt) REVERT: C 415 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7770 (mm-30) REVERT: C 416 GLU cc_start: 0.8579 (tt0) cc_final: 0.8032 (tt0) REVERT: C 439 LYS cc_start: 0.8333 (pptt) cc_final: 0.7892 (mmpt) REVERT: C 446 GLN cc_start: 0.8301 (tt0) cc_final: 0.7764 (tm130) REVERT: C 466 LYS cc_start: 0.8617 (tttm) cc_final: 0.8247 (ttpt) REVERT: C 467 ASP cc_start: 0.7471 (p0) cc_final: 0.7142 (p0) REVERT: C 530 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8123 (tttm) REVERT: C 583 MET cc_start: 0.8222 (ptm) cc_final: 0.7969 (ptt) outliers start: 52 outliers final: 24 residues processed: 259 average time/residue: 0.6050 time to fit residues: 171.5061 Evaluate side-chains 266 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 104 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 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 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 52 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** A 503 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 = 0.4116 r_free = 0.4116 target = 0.195967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.157472 restraints weight = 14567.864| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.53 r_work: 0.3056 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.004 0.054 16820 Z= 0.176 Angle : 0.629 12.209 22780 Z= 0.327 Chirality : 0.044 0.258 2548 Planarity : 0.004 0.039 2860 Dihedral : 5.375 39.271 2180 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.71 % Allowed : 15.71 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.19), residues: 1968 helix: 0.06 (0.15), residues: 1300 sheet: 0.97 (0.51), residues: 92 loop : -0.36 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 422 TYR 0.015 0.001 TYR A 306 PHE 0.026 0.002 PHE A 227 TRP 0.016 0.002 TRP D 427 HIS 0.002 0.001 HIS D 475 Details of bonding type rmsd covalent geometry : bond 0.00425 (16808) covalent geometry : angle 0.62543 (22756) SS BOND : bond 0.00260 ( 12) SS BOND : angle 2.10837 ( 24) hydrogen bonds : bond 0.04179 ( 848) hydrogen bonds : angle 4.22253 ( 2382) *********************** 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: 49 poor density : 229 time to evaluate : 0.674 Fit side-chains REVERT: D 320 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7699 (mm-30) REVERT: D 369 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8678 (mt) REVERT: D 415 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7844 (mm-30) REVERT: D 439 LYS cc_start: 0.8389 (pptt) cc_final: 0.8113 (mmpt) REVERT: D 445 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8159 (mp0) REVERT: D 446 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7955 (tm130) REVERT: D 466 LYS cc_start: 0.8707 (tttm) cc_final: 0.8426 (ttpt) REVERT: D 467 ASP cc_start: 0.7607 (p0) cc_final: 0.7278 (p0) REVERT: D 474 ARG cc_start: 0.8383 (mtp-110) cc_final: 0.8180 (mtp85) REVERT: D 501 ARG cc_start: 0.8103 (mtt90) cc_final: 0.7896 (mtt-85) REVERT: D 518 ASP cc_start: 0.7719 (m-30) cc_final: 0.7372 (m-30) REVERT: D 530 LYS cc_start: 0.8639 (tttt) cc_final: 0.8416 (tttt) REVERT: D 532 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8294 (tp) REVERT: D 580 ARG cc_start: 0.8169 (ttm-80) cc_final: 0.7931 (mtp180) REVERT: A 369 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8689 (mt) REVERT: A 439 LYS cc_start: 0.8401 (pptt) cc_final: 0.8032 (mmpt) REVERT: A 445 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8155 (mp0) REVERT: A 446 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7931 (tm130) REVERT: A 474 ARG cc_start: 0.8288 (mtp-110) cc_final: 0.7989 (mtt90) REVERT: A 518 ASP cc_start: 0.7786 (m-30) cc_final: 0.7385 (m-30) REVERT: A 532 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8273 (tp) REVERT: A 577 ARG cc_start: 0.7304 (mtm110) cc_final: 0.7047 (mtp-110) REVERT: B 320 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 369 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8724 (mt) REVERT: B 415 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7951 (mm-30) REVERT: B 416 GLU cc_start: 0.8643 (tt0) cc_final: 0.8099 (tt0) REVERT: B 439 LYS cc_start: 0.8351 (pptt) cc_final: 0.8031 (mmmt) REVERT: B 446 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7879 (tm130) REVERT: B 466 LYS cc_start: 0.8697 (tttm) cc_final: 0.8426 (ttpt) REVERT: B 467 ASP cc_start: 0.7577 (p0) cc_final: 0.7219 (p0) REVERT: B 518 ASP cc_start: 0.7791 (m-30) cc_final: 0.7475 (m-30) REVERT: B 530 LYS cc_start: 0.8651 (tttt) cc_final: 0.8421 (tttt) REVERT: B 557 GLU cc_start: 0.7597 (pm20) cc_final: 0.7217 (pm20) REVERT: C 209 HIS cc_start: 0.7333 (m90) cc_final: 0.7005 (m-70) REVERT: C 230 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.7016 (t80) REVERT: C 369 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8691 (mt) REVERT: C 415 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7881 (mm-30) REVERT: C 416 GLU cc_start: 0.8680 (tt0) cc_final: 0.8185 (tt0) REVERT: C 439 LYS cc_start: 0.8361 (pptt) cc_final: 0.8075 (mmpt) REVERT: C 446 GLN cc_start: 0.8346 (tt0) cc_final: 0.7892 (tm130) REVERT: C 466 LYS cc_start: 0.8719 (tttm) cc_final: 0.8419 (ttpt) REVERT: C 467 ASP cc_start: 0.7605 (p0) cc_final: 0.7241 (p0) REVERT: C 530 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8370 (tttt) REVERT: C 583 MET cc_start: 0.8268 (ptm) cc_final: 0.8048 (ptt) outliers start: 49 outliers final: 25 residues processed: 258 average time/residue: 0.6454 time to fit residues: 182.2118 Evaluate side-chains 261 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 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 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 230 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 199 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 168 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN ** 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 503 GLN ** 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 = 0.4130 r_free = 0.4130 target = 0.197303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.152369 restraints weight = 14577.724| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.73 r_work: 0.3028 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3787 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= 0.139 Angle : 0.597 12.509 22780 Z= 0.309 Chirality : 0.043 0.248 2548 Planarity : 0.004 0.039 2860 Dihedral : 5.247 37.946 2180 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.43 % Allowed : 16.48 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.19), residues: 1968 helix: 0.17 (0.15), residues: 1300 sheet: 1.00 (0.51), residues: 92 loop : -0.31 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 474 TYR 0.013 0.001 TYR A 306 PHE 0.012 0.001 PHE B 227 TRP 0.010 0.002 TRP B 427 HIS 0.002 0.001 HIS C 475 Details of bonding type rmsd covalent geometry : bond 0.00329 (16808) covalent geometry : angle 0.59466 (22756) SS BOND : bond 0.00183 ( 12) SS BOND : angle 1.81367 ( 24) hydrogen bonds : bond 0.03803 ( 848) hydrogen bonds : angle 4.14384 ( 2382) ********************** 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 267 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 0.564 Fit side-chains REVERT: D 230 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7263 (t80) REVERT: D 320 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7543 (mm-30) REVERT: D 369 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8692 (mt) REVERT: D 415 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: D 439 LYS cc_start: 0.8325 (pptt) cc_final: 0.7931 (mmpt) REVERT: D 445 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8100 (mp0) REVERT: D 446 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7811 (tm130) REVERT: D 466 LYS cc_start: 0.8622 (tttm) cc_final: 0.8255 (ttpt) REVERT: D 467 ASP cc_start: 0.7459 (p0) cc_final: 0.7094 (p0) REVERT: D 474 ARG cc_start: 0.8402 (mtp-110) cc_final: 0.8162 (mtp85) REVERT: D 501 ARG cc_start: 0.8048 (mtt90) cc_final: 0.7781 (mtt-85) REVERT: D 518 ASP cc_start: 0.7622 (m-30) cc_final: 0.7394 (m-30) REVERT: D 530 LYS cc_start: 0.8596 (tttt) cc_final: 0.8314 (tttt) REVERT: D 532 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8070 (tp) REVERT: A 369 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8709 (mt) REVERT: A 439 LYS cc_start: 0.8369 (pptt) cc_final: 0.7849 (mmpt) REVERT: A 445 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8095 (mp0) REVERT: A 446 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7860 (tm130) REVERT: A 467 ASP cc_start: 0.8295 (t70) cc_final: 0.7183 (p0) REVERT: A 474 ARG cc_start: 0.8261 (mtp-110) cc_final: 0.7858 (mtt90) REVERT: A 518 ASP cc_start: 0.7834 (m-30) cc_final: 0.7467 (m-30) REVERT: A 521 ASP cc_start: 0.7849 (p0) cc_final: 0.7634 (p0) REVERT: A 532 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8056 (tp) REVERT: A 577 ARG cc_start: 0.7200 (mtm110) cc_final: 0.6887 (mtp-110) REVERT: B 230 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7235 (t80) REVERT: B 320 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7539 (mm-30) REVERT: B 369 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8706 (mt) REVERT: B 415 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: B 416 GLU cc_start: 0.8552 (tt0) cc_final: 0.7979 (tt0) REVERT: B 439 LYS cc_start: 0.8323 (pptt) cc_final: 0.7867 (mmmt) REVERT: B 445 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8068 (mp0) REVERT: B 446 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7798 (tm130) REVERT: B 466 LYS cc_start: 0.8654 (tttm) cc_final: 0.8291 (ttpt) REVERT: B 467 ASP cc_start: 0.7420 (p0) cc_final: 0.7065 (p0) REVERT: B 474 ARG cc_start: 0.8376 (mtp-110) cc_final: 0.7876 (mtt90) REVERT: B 518 ASP cc_start: 0.7780 (m-30) cc_final: 0.7468 (m-30) REVERT: B 530 LYS cc_start: 0.8594 (tttt) cc_final: 0.8308 (tttt) REVERT: B 557 GLU cc_start: 0.7539 (pm20) cc_final: 0.7213 (pm20) REVERT: B 580 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7414 (tpp80) REVERT: C 209 HIS cc_start: 0.7166 (m90) cc_final: 0.6760 (m-70) REVERT: C 230 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.6957 (t80) REVERT: C 369 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8738 (mt) REVERT: C 415 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7771 (mm-30) REVERT: C 416 GLU cc_start: 0.8614 (tt0) cc_final: 0.8059 (tt0) REVERT: C 439 LYS cc_start: 0.8304 (pptt) cc_final: 0.7892 (mmpt) REVERT: C 446 GLN cc_start: 0.8322 (tt0) cc_final: 0.7777 (tm130) REVERT: C 466 LYS cc_start: 0.8635 (tttm) cc_final: 0.8256 (ttpt) REVERT: C 467 ASP cc_start: 0.7460 (p0) cc_final: 0.7064 (p0) REVERT: C 530 LYS cc_start: 0.8485 (tttt) cc_final: 0.8120 (tttm) REVERT: C 580 ARG cc_start: 0.8134 (ttt90) cc_final: 0.7887 (mtp85) REVERT: C 583 MET cc_start: 0.8228 (ptm) cc_final: 0.7986 (ptt) outliers start: 44 outliers final: 23 residues processed: 246 average time/residue: 0.6862 time to fit residues: 184.5778 Evaluate side-chains 257 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 230 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 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 230 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 195 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 230 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 533 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 132 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 144 optimal weight: 0.0020 chunk 56 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 146 optimal weight: 0.0970 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.198496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.152386 restraints weight = 14642.985| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.75 r_work: 0.3047 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3865 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= 0.121 Angle : 0.578 12.421 22780 Z= 0.298 Chirality : 0.042 0.230 2548 Planarity : 0.004 0.039 2860 Dihedral : 5.084 36.745 2180 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.16 % Allowed : 16.70 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.19), residues: 1968 helix: 0.29 (0.15), residues: 1300 sheet: 1.14 (0.52), residues: 92 loop : -0.25 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 474 TYR 0.013 0.001 TYR A 306 PHE 0.012 0.001 PHE C 227 TRP 0.010 0.001 TRP D 277 HIS 0.002 0.000 HIS D 475 Details of bonding type rmsd covalent geometry : bond 0.00283 (16808) covalent geometry : angle 0.57595 (22756) SS BOND : bond 0.00162 ( 12) SS BOND : angle 1.71264 ( 24) hydrogen bonds : bond 0.03603 ( 848) hydrogen bonds : angle 4.07544 ( 2382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5489.59 seconds wall clock time: 93 minutes 58.71 seconds (5638.71 seconds total)