Starting phenix.real_space_refine on Tue Jul 7 06:51:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gf8_29981/07_2026/8gf8_29981_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gf8_29981/07_2026/8gf8_29981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gf8_29981/07_2026/8gf8_29981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gf8_29981/07_2026/8gf8_29981.map" model { file = "/net/cci-nas-00/data/ceres_data/8gf8_29981/07_2026/8gf8_29981_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gf8_29981/07_2026/8gf8_29981_neut_trim.cif" } resolution = 2.9 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= 0.021 sd= 0.104 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: 7 Type Number sf(0) Gaussians P 36 5.49 5 S 136 5.16 5 Na 2 4.78 5 C 14780 2.51 5 N 3340 2.21 5 O 3992 1.98 5 H 20452 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42738 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 10196 Classifications: {'peptide': 630} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 613} Chain breaks: 1 Chain: "B" Number of atoms: 10196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 10196 Classifications: {'peptide': 630} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 613} Chain breaks: 1 Chain: "C" Number of atoms: 10196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 10196 Classifications: {'peptide': 630} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 613} Chain breaks: 1 Chain: "D" Number of atoms: 10196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 10196 Classifications: {'peptide': 630} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 613} Chain breaks: 1 Chain: "A" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 488 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'8IJ': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 592 Unusual residues: {'8IJ': 1, 'POV': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 488 Unusual residues: {'8IJ': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 384 Unusual residues: {'8IJ': 1, 'POV': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 7.32, per 1000 atoms: 0.17 Number of scatterers: 42738 At special positions: 0 Unit cell: (129.525, 129.525, 117.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 136 16.00 P 36 15.00 Na 2 11.00 O 3992 8.00 N 3340 7.00 C 14780 6.00 H 20452 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 391 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 391 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 391 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 391 " 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: 4.08 Conformation dependent library (CDL) restraints added in 1.4 seconds 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 61.8% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.514A pdb=" N PHE A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.502A pdb=" N GLN A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 150 removed outlier: 3.904A pdb=" N ASN A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 165 Processing helix chain 'A' and resid 173 through 184 Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.529A pdb=" N ASN A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.858A pdb=" N ILE A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.909A pdb=" N LEU A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 261 through 270 removed outlier: 3.513A pdb=" N LEU A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.831A pdb=" N SER A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A 311 " --> pdb=" O THR A 307 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 removed outlier: 3.824A pdb=" N GLU A 328 " --> pdb=" O LYS A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 Processing helix chain 'A' and resid 346 through 355 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 411 through 415 removed outlier: 4.165A pdb=" N LEU A 414 " --> pdb=" O HIS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 430 removed outlier: 3.513A pdb=" N GLN A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 455 removed outlier: 3.845A pdb=" N ILE A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 455 " --> pdb=" O MET A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 494 removed outlier: 3.663A pdb=" N TYR A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 473 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 502 through 507 removed outlier: 4.460A pdb=" N PHE A 507 " --> pdb=" O MET A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.752A pdb=" N VAL A 527 " --> pdb=" O MET A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.536A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 removed outlier: 3.743A pdb=" N THR A 556 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 599 removed outlier: 3.917A pdb=" N MET A 572 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 639 removed outlier: 3.728A pdb=" N GLU A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 Processing helix chain 'A' and resid 674 through 690 Processing helix chain 'A' and resid 694 through 713 removed outlier: 3.540A pdb=" N LEU A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 124 Processing helix chain 'B' and resid 126 through 138 removed outlier: 3.501A pdb=" N GLN B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 150 removed outlier: 3.903A pdb=" N ASN B 147 " --> pdb=" O HIS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 165 Processing helix chain 'B' and resid 173 through 184 Processing helix chain 'B' and resid 187 through 192 removed outlier: 3.529A pdb=" N ASN B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.858A pdb=" N ILE B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.909A pdb=" N LEU B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 261 through 270 removed outlier: 3.513A pdb=" N LEU B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 299 through 321 removed outlier: 3.831A pdb=" N SER B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN B 311 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 329 removed outlier: 3.825A pdb=" N GLU B 328 " --> pdb=" O LYS B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 411 through 415 removed outlier: 4.164A pdb=" N LEU B 414 " --> pdb=" O HIS B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 430 removed outlier: 3.514A pdb=" N GLN B 424 " --> pdb=" O ASN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 455 removed outlier: 3.843A pdb=" N ILE B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 455 " --> pdb=" O MET B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 494 removed outlier: 3.663A pdb=" N TYR B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 502 through 507 removed outlier: 4.460A pdb=" N PHE B 507 " --> pdb=" O MET B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 532 removed outlier: 3.751A pdb=" N VAL B 527 " --> pdb=" O MET B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.535A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 558 removed outlier: 3.743A pdb=" N THR B 556 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY B 558 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 599 removed outlier: 3.918A pdb=" N MET B 572 " --> pdb=" O MET B 568 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 639 removed outlier: 3.729A pdb=" N GLU B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 Processing helix chain 'B' and resid 674 through 690 Processing helix chain 'B' and resid 694 through 713 removed outlier: 3.539A pdb=" N LEU B 700 " --> pdb=" O ASN B 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 124 Processing helix chain 'C' and resid 126 through 138 removed outlier: 3.502A pdb=" N GLN C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 150 removed outlier: 3.904A pdb=" N ASN C 147 " --> pdb=" O HIS C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 165 Processing helix chain 'C' and resid 173 through 184 Processing helix chain 'C' and resid 187 through 192 removed outlier: 3.529A pdb=" N ASN C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.859A pdb=" N ILE C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.908A pdb=" N LEU C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 261 through 270 removed outlier: 3.513A pdb=" N LEU C 269 " --> pdb=" O VAL C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 299 through 321 removed outlier: 3.831A pdb=" N SER C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN C 311 " --> pdb=" O THR C 307 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 329 removed outlier: 3.824A pdb=" N GLU C 328 " --> pdb=" O LYS C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 344 Processing helix chain 'C' and resid 346 through 355 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 411 through 415 removed outlier: 4.164A pdb=" N LEU C 414 " --> pdb=" O HIS C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 430 removed outlier: 3.514A pdb=" N GLN C 424 " --> pdb=" O ASN C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 455 removed outlier: 3.844A pdb=" N ILE C 434 " --> pdb=" O PHE C 430 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR C 455 " --> pdb=" O MET C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 494 removed outlier: 3.663A pdb=" N TYR C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE C 473 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY C 484 " --> pdb=" O LEU C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 502 through 507 removed outlier: 4.460A pdb=" N PHE C 507 " --> pdb=" O MET C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 532 removed outlier: 3.752A pdb=" N VAL C 527 " --> pdb=" O MET C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.535A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 558 removed outlier: 3.744A pdb=" N THR C 556 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY C 558 " --> pdb=" O TYR C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 599 removed outlier: 3.918A pdb=" N MET C 572 " --> pdb=" O MET C 568 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 598 " --> pdb=" O ALA C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 639 removed outlier: 3.729A pdb=" N GLU C 637 " --> pdb=" O SER C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 672 Processing helix chain 'C' and resid 674 through 690 Processing helix chain 'C' and resid 694 through 713 removed outlier: 3.539A pdb=" N LEU C 700 " --> pdb=" O ASN C 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 124 Processing helix chain 'D' and resid 126 through 138 removed outlier: 3.503A pdb=" N GLN D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 150 removed outlier: 3.904A pdb=" N ASN D 147 " --> pdb=" O HIS D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 165 Processing helix chain 'D' and resid 173 through 184 Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.529A pdb=" N ASN D 192 " --> pdb=" O LYS D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.858A pdb=" N ILE D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.909A pdb=" N LEU D 220 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 258 Processing helix chain 'D' and resid 261 through 270 removed outlier: 3.513A pdb=" N LEU D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 299 through 321 removed outlier: 3.831A pdb=" N SER D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN D 311 " --> pdb=" O THR D 307 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 329 removed outlier: 3.824A pdb=" N GLU D 328 " --> pdb=" O LYS D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 Processing helix chain 'D' and resid 346 through 355 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 411 through 415 removed outlier: 4.164A pdb=" N LEU D 414 " --> pdb=" O HIS D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 430 removed outlier: 3.514A pdb=" N GLN D 424 " --> pdb=" O ASN D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 455 removed outlier: 3.844A pdb=" N ILE D 434 " --> pdb=" O PHE D 430 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR D 455 " --> pdb=" O MET D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 494 removed outlier: 3.663A pdb=" N TYR D 472 " --> pdb=" O LYS D 468 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE D 473 " --> pdb=" O THR D 469 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY D 484 " --> pdb=" O LEU D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 502 through 507 removed outlier: 4.460A pdb=" N PHE D 507 " --> pdb=" O MET D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 532 removed outlier: 3.751A pdb=" N VAL D 527 " --> pdb=" O MET D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.535A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 558 removed outlier: 3.743A pdb=" N THR D 556 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY D 558 " --> pdb=" O TYR D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 599 removed outlier: 3.916A pdb=" N MET D 572 " --> pdb=" O MET D 568 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 598 " --> pdb=" O ALA D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 639 removed outlier: 3.728A pdb=" N GLU D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 672 Processing helix chain 'D' and resid 674 through 690 Processing helix chain 'D' and resid 694 through 713 removed outlier: 3.539A pdb=" N LEU D 700 " --> pdb=" O ASN D 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 374 removed outlier: 3.678A pdb=" N PHE A 370 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER A 380 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA A 374 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 369 through 374 removed outlier: 3.679A pdb=" N PHE B 370 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER B 380 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA B 374 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 369 through 374 removed outlier: 3.679A pdb=" N PHE C 370 " --> pdb=" O LEU C 382 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER C 380 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA C 374 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 369 through 374 removed outlier: 3.679A pdb=" N PHE D 370 " --> pdb=" O LEU D 382 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER D 380 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA D 374 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) 1012 hydrogen bonds defined for protein. 2964 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: 11.30 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 20412 1.03 - 1.23: 475 1.23 - 1.43: 8629 1.43 - 1.63: 13408 1.63 - 1.83: 224 Bond restraints: 43148 Sorted by residual: bond pdb=" O12 POV B1204 " pdb=" P POV B1204 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" O12 POV C1202 " pdb=" P POV C1202 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 9.80e+00 bond pdb=" O12 POV A1201 " pdb=" P POV A1201 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 9.78e+00 bond pdb=" O12 POV A1207 " pdb=" P POV A1207 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 9.77e+00 bond pdb=" O12 POV D1201 " pdb=" P POV D1201 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.72e+00 ... (remaining 43143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 75703 3.06 - 6.12: 883 6.12 - 9.19: 62 9.19 - 12.25: 4 12.25 - 15.31: 4 Bond angle restraints: 76656 Sorted by residual: angle pdb=" CA LEU A 675 " pdb=" CB LEU A 675 " pdb=" CG LEU A 675 " ideal model delta sigma weight residual 116.30 131.61 -15.31 3.50e+00 8.16e-02 1.91e+01 angle pdb=" CA LEU D 675 " pdb=" CB LEU D 675 " pdb=" CG LEU D 675 " ideal model delta sigma weight residual 116.30 131.60 -15.30 3.50e+00 8.16e-02 1.91e+01 angle pdb=" CA LEU B 675 " pdb=" CB LEU B 675 " pdb=" CG LEU B 675 " ideal model delta sigma weight residual 116.30 131.59 -15.29 3.50e+00 8.16e-02 1.91e+01 angle pdb=" CA LEU C 675 " pdb=" CB LEU C 675 " pdb=" CG LEU C 675 " ideal model delta sigma weight residual 116.30 131.56 -15.26 3.50e+00 8.16e-02 1.90e+01 angle pdb=" C GLN B 124 " pdb=" N ASN B 125 " pdb=" CA ASN B 125 " ideal model delta sigma weight residual 122.46 127.75 -5.29 1.41e+00 5.03e-01 1.41e+01 ... (remaining 76651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.58: 20303 34.58 - 69.16: 671 69.16 - 103.74: 85 103.74 - 138.32: 21 138.32 - 172.89: 20 Dihedral angle restraints: 21100 sinusoidal: 12076 harmonic: 9024 Sorted by residual: dihedral pdb=" CA SER D 272 " pdb=" C SER D 272 " pdb=" N TRP D 273 " pdb=" CA TRP D 273 " ideal model delta harmonic sigma weight residual -180.00 -145.92 -34.08 0 5.00e+00 4.00e-02 4.65e+01 dihedral pdb=" CA SER A 272 " pdb=" C SER A 272 " pdb=" N TRP A 273 " pdb=" CA TRP A 273 " ideal model delta harmonic sigma weight residual -180.00 -145.99 -34.01 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CA SER C 272 " pdb=" C SER C 272 " pdb=" N TRP C 273 " pdb=" CA TRP C 273 " ideal model delta harmonic sigma weight residual -180.00 -146.01 -33.99 0 5.00e+00 4.00e-02 4.62e+01 ... (remaining 21097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2343 0.047 - 0.093: 750 0.093 - 0.140: 122 0.140 - 0.187: 25 0.187 - 0.233: 4 Chirality restraints: 3244 Sorted by residual: chirality pdb=" C2 POV B1204 " pdb=" C1 POV B1204 " pdb=" C3 POV B1204 " pdb=" O21 POV B1204 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C2 POV D1201 " pdb=" C1 POV D1201 " pdb=" C3 POV D1201 " pdb=" O21 POV D1201 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C2 POV A1201 " pdb=" C1 POV A1201 " pdb=" C3 POV A1201 " pdb=" O21 POV A1201 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 3241 not shown) Planarity restraints: 6064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 420 " -0.093 2.00e-02 2.50e+03 1.00e-01 1.51e+02 pdb=" CG ASN C 420 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 420 " 0.086 2.00e-02 2.50e+03 pdb=" ND2 ASN C 420 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 420 " 0.143 2.00e-02 2.50e+03 pdb="HD22 ASN C 420 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 420 " 0.093 2.00e-02 2.50e+03 1.00e-01 1.50e+02 pdb=" CG ASN B 420 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 420 " -0.085 2.00e-02 2.50e+03 pdb=" ND2 ASN B 420 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 420 " -0.142 2.00e-02 2.50e+03 pdb="HD22 ASN B 420 " 0.153 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 420 " 0.093 2.00e-02 2.50e+03 1.00e-01 1.50e+02 pdb=" CG ASN A 420 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 420 " -0.085 2.00e-02 2.50e+03 pdb=" ND2 ASN A 420 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 420 " -0.142 2.00e-02 2.50e+03 pdb="HD22 ASN A 420 " 0.153 2.00e-02 2.50e+03 ... (remaining 6061 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.27: 4837 2.27 - 2.85: 97447 2.85 - 3.43: 112931 3.43 - 4.02: 157412 4.02 - 4.60: 243100 Nonbonded interactions: 615727 Sorted by model distance: nonbonded pdb=" O ARG C 356 " pdb=" H ARG C 368 " model vdw 1.684 2.450 nonbonded pdb=" O ARG D 356 " pdb=" H ARG D 368 " model vdw 1.684 2.450 nonbonded pdb=" O ARG B 356 " pdb=" H ARG B 368 " model vdw 1.684 2.450 nonbonded pdb=" O ARG A 356 " pdb=" H ARG A 368 " model vdw 1.685 2.450 nonbonded pdb=" O ASN B 147 " pdb=" HZ3 LYS B 150 " model vdw 1.709 2.450 ... (remaining 615722 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 115 through 1201 or resid 1204 or (resid 1206 and (name C3 \ 4 or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or na \ me C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or re \ sid 1207 or (resid 1208 and (name C34 or name C35 or name C36 or name C37 or nam \ e C38 or name C39 or name C310 or name C311 or name C312 or name C313 or name C3 \ 14 or name C315 or name C316)))) selection = (chain 'B' and (resid 115 through 1201 or resid 1204 or (resid 1206 and (name C3 \ 4 or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or na \ me C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or re \ sid 1207 through 1208)) selection = (chain 'C' and (resid 115 through 1201 or resid 1204 or resid 1206 through 1207 \ or (resid 1208 and (name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name C310 or name C311 or name C312 or name C313 or name C314 or nam \ e C315 or name C316)))) selection = (chain 'D' and (resid 115 through 1201 or resid 1204 or (resid 1206 and (name C3 \ 4 or name C35 or name C36 or name C37 or name C38 or name C39 or name C310 or na \ me C311 or name C312 or name C313 or name C314 or name C315 or name C316)) or re \ sid 1207 or (resid 1208 and (name C34 or name C35 or name C36 or name C37 or nam \ e C38 or name C39 or name C310 or name C311 or name C312 or name C313 or name C3 \ 14 or name C315 or name C316)))) } 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: 0.010 Normalize map: mean=0, sd=1: 1.530 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: 0.310 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 40.990 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 : 0.008 0.063 22700 Z= 0.351 Angle : 1.047 15.311 30336 Z= 0.497 Chirality : 0.046 0.233 3244 Planarity : 0.005 0.046 3616 Dihedral : 19.171 172.895 9300 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 0.18 % Allowed : 3.96 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.60 (0.12), residues: 2504 helix: -3.55 (0.09), residues: 1460 sheet: -3.99 (0.43), residues: 92 loop : -3.73 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 212 TYR 0.022 0.003 TYR B 739 PHE 0.026 0.003 PHE B 721 TRP 0.018 0.002 TRP B 698 HIS 0.010 0.002 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00764 / 0.35 (22696) covalent geometry : angle 1.04719 / 0.50 (30328) SS BOND : bond 0.00177 / 0.09 ( 4) SS BOND : angle 1.87204 / 1.33 ( 8) hydrogen bonds : bond 0.26118 / 17.23 ( 1012) hydrogen bonds : angle 10.41642 / 7.13 ( 2964) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 506 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 HIS cc_start: 0.5396 (p90) cc_final: 0.4819 (p90) REVERT: A 340 LEU cc_start: 0.8042 (tp) cc_final: 0.7785 (tp) REVERT: A 523 MET cc_start: 0.7674 (tpt) cc_final: 0.7338 (tpt) REVERT: A 599 ILE cc_start: 0.8337 (mt) cc_final: 0.8011 (mp) REVERT: A 753 TRP cc_start: 0.3020 (m100) cc_final: 0.2499 (p-90) REVERT: B 233 HIS cc_start: 0.5392 (p90) cc_final: 0.4765 (p90) REVERT: B 340 LEU cc_start: 0.8038 (tp) cc_final: 0.7761 (tp) REVERT: B 523 MET cc_start: 0.7672 (tpt) cc_final: 0.7384 (tpt) REVERT: B 753 TRP cc_start: 0.3090 (m100) cc_final: 0.2468 (p-90) REVERT: C 340 LEU cc_start: 0.8064 (tp) cc_final: 0.7797 (tp) REVERT: C 753 TRP cc_start: 0.3049 (m100) cc_final: 0.2476 (p-90) REVERT: D 233 HIS cc_start: 0.5409 (p90) cc_final: 0.4805 (p90) REVERT: D 340 LEU cc_start: 0.8073 (tp) cc_final: 0.7808 (tp) REVERT: D 523 MET cc_start: 0.7688 (tpt) cc_final: 0.7341 (tpt) REVERT: D 753 TRP cc_start: 0.2966 (m100) cc_final: 0.2387 (p-90) outliers start: 4 outliers final: 0 residues processed: 510 average time/residue: 1.2997 time to fit residues: 766.8654 Evaluate side-chains 282 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 30.0000 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 50.0000 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN A 311 ASN A 355 GLN A 561 GLN A 728 GLN B 224 ASN B 271 ASN B 311 ASN B 355 GLN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN B 629 ASN B 728 GLN C 224 ASN C 311 ASN C 355 GLN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 GLN C 629 ASN C 728 GLN D 224 ASN D 311 ASN D 355 GLN D 561 GLN D 629 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.213820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.169758 restraints weight = 65329.644| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.76 r_work: 0.3614 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22700 Z= 0.206 Angle : 0.667 6.696 30336 Z= 0.348 Chirality : 0.038 0.123 3244 Planarity : 0.005 0.040 3616 Dihedral : 22.516 179.732 4472 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 1.93 % Allowed : 13.04 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: -3.77 (0.15), residues: 2504 helix: -1.84 (0.11), residues: 1536 sheet: -3.90 (0.43), residues: 92 loop : -3.37 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 421 TYR 0.017 0.002 TYR D 584 PHE 0.014 0.002 PHE C 305 TRP 0.016 0.002 TRP C 698 HIS 0.012 0.001 HIS D 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (22696) covalent geometry : angle 0.66592 / 0.35 (30328) SS BOND : bond 0.00190 / 0.10 ( 4) SS BOND : angle 1.99928 / 1.42 ( 8) hydrogen bonds : bond 0.04580 / 3.00 ( 1012) hydrogen bonds : angle 5.50887 / 3.75 ( 2964) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 311 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.6615 (ttp) REVERT: A 498 GLN cc_start: 0.6471 (mt0) cc_final: 0.6257 (mt0) REVERT: A 523 MET cc_start: 0.8675 (tpt) cc_final: 0.8254 (tpt) REVERT: A 747 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7175 (tp30) REVERT: B 163 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6692 (ttp) REVERT: B 233 HIS cc_start: 0.5745 (p90) cc_final: 0.5068 (p-80) REVERT: B 305 PHE cc_start: 0.8097 (t80) cc_final: 0.7490 (t80) REVERT: B 523 MET cc_start: 0.8607 (tpt) cc_final: 0.8205 (tpt) REVERT: B 747 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7184 (tp30) REVERT: C 295 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7749 (m) REVERT: C 305 PHE cc_start: 0.8113 (t80) cc_final: 0.7269 (t80) REVERT: C 326 LEU cc_start: 0.8516 (tp) cc_final: 0.8266 (mt) REVERT: C 523 MET cc_start: 0.8669 (tpt) cc_final: 0.8382 (tpt) REVERT: C 747 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7103 (tp30) REVERT: D 163 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6477 (ttp) REVERT: D 305 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7515 (t80) REVERT: D 523 MET cc_start: 0.8671 (tpt) cc_final: 0.8275 (tpt) REVERT: D 747 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7166 (tp30) outliers start: 43 outliers final: 3 residues processed: 331 average time/residue: 1.1125 time to fit residues: 436.1535 Evaluate side-chains 264 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 252 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 747 GLU Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 747 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 237 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 177 optimal weight: 0.0270 chunk 165 optimal weight: 0.9980 chunk 236 optimal weight: 0.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 GLN B 271 ASN B 355 GLN B 629 ASN C 355 GLN C 629 ASN D 355 GLN D 629 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.213990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.169374 restraints weight = 66013.230| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.94 r_work: 0.3587 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22700 Z= 0.145 Angle : 0.550 5.007 30336 Z= 0.290 Chirality : 0.035 0.120 3244 Planarity : 0.004 0.040 3616 Dihedral : 21.360 179.748 4472 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.11 % Allowed : 12.99 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: -2.67 (0.16), residues: 2504 helix: -0.76 (0.12), residues: 1548 sheet: -3.61 (0.46), residues: 92 loop : -3.38 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 421 TYR 0.013 0.001 TYR A 584 PHE 0.013 0.001 PHE A 449 TRP 0.013 0.001 TRP B 698 HIS 0.004 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (22696) covalent geometry : angle 0.54966 / 0.29 (30328) SS BOND : bond 0.00810 / 0.41 ( 4) SS BOND : angle 1.68669 / 1.20 ( 8) hydrogen bonds : bond 0.04088 / 2.68 ( 1012) hydrogen bonds : angle 4.86045 / 3.30 ( 2964) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 286 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7090 (mtm) cc_final: 0.6752 (ttp) REVERT: A 295 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.7951 (t) REVERT: A 372 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7112 (tp30) REVERT: A 523 MET cc_start: 0.8778 (tpt) cc_final: 0.8289 (tpt) REVERT: A 685 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7278 (tp30) REVERT: B 163 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6691 (ttp) REVERT: B 305 PHE cc_start: 0.7991 (t80) cc_final: 0.7126 (t80) REVERT: B 372 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7114 (tp30) REVERT: B 498 GLN cc_start: 0.6463 (mt0) cc_final: 0.6246 (mt0) REVERT: B 523 MET cc_start: 0.8765 (tpt) cc_final: 0.8355 (tpt) REVERT: B 685 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7289 (tp30) REVERT: C 295 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7830 (t) REVERT: C 305 PHE cc_start: 0.7995 (t80) cc_final: 0.7472 (t80) REVERT: C 326 LEU cc_start: 0.8394 (tp) cc_final: 0.8123 (mt) REVERT: C 372 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7160 (tp30) REVERT: C 523 MET cc_start: 0.8791 (tpt) cc_final: 0.8462 (tpt) REVERT: C 685 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7259 (tp30) REVERT: C 689 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7685 (mmmt) REVERT: D 163 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6541 (ttp) REVERT: D 215 MET cc_start: 0.6070 (ttp) cc_final: 0.5841 (ttp) REVERT: D 295 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7877 (t) REVERT: D 372 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7166 (tp30) REVERT: D 523 MET cc_start: 0.8769 (tpt) cc_final: 0.8314 (tpt) REVERT: D 685 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7332 (tp30) outliers start: 47 outliers final: 7 residues processed: 316 average time/residue: 1.0369 time to fit residues: 390.7724 Evaluate side-chains 267 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 251 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain D residue 542 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 11 optimal weight: 30.0000 chunk 220 optimal weight: 2.9990 chunk 199 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 ASN A 355 GLN A 629 ASN B 311 ASN B 355 GLN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN C 311 ASN C 355 GLN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN D 311 ASN ** D 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN D 728 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.211060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.166810 restraints weight = 66008.952| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.10 r_work: 0.3513 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22700 Z= 0.202 Angle : 0.579 5.299 30336 Z= 0.302 Chirality : 0.036 0.123 3244 Planarity : 0.004 0.033 3616 Dihedral : 20.843 179.759 4472 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 2.29 % Allowed : 13.85 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.16), residues: 2504 helix: -0.39 (0.13), residues: 1528 sheet: -3.68 (0.44), residues: 92 loop : -3.03 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 474 TYR 0.014 0.002 TYR C 352 PHE 0.016 0.002 PHE B 449 TRP 0.013 0.002 TRP A 698 HIS 0.006 0.001 HIS D 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (22696) covalent geometry : angle 0.57781 / 0.30 (30328) SS BOND : bond 0.01128 / 0.56 ( 4) SS BOND : angle 2.08930 / 1.51 ( 8) hydrogen bonds : bond 0.04034 / 2.65 ( 1012) hydrogen bonds : angle 4.75043 / 3.22 ( 2964) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 279 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6726 (ttp) REVERT: A 295 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8050 (t) REVERT: A 305 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7682 (t80) REVERT: A 523 MET cc_start: 0.8796 (tpt) cc_final: 0.8314 (tpt) REVERT: A 572 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.7689 (mpp) REVERT: B 163 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6633 (ttp) REVERT: B 305 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7685 (t80) REVERT: B 372 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7184 (tp30) REVERT: B 523 MET cc_start: 0.8855 (tpt) cc_final: 0.8447 (tpt) REVERT: B 560 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: C 163 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6576 (ttp) REVERT: C 295 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8040 (t) REVERT: C 305 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7670 (t80) REVERT: C 523 MET cc_start: 0.8825 (tpt) cc_final: 0.8398 (tpt) REVERT: C 560 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.7837 (tm-30) REVERT: C 685 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7470 (tp30) REVERT: D 163 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6569 (ttp) REVERT: D 295 VAL cc_start: 0.8336 (OUTLIER) cc_final: 0.8037 (t) REVERT: D 523 MET cc_start: 0.8823 (tpt) cc_final: 0.8347 (tpt) outliers start: 51 outliers final: 8 residues processed: 304 average time/residue: 0.9958 time to fit residues: 365.2156 Evaluate side-chains 269 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 542 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 206 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 238 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 4 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.210805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.167723 restraints weight = 65794.741| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.01 r_work: 0.3509 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22700 Z= 0.205 Angle : 0.565 5.978 30336 Z= 0.292 Chirality : 0.036 0.145 3244 Planarity : 0.004 0.035 3616 Dihedral : 19.714 179.452 4472 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 2.83 % Allowed : 14.70 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: -1.95 (0.16), residues: 2504 helix: -0.22 (0.13), residues: 1524 sheet: -3.56 (0.44), residues: 92 loop : -2.92 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 474 TYR 0.012 0.002 TYR A 584 PHE 0.012 0.001 PHE B 449 TRP 0.012 0.002 TRP C 698 HIS 0.004 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.21 (22696) covalent geometry : angle 0.56372 / 0.29 (30328) SS BOND : bond 0.00578 / 0.29 ( 4) SS BOND : angle 1.94397 / 1.36 ( 8) hydrogen bonds : bond 0.03917 / 2.57 ( 1012) hydrogen bonds : angle 4.62158 / 3.12 ( 2964) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 241 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6631 (ttp) REVERT: A 295 VAL cc_start: 0.8359 (OUTLIER) cc_final: 0.8140 (t) REVERT: A 372 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7045 (tp30) REVERT: A 523 MET cc_start: 0.8809 (tpt) cc_final: 0.8375 (tpt) REVERT: B 163 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6626 (ttp) REVERT: B 372 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7064 (tp30) REVERT: B 523 MET cc_start: 0.8826 (tpt) cc_final: 0.8402 (tpt) REVERT: C 295 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8098 (t) REVERT: C 326 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8088 (mt) REVERT: C 372 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6995 (tp30) REVERT: C 523 MET cc_start: 0.8828 (tpt) cc_final: 0.8387 (tpt) REVERT: C 560 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: D 163 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6523 (ttp) REVERT: D 295 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.8134 (t) REVERT: D 372 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6995 (tp30) REVERT: D 523 MET cc_start: 0.8789 (tpt) cc_final: 0.8354 (tpt) outliers start: 63 outliers final: 12 residues processed: 280 average time/residue: 0.9196 time to fit residues: 310.2065 Evaluate side-chains 252 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 167 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain D residue 542 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 160 optimal weight: 2.9990 chunk 200 optimal weight: 30.0000 chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 195 optimal weight: 30.0000 chunk 136 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 125 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.209215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.165611 restraints weight = 65851.137| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.06 r_work: 0.3483 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 22700 Z= 0.256 Angle : 0.596 5.531 30336 Z= 0.309 Chirality : 0.038 0.155 3244 Planarity : 0.004 0.053 3616 Dihedral : 19.785 178.122 4472 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 2.97 % Allowed : 15.69 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.16), residues: 2504 helix: -0.25 (0.13), residues: 1520 sheet: -3.65 (0.43), residues: 92 loop : -2.89 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 364 TYR 0.016 0.002 TYR B 584 PHE 0.013 0.002 PHE A 650 TRP 0.013 0.002 TRP D 698 HIS 0.004 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.26 (22696) covalent geometry : angle 0.59439 / 0.31 (30328) SS BOND : bond 0.00623 / 0.31 ( 4) SS BOND : angle 3.00096 / 1.64 ( 8) hydrogen bonds : bond 0.04075 / 2.68 ( 1012) hydrogen bonds : angle 4.68512 / 3.16 ( 2964) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 243 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6603 (ttp) REVERT: A 372 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7103 (tp30) REVERT: A 523 MET cc_start: 0.8835 (tpt) cc_final: 0.8384 (tpt) REVERT: A 572 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.7687 (mpp) REVERT: B 163 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6554 (ttp) REVERT: B 206 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7248 (tt) REVERT: B 333 LYS cc_start: 0.8273 (ptpp) cc_final: 0.8022 (tptm) REVERT: B 523 MET cc_start: 0.8844 (tpt) cc_final: 0.8436 (tpt) REVERT: B 560 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: C 326 LEU cc_start: 0.8300 (tt) cc_final: 0.8084 (mt) REVERT: C 372 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7050 (tp30) REVERT: C 560 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: D 372 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7084 (tp30) REVERT: D 523 MET cc_start: 0.8801 (tpt) cc_final: 0.8359 (tpt) outliers start: 66 outliers final: 22 residues processed: 286 average time/residue: 0.7836 time to fit residues: 271.0385 Evaluate side-chains 260 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 229 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 542 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 184 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 chunk 223 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.211106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.165719 restraints weight = 65394.702| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.90 r_work: 0.3548 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22700 Z= 0.148 Angle : 0.527 5.542 30336 Z= 0.274 Chirality : 0.035 0.139 3244 Planarity : 0.003 0.040 3616 Dihedral : 18.500 177.446 4472 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 2.61 % Allowed : 16.23 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: -1.54 (0.17), residues: 2504 helix: 0.05 (0.13), residues: 1528 sheet: -3.29 (0.46), residues: 92 loop : -2.67 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 364 TYR 0.015 0.002 TYR D 310 PHE 0.009 0.001 PHE D 305 TRP 0.011 0.001 TRP D 698 HIS 0.003 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (22696) covalent geometry : angle 0.52464 / 0.27 (30328) SS BOND : bond 0.00573 / 0.29 ( 4) SS BOND : angle 2.97882 / 1.57 ( 8) hydrogen bonds : bond 0.03665 / 2.40 ( 1012) hydrogen bonds : angle 4.38370 / 2.96 ( 2964) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 248 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6647 (ttp) REVERT: A 372 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6939 (tp30) REVERT: A 523 MET cc_start: 0.8718 (tpt) cc_final: 0.8246 (tpt) REVERT: B 163 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6560 (ttp) REVERT: B 206 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7200 (tt) REVERT: B 333 LYS cc_start: 0.8212 (ptpp) cc_final: 0.7970 (tptm) REVERT: B 372 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6851 (tp30) REVERT: B 523 MET cc_start: 0.8744 (tpt) cc_final: 0.8283 (tpt) REVERT: B 560 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7703 (tm-30) REVERT: C 326 LEU cc_start: 0.8261 (tt) cc_final: 0.8061 (mt) REVERT: C 372 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6908 (tp30) REVERT: C 523 MET cc_start: 0.8739 (tpt) cc_final: 0.8275 (tpt) REVERT: C 560 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7718 (tm-30) REVERT: D 206 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7251 (tt) REVERT: D 372 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6915 (tp30) REVERT: D 523 MET cc_start: 0.8709 (tpt) cc_final: 0.8236 (tpt) outliers start: 58 outliers final: 17 residues processed: 283 average time/residue: 0.6248 time to fit residues: 216.4983 Evaluate side-chains 252 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 542 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 68 optimal weight: 30.0000 chunk 123 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN B 728 GLN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.209734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.165508 restraints weight = 65788.492| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.93 r_work: 0.3525 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22700 Z= 0.176 Angle : 0.542 5.859 30336 Z= 0.282 Chirality : 0.035 0.148 3244 Planarity : 0.004 0.036 3616 Dihedral : 18.315 178.711 4472 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 2.20 % Allowed : 17.45 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: -1.48 (0.17), residues: 2504 helix: 0.08 (0.13), residues: 1528 sheet: -3.14 (0.49), residues: 92 loop : -2.63 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 364 TYR 0.016 0.002 TYR D 310 PHE 0.009 0.001 PHE A 449 TRP 0.010 0.001 TRP D 698 HIS 0.003 0.001 HIS C 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (22696) covalent geometry : angle 0.54099 / 0.28 (30328) SS BOND : bond 0.00583 / 0.29 ( 4) SS BOND : angle 2.27278 / 1.23 ( 8) hydrogen bonds : bond 0.03752 / 2.46 ( 1012) hydrogen bonds : angle 4.41704 / 2.99 ( 2964) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 235 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6675 (ttp) REVERT: A 372 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7030 (tp30) REVERT: A 572 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.7594 (mpp) REVERT: B 206 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7196 (tt) REVERT: B 333 LYS cc_start: 0.8225 (ptpp) cc_final: 0.8002 (tptm) REVERT: B 560 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: C 372 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.7028 (tp30) REVERT: C 523 MET cc_start: 0.8756 (tpt) cc_final: 0.8301 (tpt) REVERT: C 560 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: D 206 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7215 (tt) REVERT: D 372 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6961 (tp30) outliers start: 49 outliers final: 16 residues processed: 265 average time/residue: 0.6147 time to fit residues: 196.7373 Evaluate side-chains 245 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 542 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 227 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 74 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN A 728 GLN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.208026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.164809 restraints weight = 65570.321| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.95 r_work: 0.3492 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22700 Z= 0.245 Angle : 0.594 6.525 30336 Z= 0.307 Chirality : 0.038 0.185 3244 Planarity : 0.004 0.053 3616 Dihedral : 18.805 176.381 4472 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 2.07 % Allowed : 18.08 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: -1.66 (0.16), residues: 2504 helix: -0.07 (0.13), residues: 1524 sheet: -3.11 (0.49), residues: 92 loop : -2.66 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 364 TYR 0.020 0.002 TYR A 310 PHE 0.013 0.002 PHE C 650 TRP 0.013 0.002 TRP D 698 HIS 0.003 0.001 HIS B 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.25 (22696) covalent geometry : angle 0.59279 / 0.31 (30328) SS BOND : bond 0.00553 / 0.28 ( 4) SS BOND : angle 2.39061 / 1.30 ( 8) hydrogen bonds : bond 0.04016 / 2.64 ( 1012) hydrogen bonds : angle 4.58990 / 3.10 ( 2964) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.7628 (mpp) REVERT: B 206 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7210 (tt) REVERT: B 560 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: C 523 MET cc_start: 0.8809 (tpt) cc_final: 0.8407 (tpt) REVERT: C 560 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: D 206 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7250 (tt) REVERT: D 372 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7020 (tp30) outliers start: 46 outliers final: 21 residues processed: 255 average time/residue: 0.6077 time to fit residues: 186.7961 Evaluate side-chains 244 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 542 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 30 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 232 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.212264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.168839 restraints weight = 66123.625| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.85 r_work: 0.3564 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22700 Z= 0.117 Angle : 0.522 7.723 30336 Z= 0.271 Chirality : 0.034 0.148 3244 Planarity : 0.003 0.036 3616 Dihedral : 17.463 178.632 4472 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 1.62 % Allowed : 19.15 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: -1.11 (0.17), residues: 2504 helix: 0.35 (0.13), residues: 1520 sheet: -2.76 (0.54), residues: 92 loop : -2.41 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 364 TYR 0.017 0.001 TYR B 310 PHE 0.010 0.001 PHE D 305 TRP 0.012 0.001 TRP B 698 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (22696) covalent geometry : angle 0.52113 / 0.27 (30328) SS BOND : bond 0.00521 / 0.26 ( 4) SS BOND : angle 1.84282 / 1.00 ( 8) hydrogen bonds : bond 0.03528 / 2.30 ( 1012) hydrogen bonds : angle 4.23353 / 2.87 ( 2964) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6876 (tp30) REVERT: A 523 MET cc_start: 0.8487 (mmm) cc_final: 0.7942 (tpt) REVERT: B 206 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7130 (tt) REVERT: B 523 MET cc_start: 0.8526 (mmm) cc_final: 0.7986 (tpt) REVERT: B 560 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: C 372 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6900 (tp30) REVERT: C 523 MET cc_start: 0.8715 (tpt) cc_final: 0.8264 (tpt) REVERT: D 206 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7211 (tt) REVERT: D 523 MET cc_start: 0.8504 (mmm) cc_final: 0.7946 (tpt) outliers start: 36 outliers final: 12 residues processed: 257 average time/residue: 0.6227 time to fit residues: 192.6017 Evaluate side-chains 234 residues out of total 2224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 386 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 244 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 211 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 200 optimal weight: 30.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN B 728 GLN ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.210889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.167833 restraints weight = 66662.184| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.98 r_work: 0.3534 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22700 Z= 0.152 Angle : 0.537 7.652 30336 Z= 0.278 Chirality : 0.035 0.150 3244 Planarity : 0.004 0.037 3616 Dihedral : 17.446 176.725 4472 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 1.62 % Allowed : 19.51 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 are not related in a simple way. whole: -1.03 (0.17), residues: 2504 helix: 0.42 (0.13), residues: 1520 sheet: -2.69 (0.55), residues: 92 loop : -2.40 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 364 TYR 0.017 0.002 TYR C 310 PHE 0.009 0.001 PHE D 305 TRP 0.009 0.001 TRP D 698 HIS 0.004 0.001 HIS B 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (22696) covalent geometry : angle 0.53578 / 0.28 (30328) SS BOND : bond 0.00587 / 0.29 ( 4) SS BOND : angle 1.94590 / 1.05 ( 8) hydrogen bonds : bond 0.03645 / 2.39 ( 1012) hydrogen bonds : angle 4.27735 / 2.90 ( 2964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11868.38 seconds wall clock time: 201 minutes 35.81 seconds (12095.81 seconds total)