Starting phenix.real_space_refine on Fri Feb 6 00:54:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mvu_48671/02_2026/9mvu_48671.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mvu_48671/02_2026/9mvu_48671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mvu_48671/02_2026/9mvu_48671.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mvu_48671/02_2026/9mvu_48671.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mvu_48671/02_2026/9mvu_48671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mvu_48671/02_2026/9mvu_48671.map" } resolution = 2.2 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= 0.001 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 10608 2.51 5 N 2969 2.21 5 O 7541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21199 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4660 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 548} Chain breaks: 2 Chain: "B" Number of atoms: 4689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4689 Classifications: {'peptide': 580} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 552} Chain breaks: 2 Chain: "C" Number of atoms: 4638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4638 Classifications: {'peptide': 574} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 546} Chain breaks: 2 Chain: "D" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 950 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 950 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "F" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 950 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1240, 1240 Classifications: {'water': 1240} Link IDs: {None: 1239} Chain: "B" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1238, 1238 Classifications: {'water': 1238} Link IDs: {None: 1237} Chain: "C" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1250, 1250 Classifications: {'water': 1250} Link IDs: {None: 1249} Chain: "D" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 213 Classifications: {'water': 213} Link IDs: {None: 212} Chain: "E" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 214 Classifications: {'water': 214} Link IDs: {None: 213} Chain: "F" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 207 Classifications: {'water': 207} Link IDs: {None: 206} Time building chain proxies: 5.38, per 1000 atoms: 0.25 Number of scatterers: 21199 At special positions: 0 Unit cell: (148.716, 141.426, 181.521, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 7541 8.00 N 2969 7.00 C 10608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.04 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.02 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.04 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.04 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.04 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.02 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 98 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 950.9 milliseconds 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3922 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 42 sheets defined 21.1% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.521A pdb=" N GLU A 310 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 411 through 429 removed outlier: 4.039A pdb=" N ARG A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 546 removed outlier: 4.486A pdb=" N THR A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 removed outlier: 3.517A pdb=" N GLY A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 701 through 710 Processing helix chain 'A' and resid 711 through 717 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 358 through 363 removed outlier: 3.827A pdb=" N ALA B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 411 through 429 removed outlier: 4.011A pdb=" N ARG B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 427 " --> pdb=" O ARG B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 546 removed outlier: 4.361A pdb=" N THR B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 545 " --> pdb=" O GLU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 removed outlier: 3.507A pdb=" N ILE B 550 " --> pdb=" O ASN B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 660 through 664 Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 701 through 710 Processing helix chain 'B' and resid 711 through 717 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 358 through 363 removed outlier: 3.830A pdb=" N ALA C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 411 through 429 removed outlier: 3.964A pdb=" N ARG C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 546 removed outlier: 4.527A pdb=" N THR C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 removed outlier: 3.556A pdb=" N ILE C 550 " --> pdb=" O ASN C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 660 through 664 Processing helix chain 'C' and resid 690 through 697 Processing helix chain 'C' and resid 701 through 710 Processing helix chain 'C' and resid 711 through 717 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.648A pdb=" N THR D 93 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.631A pdb=" N THR E 93 " --> pdb=" O ALA E 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 6.731A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 559 through 564 removed outlier: 4.216A pdb=" N THR A 123 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A 124 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL C 667 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLN A 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 433 through 435 removed outlier: 6.100A pdb=" N LEU A 443 " --> pdb=" O ASN A 398 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN A 398 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LYS A 368 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LYS A 151 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU A 374 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY A 145 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU A 376 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N THR A 143 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 191 removed outlier: 6.515A pdb=" N GLN A 172 " --> pdb=" O MET A 183 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE A 185 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 170 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU A 187 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 168 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG A 189 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LYS A 166 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N TYR A 164 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.169A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG A 342 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASP A 323 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU A 344 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLN A 321 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR A 346 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N PHE A 319 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA7, first strand: chain 'A' and resid 210 through 215 Processing sheet with id=AA8, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AA9, first strand: chain 'A' and resid 638 through 643 removed outlier: 6.802A pdb=" N TYR A 647 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLN A 658 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR A 649 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 665 through 667 removed outlier: 3.816A pdb=" N THR A 665 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 123 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AB3, first strand: chain 'B' and resid 366 through 372 removed outlier: 5.410A pdb=" N LYS B 368 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS B 151 " --> pdb=" O LYS B 368 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 366 through 372 removed outlier: 5.410A pdb=" N LYS B 368 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LYS B 151 " --> pdb=" O LYS B 368 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 180 through 191 removed outlier: 6.505A pdb=" N GLN B 172 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 185 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL B 170 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU B 187 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 168 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG B 189 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS B 166 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N TYR B 164 " --> pdb=" O PRO B 191 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.274A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N THR B 340 " --> pdb=" O GLY B 324 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AB8, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AB9, first strand: chain 'B' and resid 375 through 380 Processing sheet with id=AC1, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AC2, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC3, first strand: chain 'B' and resid 638 through 643 removed outlier: 6.184A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 665 through 667 removed outlier: 3.815A pdb=" N THR B 665 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AC6, first strand: chain 'C' and resid 366 through 372 removed outlier: 5.393A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 366 through 372 removed outlier: 5.393A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 180 through 191 removed outlier: 6.602A pdb=" N GLN C 172 " --> pdb=" O MET C 183 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE C 185 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL C 170 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU C 187 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL C 168 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG C 189 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS C 166 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N TYR C 164 " --> pdb=" O PRO C 191 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.245A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N THR C 340 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AD2, first strand: chain 'C' and resid 210 through 215 Processing sheet with id=AD3, first strand: chain 'C' and resid 375 through 380 Processing sheet with id=AD4, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AD5, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD6, first strand: chain 'C' and resid 638 through 643 removed outlier: 5.631A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 2 through 7 Processing sheet with id=AD8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.428A pdb=" N GLY D 10 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.428A pdb=" N GLY D 10 " --> pdb=" O THR D 122 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 2 through 7 Processing sheet with id=AE2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.291A pdb=" N GLY E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.291A pdb=" N GLY E 10 " --> pdb=" O THR E 122 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 2 through 7 Processing sheet with id=AE5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.399A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.399A pdb=" N GLY F 10 " --> pdb=" O THR F 122 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2118 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: 5.76 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5613 1.34 - 1.46: 4143 1.46 - 1.58: 7363 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 17245 Sorted by residual: bond pdb=" N PRO A 578 " pdb=" CD PRO A 578 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.51e+01 bond pdb=" N PRO C 578 " pdb=" CD PRO C 578 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" N PRO B 578 " pdb=" CD PRO B 578 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" N ILE B 613 " pdb=" CA ILE B 613 " ideal model delta sigma weight residual 1.459 1.497 -0.039 1.24e-02 6.50e+03 9.71e+00 bond pdb=" N ILE C 613 " pdb=" CA ILE C 613 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.17e+00 ... (remaining 17240 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 23178 2.79 - 5.59: 213 5.59 - 8.38: 11 8.38 - 11.17: 1 11.17 - 13.97: 6 Bond angle restraints: 23409 Sorted by residual: angle pdb=" CA PRO A 578 " pdb=" N PRO A 578 " pdb=" CD PRO A 578 " ideal model delta sigma weight residual 112.00 99.29 12.71 1.40e+00 5.10e-01 8.24e+01 angle pdb=" CA PRO C 578 " pdb=" N PRO C 578 " pdb=" CD PRO C 578 " ideal model delta sigma weight residual 112.00 99.29 12.71 1.40e+00 5.10e-01 8.24e+01 angle pdb=" CA PRO B 578 " pdb=" N PRO B 578 " pdb=" CD PRO B 578 " ideal model delta sigma weight residual 112.00 99.32 12.68 1.40e+00 5.10e-01 8.20e+01 angle pdb=" CB GLU B 419 " pdb=" CG GLU B 419 " pdb=" CD GLU B 419 " ideal model delta sigma weight residual 112.60 98.63 13.97 1.70e+00 3.46e-01 6.75e+01 angle pdb=" CB GLU A 419 " pdb=" CG GLU A 419 " pdb=" CD GLU A 419 " ideal model delta sigma weight residual 112.60 100.26 12.34 1.70e+00 3.46e-01 5.27e+01 ... (remaining 23404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9424 17.97 - 35.94: 603 35.94 - 53.91: 139 53.91 - 71.88: 52 71.88 - 89.85: 29 Dihedral angle restraints: 10247 sinusoidal: 4118 harmonic: 6129 Sorted by residual: dihedral pdb=" CD ARG B 427 " pdb=" NE ARG B 427 " pdb=" CZ ARG B 427 " pdb=" NH1 ARG B 427 " ideal model delta sinusoidal sigma weight residual 0.00 -83.02 83.02 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CD ARG C 427 " pdb=" NE ARG C 427 " pdb=" CZ ARG C 427 " pdb=" NH1 ARG C 427 " ideal model delta sinusoidal sigma weight residual 0.00 -73.06 73.06 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CA LYS A 428 " pdb=" C LYS A 428 " pdb=" N TYR A 429 " pdb=" CA TYR A 429 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 10244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1854 0.047 - 0.093: 496 0.093 - 0.140: 158 0.140 - 0.186: 10 0.186 - 0.233: 9 Chirality restraints: 2527 Sorted by residual: chirality pdb=" CG LEU A 659 " pdb=" CB LEU A 659 " pdb=" CD1 LEU A 659 " pdb=" CD2 LEU A 659 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TYR C 429 " pdb=" N TYR C 429 " pdb=" C TYR C 429 " pdb=" CB TYR C 429 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA TYR A 429 " pdb=" N TYR A 429 " pdb=" C TYR A 429 " pdb=" CB TYR A 429 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 2524 not shown) Planarity restraints: 3061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 427 " -1.087 9.50e-02 1.11e+02 4.87e-01 1.43e+02 pdb=" NE ARG B 427 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG B 427 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 427 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 427 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 427 " -1.056 9.50e-02 1.11e+02 4.73e-01 1.35e+02 pdb=" NE ARG C 427 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG C 427 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 427 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 427 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 427 " 0.720 9.50e-02 1.11e+02 3.23e-01 6.35e+01 pdb=" NE ARG A 427 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG A 427 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 427 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 427 " 0.022 2.00e-02 2.50e+03 ... (remaining 3058 not shown) Histogram of nonbonded interaction distances: 0.40 - 1.30: 4 1.30 - 2.20: 9 2.20 - 3.10: 17712 3.10 - 4.00: 64736 4.00 - 4.90: 112629 Warning: very small nonbonded interaction distances. Nonbonded interactions: 195090 Sorted by model distance: nonbonded pdb=" NZ LYS C 238 " pdb=" O HOH A1508 " model vdw 0.402 3.120 nonbonded pdb=" NZ LYS A 238 " pdb=" O HOH A 801 " model vdw 0.527 3.120 nonbonded pdb=" CZ ARG C 415 " pdb=" O HOH C 801 " model vdw 1.146 3.270 nonbonded pdb=" NZ LYS B 238 " pdb=" O HOH B 801 " model vdw 1.152 3.120 nonbonded pdb=" CE LYS A 238 " pdb=" O HOH A 801 " model vdw 1.701 3.440 ... (remaining 195085 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 111 through 327 or resid 338 through 723)) selection = (chain 'B' and (resid 111 through 327 or resid 338 through 459 or resid 492 thro \ ugh 723)) selection = (chain 'C' and (resid 111 through 327 or resid 338 through 459 or resid 492 thro \ ugh 723)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.130 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17263 Z= 0.238 Angle : 0.726 13.966 23445 Z= 0.436 Chirality : 0.048 0.233 2527 Planarity : 0.018 0.487 3061 Dihedral : 14.356 89.848 6271 Min Nonbonded Distance : 0.402 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.25 % Favored : 98.65 % Rotamer: Outliers : 0.77 % Allowed : 0.33 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.24 (0.18), residues: 2081 helix: 0.75 (0.30), residues: 298 sheet: -0.28 (0.18), residues: 750 loop : -0.20 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 33 TYR 0.023 0.002 TYR A 296 PHE 0.017 0.002 PHE B 287 TRP 0.017 0.002 TRP B 539 HIS 0.015 0.002 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00404 (17245) covalent geometry : angle 0.72562 (23409) SS BOND : bond 0.00413 ( 18) SS BOND : angle 1.15631 ( 36) hydrogen bonds : bond 0.10267 ( 710) hydrogen bonds : angle 6.95587 ( 2118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 380 TYR cc_start: 0.6139 (t80) cc_final: 0.5929 (t80) REVERT: A 418 ARG cc_start: 0.7800 (tpt-90) cc_final: 0.6966 (mtm110) REVERT: A 695 LYS cc_start: 0.7261 (tptp) cc_final: 0.6678 (mmtm) REVERT: B 380 TYR cc_start: 0.6207 (t80) cc_final: 0.5891 (t80) REVERT: B 692 HIS cc_start: 0.7523 (t-90) cc_final: 0.7270 (t-90) REVERT: C 695 LYS cc_start: 0.7744 (tttt) cc_final: 0.7135 (mtmm) outliers start: 14 outliers final: 4 residues processed: 230 average time/residue: 0.7198 time to fit residues: 187.7509 Evaluate side-chains 191 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 187 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain C residue 428 LYS Chi-restraints excluded: chain C residue 614 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.0020 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN B 126 GLN B 141 ASN C 141 ASN C 248 HIS C 674 ASN D 3 GLN D 79 ASN E 39 GLN E 86 ASN F 3 GLN F 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.183597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120291 restraints weight = 17503.785| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.45 r_work: 0.3226 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17263 Z= 0.143 Angle : 0.554 8.292 23445 Z= 0.305 Chirality : 0.043 0.151 2527 Planarity : 0.005 0.070 3061 Dihedral : 5.730 75.026 2387 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.16 % Allowed : 4.48 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.08 (0.18), residues: 2081 helix: 1.44 (0.30), residues: 301 sheet: -0.16 (0.18), residues: 747 loop : -0.07 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 215 TYR 0.018 0.001 TYR A 296 PHE 0.018 0.002 PHE A 287 TRP 0.015 0.002 TRP C 539 HIS 0.012 0.002 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00304 (17245) covalent geometry : angle 0.55295 (23409) SS BOND : bond 0.00356 ( 18) SS BOND : angle 0.95012 ( 36) hydrogen bonds : bond 0.04489 ( 710) hydrogen bonds : angle 5.96149 ( 2118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.908 Fit side-chains REVERT: A 227 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: A 297 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8341 (ttt) REVERT: A 380 TYR cc_start: 0.6164 (t80) cc_final: 0.5935 (t80) REVERT: A 416 ASP cc_start: 0.7715 (m-30) cc_final: 0.7494 (m-30) REVERT: A 418 ARG cc_start: 0.7899 (tpt-90) cc_final: 0.7252 (ttp-170) REVERT: A 695 LYS cc_start: 0.7416 (tptp) cc_final: 0.6750 (mmtm) REVERT: B 380 TYR cc_start: 0.6211 (t80) cc_final: 0.5947 (t80) REVERT: B 692 HIS cc_start: 0.7550 (t-90) cc_final: 0.7301 (t-90) REVERT: C 438 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7563 (mp10) REVERT: C 695 LYS cc_start: 0.7813 (tttt) cc_final: 0.7188 (mtmt) REVERT: E 3 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7749 (mm-40) REVERT: F 3 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7540 (mm110) outliers start: 21 outliers final: 6 residues processed: 206 average time/residue: 0.6654 time to fit residues: 155.4922 Evaluate side-chains 200 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 3 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 104 optimal weight: 0.1980 chunk 86 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 197 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN A 141 ASN A 255 ASN B 126 GLN B 141 ASN B 177 HIS C 126 GLN C 141 ASN C 674 ASN D 3 GLN E 39 GLN F 3 GLN F 39 GLN F 84 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.182594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118908 restraints weight = 17522.079| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.45 r_work: 0.3205 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17263 Z= 0.155 Angle : 0.545 7.038 23445 Z= 0.301 Chirality : 0.043 0.142 2527 Planarity : 0.004 0.061 3061 Dihedral : 5.288 66.180 2380 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.16 % Allowed : 5.25 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.14 (0.18), residues: 2081 helix: 1.54 (0.29), residues: 302 sheet: -0.16 (0.18), residues: 756 loop : -0.01 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 215 TYR 0.016 0.001 TYR A 296 PHE 0.020 0.002 PHE A 287 TRP 0.013 0.002 TRP A 539 HIS 0.010 0.002 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00330 (17245) covalent geometry : angle 0.54428 (23409) SS BOND : bond 0.00443 ( 18) SS BOND : angle 0.95358 ( 36) hydrogen bonds : bond 0.04460 ( 710) hydrogen bonds : angle 5.81451 ( 2118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.855 Fit side-chains REVERT: A 227 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8386 (m-30) REVERT: A 297 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8479 (ttt) REVERT: A 380 TYR cc_start: 0.6225 (t80) cc_final: 0.5998 (t80) REVERT: A 416 ASP cc_start: 0.7773 (m-30) cc_final: 0.7550 (m-30) REVERT: A 418 ARG cc_start: 0.7942 (tpt-90) cc_final: 0.7279 (ttp-170) REVERT: A 695 LYS cc_start: 0.7507 (tptp) cc_final: 0.6806 (mmtm) REVERT: B 380 TYR cc_start: 0.6211 (t80) cc_final: 0.5969 (t80) REVERT: B 494 ARG cc_start: 0.7894 (mtm180) cc_final: 0.7665 (mtm-85) REVERT: B 692 HIS cc_start: 0.7531 (t-90) cc_final: 0.7287 (t-90) REVERT: C 438 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7518 (mp10) REVERT: C 587 MET cc_start: 0.5446 (mpp) cc_final: 0.5012 (mtm) REVERT: C 672 ASP cc_start: 0.9003 (m-30) cc_final: 0.8647 (m-30) REVERT: C 695 LYS cc_start: 0.7807 (tttt) cc_final: 0.7189 (mttt) outliers start: 21 outliers final: 8 residues processed: 206 average time/residue: 0.7436 time to fit residues: 173.4690 Evaluate side-chains 199 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 44 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 199 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN A 141 ASN A 616 GLN B 126 GLN B 141 ASN B 255 ASN C 141 ASN C 674 ASN D 3 GLN E 39 GLN F 3 GLN F 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.179954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.115686 restraints weight = 17471.295| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.45 r_work: 0.3157 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17263 Z= 0.243 Angle : 0.628 9.613 23445 Z= 0.347 Chirality : 0.046 0.152 2527 Planarity : 0.005 0.054 3061 Dihedral : 5.682 66.014 2380 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.33 % Allowed : 6.25 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.11 (0.18), residues: 2081 helix: 1.50 (0.29), residues: 302 sheet: -0.18 (0.18), residues: 752 loop : -0.02 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 215 TYR 0.017 0.002 TYR A 296 PHE 0.024 0.002 PHE A 287 TRP 0.011 0.002 TRP C 354 HIS 0.010 0.002 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00531 (17245) covalent geometry : angle 0.62659 (23409) SS BOND : bond 0.00545 ( 18) SS BOND : angle 1.18504 ( 36) hydrogen bonds : bond 0.05126 ( 710) hydrogen bonds : angle 5.95299 ( 2118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.884 Fit side-chains REVERT: A 227 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8450 (m-30) REVERT: A 380 TYR cc_start: 0.6288 (t80) cc_final: 0.6048 (t80) REVERT: A 416 ASP cc_start: 0.7834 (m-30) cc_final: 0.7579 (m-30) REVERT: A 418 ARG cc_start: 0.8094 (tpt-90) cc_final: 0.7366 (mtp180) REVERT: A 695 LYS cc_start: 0.7610 (tptp) cc_final: 0.6856 (mmtm) REVERT: B 227 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8424 (m-30) REVERT: B 380 TYR cc_start: 0.6307 (t80) cc_final: 0.6007 (t80) REVERT: B 494 ARG cc_start: 0.7929 (mtm180) cc_final: 0.7696 (mtm-85) REVERT: B 692 HIS cc_start: 0.7581 (t-90) cc_final: 0.7330 (t-90) REVERT: B 695 LYS cc_start: 0.8098 (tmtt) cc_final: 0.7256 (mmtm) REVERT: C 438 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7547 (mp10) REVERT: C 587 MET cc_start: 0.5689 (mpp) cc_final: 0.5424 (mtm) REVERT: C 672 ASP cc_start: 0.9080 (m-30) cc_final: 0.8749 (m-30) REVERT: C 695 LYS cc_start: 0.7807 (tttt) cc_final: 0.7132 (mttt) REVERT: D 39 GLN cc_start: 0.7466 (tp-100) cc_final: 0.7175 (tp40) REVERT: E 3 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7883 (mm-40) REVERT: F 3 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7693 (mm110) outliers start: 24 outliers final: 12 residues processed: 204 average time/residue: 0.6948 time to fit residues: 161.1773 Evaluate side-chains 201 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 122 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 197 optimal weight: 0.7980 chunk 163 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN A 141 ASN B 126 GLN B 141 ASN C 141 ASN C 546 ASN C 674 ASN D 3 GLN E 39 GLN F 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.181893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.118103 restraints weight = 17473.274| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.45 r_work: 0.3190 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17263 Z= 0.157 Angle : 0.542 7.333 23445 Z= 0.300 Chirality : 0.043 0.140 2527 Planarity : 0.004 0.049 3061 Dihedral : 5.340 63.367 2380 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.22 % Allowed : 7.30 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.18 (0.18), residues: 2081 helix: 1.62 (0.30), residues: 303 sheet: -0.15 (0.18), residues: 711 loop : -0.01 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 215 TYR 0.014 0.001 TYR A 296 PHE 0.020 0.002 PHE A 287 TRP 0.012 0.002 TRP A 539 HIS 0.009 0.002 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00335 (17245) covalent geometry : angle 0.54095 (23409) SS BOND : bond 0.00379 ( 18) SS BOND : angle 1.00684 ( 36) hydrogen bonds : bond 0.04486 ( 710) hydrogen bonds : angle 5.76865 ( 2118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.930 Fit side-chains REVERT: A 227 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8429 (m-30) REVERT: A 418 ARG cc_start: 0.8080 (tpt-90) cc_final: 0.7331 (mtp180) REVERT: A 695 LYS cc_start: 0.7610 (tptp) cc_final: 0.6866 (mmtm) REVERT: B 227 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8432 (m-30) REVERT: B 380 TYR cc_start: 0.6199 (t80) cc_final: 0.5984 (t80) REVERT: B 494 ARG cc_start: 0.7899 (mtm180) cc_final: 0.7663 (mtm-85) REVERT: B 692 HIS cc_start: 0.7531 (t-90) cc_final: 0.7293 (t-90) REVERT: C 438 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7485 (mp10) REVERT: C 587 MET cc_start: 0.5819 (mpp) cc_final: 0.5566 (mtm) REVERT: C 672 ASP cc_start: 0.9042 (m-30) cc_final: 0.8694 (m-30) REVERT: C 695 LYS cc_start: 0.7791 (tttt) cc_final: 0.7140 (mttt) REVERT: D 39 GLN cc_start: 0.7477 (tp-100) cc_final: 0.7273 (tp40) REVERT: E 3 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7710 (mm-40) outliers start: 22 outliers final: 12 residues processed: 207 average time/residue: 0.6736 time to fit residues: 159.4453 Evaluate side-chains 202 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 162 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 169 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN A 141 ASN B 126 GLN B 141 ASN C 141 ASN C 546 ASN C 674 ASN D 3 GLN E 39 GLN F 3 GLN F 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.179280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114995 restraints weight = 17348.726| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.44 r_work: 0.3153 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17263 Z= 0.273 Angle : 0.647 10.279 23445 Z= 0.359 Chirality : 0.047 0.167 2527 Planarity : 0.006 0.046 3061 Dihedral : 5.719 65.217 2379 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.33 % Allowed : 7.85 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.11 (0.18), residues: 2081 helix: 1.53 (0.29), residues: 303 sheet: -0.22 (0.18), residues: 714 loop : -0.02 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 215 TYR 0.018 0.002 TYR A 380 PHE 0.024 0.003 PHE A 287 TRP 0.012 0.003 TRP C 354 HIS 0.009 0.002 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00600 (17245) covalent geometry : angle 0.64593 (23409) SS BOND : bond 0.00593 ( 18) SS BOND : angle 1.23572 ( 36) hydrogen bonds : bond 0.05277 ( 710) hydrogen bonds : angle 5.96587 ( 2118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.865 Fit side-chains REVERT: A 227 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8465 (m-30) REVERT: A 418 ARG cc_start: 0.8126 (tpt-90) cc_final: 0.7356 (mtp180) REVERT: A 613 ILE cc_start: 0.4093 (OUTLIER) cc_final: 0.3859 (tt) REVERT: A 695 LYS cc_start: 0.7674 (tptp) cc_final: 0.6904 (mmtm) REVERT: B 124 VAL cc_start: 0.7342 (OUTLIER) cc_final: 0.7056 (p) REVERT: B 227 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8442 (m-30) REVERT: B 380 TYR cc_start: 0.6277 (t80) cc_final: 0.6015 (t80) REVERT: B 494 ARG cc_start: 0.7934 (mtm180) cc_final: 0.7680 (mtm-85) REVERT: B 692 HIS cc_start: 0.7583 (t-90) cc_final: 0.7351 (t-170) REVERT: B 695 LYS cc_start: 0.8135 (tmtt) cc_final: 0.7277 (mmtm) REVERT: C 438 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7516 (mp10) REVERT: C 695 LYS cc_start: 0.7781 (tttt) cc_final: 0.7146 (mttt) REVERT: D 39 GLN cc_start: 0.7599 (tp-100) cc_final: 0.7373 (tp40) REVERT: E 3 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7789 (mm-40) REVERT: F 117 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7053 (mm-40) outliers start: 24 outliers final: 13 residues processed: 208 average time/residue: 0.7219 time to fit residues: 170.6235 Evaluate side-chains 206 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 563 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 199 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 GLN A 141 ASN B 126 GLN B 141 ASN C 141 ASN C 674 ASN D 3 GLN E 39 GLN E 56 ASN F 3 GLN F 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.181745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.117968 restraints weight = 17323.099| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.45 r_work: 0.3190 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17263 Z= 0.160 Angle : 0.544 7.419 23445 Z= 0.301 Chirality : 0.043 0.139 2527 Planarity : 0.004 0.044 3061 Dihedral : 5.321 61.569 2379 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.22 % Allowed : 8.57 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.17 (0.18), residues: 2081 helix: 1.72 (0.30), residues: 304 sheet: -0.17 (0.18), residues: 714 loop : -0.03 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 215 TYR 0.013 0.001 TYR A 296 PHE 0.020 0.002 PHE A 287 TRP 0.013 0.002 TRP A 539 HIS 0.008 0.002 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00340 (17245) covalent geometry : angle 0.54311 (23409) SS BOND : bond 0.00375 ( 18) SS BOND : angle 1.00032 ( 36) hydrogen bonds : bond 0.04491 ( 710) hydrogen bonds : angle 5.73752 ( 2118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.838 Fit side-chains REVERT: A 227 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8462 (m-30) REVERT: A 418 ARG cc_start: 0.8104 (tpt-90) cc_final: 0.7359 (mtp180) REVERT: A 695 LYS cc_start: 0.7647 (tptp) cc_final: 0.6876 (mmtm) REVERT: B 124 VAL cc_start: 0.7335 (OUTLIER) cc_final: 0.7064 (p) REVERT: B 227 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8459 (m-30) REVERT: B 380 TYR cc_start: 0.6190 (t80) cc_final: 0.5981 (t80) REVERT: B 494 ARG cc_start: 0.7944 (mtm180) cc_final: 0.7685 (mtm-85) REVERT: B 692 HIS cc_start: 0.7529 (t-90) cc_final: 0.7291 (t-90) REVERT: B 695 LYS cc_start: 0.8090 (tmtt) cc_final: 0.7276 (mmtm) REVERT: C 233 GLU cc_start: 0.8563 (tt0) cc_final: 0.8328 (mp0) REVERT: C 438 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7466 (mp10) REVERT: C 695 LYS cc_start: 0.7751 (tttt) cc_final: 0.7121 (mttt) REVERT: E 3 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7781 (mm-40) REVERT: F 3 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7641 (mm110) outliers start: 22 outliers final: 12 residues processed: 212 average time/residue: 0.6349 time to fit residues: 152.8677 Evaluate side-chains 206 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 119 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 540 ASN B 126 GLN B 141 ASN C 141 ASN C 674 ASN D 3 GLN E 39 GLN F 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.179866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.115889 restraints weight = 17429.738| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.44 r_work: 0.3166 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17263 Z= 0.218 Angle : 0.599 8.786 23445 Z= 0.331 Chirality : 0.045 0.216 2527 Planarity : 0.005 0.043 3061 Dihedral : 5.501 61.044 2379 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.22 % Allowed : 8.73 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.17 (0.18), residues: 2081 helix: 1.67 (0.30), residues: 304 sheet: -0.17 (0.18), residues: 713 loop : -0.03 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 215 TYR 0.014 0.002 TYR A 296 PHE 0.023 0.002 PHE A 287 TRP 0.010 0.002 TRP C 354 HIS 0.008 0.002 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00473 (17245) covalent geometry : angle 0.59737 (23409) SS BOND : bond 0.00501 ( 18) SS BOND : angle 1.14845 ( 36) hydrogen bonds : bond 0.04903 ( 710) hydrogen bonds : angle 5.83397 ( 2118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.886 Fit side-chains REVERT: A 227 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8466 (m-30) REVERT: A 418 ARG cc_start: 0.8127 (tpt-90) cc_final: 0.7374 (mtp180) REVERT: A 695 LYS cc_start: 0.7664 (tptp) cc_final: 0.6898 (mmtm) REVERT: B 124 VAL cc_start: 0.7365 (OUTLIER) cc_final: 0.7095 (p) REVERT: B 227 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8464 (m-30) REVERT: B 380 TYR cc_start: 0.6233 (t80) cc_final: 0.6021 (t80) REVERT: B 494 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7694 (mtm-85) REVERT: B 692 HIS cc_start: 0.7558 (t-90) cc_final: 0.7316 (t-90) REVERT: B 695 LYS cc_start: 0.8113 (tmtt) cc_final: 0.7263 (mmtm) REVERT: C 438 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7518 (mp10) REVERT: C 695 LYS cc_start: 0.7754 (tttt) cc_final: 0.7096 (mttt) REVERT: E 3 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7770 (mm-40) outliers start: 22 outliers final: 14 residues processed: 208 average time/residue: 0.6459 time to fit residues: 152.3866 Evaluate side-chains 207 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 563 MET Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 32 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 186 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 170 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN B 126 GLN B 141 ASN C 141 ASN C 674 ASN D 3 GLN E 39 GLN F 3 GLN F 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.181299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.117532 restraints weight = 17400.421| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.45 r_work: 0.3181 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17263 Z= 0.165 Angle : 0.549 7.352 23445 Z= 0.304 Chirality : 0.043 0.146 2527 Planarity : 0.004 0.043 3061 Dihedral : 5.275 58.021 2379 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.22 % Allowed : 9.07 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.22 (0.18), residues: 2081 helix: 1.81 (0.30), residues: 304 sheet: -0.15 (0.18), residues: 713 loop : -0.02 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 215 TYR 0.013 0.001 TYR A 296 PHE 0.019 0.002 PHE C 287 TRP 0.012 0.002 TRP A 539 HIS 0.008 0.002 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00353 (17245) covalent geometry : angle 0.54801 (23409) SS BOND : bond 0.00408 ( 18) SS BOND : angle 1.02550 ( 36) hydrogen bonds : bond 0.04515 ( 710) hydrogen bonds : angle 5.71044 ( 2118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.770 Fit side-chains REVERT: A 227 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8454 (m-30) REVERT: A 418 ARG cc_start: 0.8094 (tpt-90) cc_final: 0.7339 (mtp180) REVERT: A 695 LYS cc_start: 0.7649 (tptp) cc_final: 0.6881 (mmtm) REVERT: B 124 VAL cc_start: 0.7313 (OUTLIER) cc_final: 0.7044 (p) REVERT: B 227 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8460 (m-30) REVERT: B 494 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7696 (mtm-85) REVERT: B 692 HIS cc_start: 0.7526 (t-90) cc_final: 0.7289 (t-90) REVERT: B 695 LYS cc_start: 0.8097 (tmtt) cc_final: 0.7286 (mmtm) REVERT: C 438 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7462 (mp10) REVERT: C 695 LYS cc_start: 0.7716 (tttt) cc_final: 0.7125 (mttt) REVERT: E 3 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7786 (mm-40) REVERT: F 3 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7653 (mm110) outliers start: 22 outliers final: 14 residues processed: 211 average time/residue: 0.6314 time to fit residues: 151.8381 Evaluate side-chains 210 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 178 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN B 126 GLN B 141 ASN C 141 ASN D 3 GLN E 39 GLN F 3 GLN F 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.181381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117382 restraints weight = 17444.892| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.44 r_work: 0.3187 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17263 Z= 0.165 Angle : 0.552 7.281 23445 Z= 0.305 Chirality : 0.043 0.139 2527 Planarity : 0.004 0.043 3061 Dihedral : 5.255 56.537 2379 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.16 % Allowed : 9.01 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.26 (0.18), residues: 2081 helix: 1.83 (0.30), residues: 304 sheet: -0.12 (0.18), residues: 709 loop : 0.01 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 661 TYR 0.013 0.001 TYR A 296 PHE 0.020 0.002 PHE A 287 TRP 0.012 0.002 TRP A 539 HIS 0.008 0.002 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00355 (17245) covalent geometry : angle 0.55106 (23409) SS BOND : bond 0.00397 ( 18) SS BOND : angle 1.02943 ( 36) hydrogen bonds : bond 0.04515 ( 710) hydrogen bonds : angle 5.70253 ( 2118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4162 Ramachandran restraints generated. 2081 Oldfield, 0 Emsley, 2081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.579 Fit side-chains REVERT: A 227 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8459 (m-30) REVERT: A 418 ARG cc_start: 0.8106 (tpt-90) cc_final: 0.7350 (mtp180) REVERT: A 695 LYS cc_start: 0.7649 (tptp) cc_final: 0.6878 (mmtm) REVERT: B 124 VAL cc_start: 0.7319 (OUTLIER) cc_final: 0.7048 (p) REVERT: B 227 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8467 (m-30) REVERT: B 494 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7695 (mtm-85) REVERT: B 692 HIS cc_start: 0.7523 (t-90) cc_final: 0.7282 (t-90) REVERT: B 695 LYS cc_start: 0.8105 (tmtt) cc_final: 0.7293 (mmtm) REVERT: C 233 GLU cc_start: 0.8571 (tt0) cc_final: 0.8329 (mp0) REVERT: C 438 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7456 (mp10) REVERT: C 695 LYS cc_start: 0.7703 (tttt) cc_final: 0.7114 (mttt) REVERT: E 3 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7819 (mm-40) REVERT: F 3 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7757 (mm110) outliers start: 21 outliers final: 14 residues processed: 209 average time/residue: 0.6325 time to fit residues: 150.0708 Evaluate side-chains 211 residues out of total 1809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 139 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN B 126 GLN B 141 ASN C 141 ASN D 3 GLN E 39 GLN F 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.179831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.115593 restraints weight = 17415.543| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.44 r_work: 0.3160 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17263 Z= 0.230 Angle : 0.608 8.895 23445 Z= 0.336 Chirality : 0.045 0.147 2527 Planarity : 0.005 0.042 3061 Dihedral : 5.498 57.057 2379 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.16 % Allowed : 9.07 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.20 (0.18), residues: 2081 helix: 1.74 (0.30), residues: 303 sheet: -0.14 (0.18), residues: 709 loop : -0.03 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 215 TYR 0.014 0.002 TYR B 380 PHE 0.022 0.002 PHE A 287 TRP 0.010 0.002 TRP C 354 HIS 0.008 0.002 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00501 (17245) covalent geometry : angle 0.60700 (23409) SS BOND : bond 0.00519 ( 18) SS BOND : angle 1.19042 ( 36) hydrogen bonds : bond 0.04965 ( 710) hydrogen bonds : angle 5.82914 ( 2118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11566.56 seconds wall clock time: 196 minutes 48.95 seconds (11808.95 seconds total)