Starting phenix.real_space_refine on Mon Jul 6 02:06:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9raf_53876/07_2026/9raf_53876.cif Found real_map, /net/cci-nas-00/data/ceres_data/9raf_53876/07_2026/9raf_53876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9raf_53876/07_2026/9raf_53876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9raf_53876/07_2026/9raf_53876.map" model { file = "/net/cci-nas-00/data/ceres_data/9raf_53876/07_2026/9raf_53876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9raf_53876/07_2026/9raf_53876.cif" } resolution = 2.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 86 5.49 5 Mg 3 5.21 5 S 103 5.16 5 C 9557 2.51 5 N 2725 2.21 5 O 3859 1.98 5 H 14762 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31095 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 11606 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 716, 11546 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 33, 'TRANS': 682} Conformer: "B" Number of residues, atoms: 716, 11546 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 33, 'TRANS': 682} bond proxies already assigned to first conformer: 11607 Chain: "C" Number of atoms: 4139 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 250, 4107 Classifications: {'peptide': 250} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 250, 4107 Classifications: {'peptide': 250} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 237} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 4113 Chain: "G" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 351 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 7, 'TRANS': 17} Chain: "M" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 422 Classifications: {'RNA': 13} Modifications used: {'3*END': 1, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna3p': 12} Chain: "B" Number of atoms: 11679 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 725, 11589 Classifications: {'peptide': 725} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 694} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 725, 11589 Classifications: {'peptide': 725} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 694} Chain breaks: 3 bond proxies already assigned to first conformer: 11606 Chain: "T" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 2243 Classifications: {'RNA': 70} Modifications used: {'3*END': 1, 'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 27, 'rna3p_pyr': 25} Link IDs: {'rna2p': 17, 'rna3p': 52} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 226 Classifications: {'water': 226} Link IDs: {None: 225} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "M" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 254 Classifications: {'water': 254} Link IDs: {None: 253} Chain: "T" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ALYS A 378 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS A 378 " occ=0.50 residue: pdb=" N AILE A 465 " occ=0.50 ... (36 atoms not shown) pdb="HD13BILE A 465 " occ=0.50 residue: pdb=" N AVAL A 557 " occ=0.60 ... (30 atoms not shown) pdb="HG23BVAL A 557 " occ=0.40 residue: pdb=" N AMET C 50 " occ=0.50 ... (32 atoms not shown) pdb=" HE3BMET C 50 " occ=0.50 residue: pdb=" N AASN C 148 " occ=0.40 ... (26 atoms not shown) pdb="HD22BASN C 148 " occ=0.60 residue: pdb=" N AILE B 322 " occ=0.50 ... (36 atoms not shown) pdb="HD13BILE B 322 " occ=0.50 residue: pdb=" N AARG B 334 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG B 334 " occ=0.50 residue: pdb=" N ALEU B 337 " occ=0.50 ... (36 atoms not shown) pdb="HD23BLEU B 337 " occ=0.50 residue: pdb=" N AARG B 350 " occ=0.60 ... (46 atoms not shown) pdb="HH22BARG B 350 " occ=0.40 Time building chain proxies: 8.92, per 1000 atoms: 0.29 Number of scatterers: 31095 At special positions: 0 Unit cell: (100.74, 102.2, 143.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 103 16.00 P 86 15.00 Mg 3 11.99 O 3859 8.00 N 2725 7.00 C 9557 6.00 H 14762 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.2 seconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3264 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 16 sheets defined 53.9% alpha, 12.8% beta 24 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 5.70 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 24 removed outlier: 4.055A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 139 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 195 through 200 removed outlier: 3.831A pdb=" N GLU A 199 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR A 200 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.961A pdb=" N PHE A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 removed outlier: 3.694A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.657A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 529 through 538 Proline residue: A 534 - end of helix removed outlier: 3.546A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 582 through 604 removed outlier: 3.970A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.934A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 697 through 715 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.668A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 24 through 37 removed outlier: 3.622A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.649A pdb=" N MET C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.699A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.767A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 231 removed outlier: 3.897A pdb=" N VAL C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.686A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 176 removed outlier: 3.619A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 265 removed outlier: 4.225A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 294 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.487A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.034A pdb=" N TYR B 380 " --> pdb=" O ASP B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 473 Processing helix chain 'B' and resid 505 through 512 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.977A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 685 through 700 removed outlier: 3.725A pdb=" N TYR B 689 " --> pdb=" O ASP B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.357A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 Processing helix chain 'B' and resid 736 through 756 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.481A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.253A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY A 555 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG A 551 " --> pdb=" O GLY A 555 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N AVAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU A 549 " --> pdb=" O AVAL A 557 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU A 544 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 11.428A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.285A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 379 removed outlier: 4.359A pdb=" N GLN B 367 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 628 through 631 removed outlier: 6.035A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 80 removed outlier: 4.482A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.596A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.600A pdb=" N LYS C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AB3, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB5, first strand: chain 'B' and resid 187 through 188 Processing sheet with id=AB6, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.917A pdb=" N LEU B 224 " --> pdb=" O AARG B 350 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 489 through 492 736 hydrogen bonds defined for protein. 2038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 6.87 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14733 1.03 - 1.23: 64 1.23 - 1.42: 6898 1.42 - 1.62: 9068 1.62 - 1.81: 177 Bond restraints: 30940 Sorted by residual: bond pdb=" C ARG C 46 " pdb=" O ARG C 46 " ideal model delta sigma weight residual 1.236 1.129 0.108 1.15e-02 7.56e+03 8.82e+01 bond pdb=" N ARG C 46 " pdb=" H ARG C 46 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" C LEU C 45 " pdb=" N ARG C 46 " ideal model delta sigma weight residual 1.334 1.309 0.026 1.27e-02 6.20e+03 4.08e+00 bond pdb=" NE ARG C 46 " pdb=" HE ARG C 46 " ideal model delta sigma weight residual 0.860 0.900 -0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" NH2 ARG C 46 " pdb="HH21 ARG C 46 " ideal model delta sigma weight residual 0.860 0.899 -0.039 2.00e-02 2.50e+03 3.79e+00 ... (remaining 30935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 51136 0.91 - 1.81: 4258 1.81 - 2.72: 335 2.72 - 3.63: 145 3.63 - 4.54: 16 Bond angle restraints: 55890 Sorted by residual: angle pdb=" CA ARG C 46 " pdb=" C ARG C 46 " pdb=" N MET C 47 " ideal model delta sigma weight residual 117.07 121.61 -4.54 1.14e+00 7.69e-01 1.58e+01 angle pdb=" CA ARG C 46 " pdb=" C ARG C 46 " pdb=" O ARG C 46 " ideal model delta sigma weight residual 120.82 116.83 3.99 1.05e+00 9.07e-01 1.44e+01 angle pdb=" N ARG C 46 " pdb=" CA ARG C 46 " pdb=" C ARG C 46 " ideal model delta sigma weight residual 111.07 107.05 4.02 1.07e+00 8.73e-01 1.41e+01 angle pdb=" O2 C T 57 " pdb=" C2 C T 57 " pdb=" N3 C T 57 " ideal model delta sigma weight residual 121.90 119.33 2.57 7.00e-01 2.04e+00 1.35e+01 angle pdb=" N1 G T 62 " pdb=" C2 G T 62 " pdb=" N2 G T 62 " ideal model delta sigma weight residual 116.20 113.43 2.77 9.00e-01 1.23e+00 9.45e+00 ... (remaining 55885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.32: 13981 34.32 - 68.64: 634 68.64 - 102.96: 56 102.96 - 137.27: 0 137.27 - 171.59: 4 Dihedral angle restraints: 14675 sinusoidal: 8793 harmonic: 5882 Sorted by residual: dihedral pdb=" O4' C T 47 " pdb=" C1' C T 47 " pdb=" N1 C T 47 " pdb=" C2 C T 47 " ideal model delta sinusoidal sigma weight residual 200.00 41.80 158.20 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" C4' U T 46 " pdb=" C3' U T 46 " pdb=" O3' U T 46 " pdb=" P C T 47 " ideal model delta sinusoidal sigma weight residual -110.00 61.59 -171.59 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' U T 15 " pdb=" C3' U T 15 " pdb=" O3' U T 15 " pdb=" P C T 16 " ideal model delta sinusoidal sigma weight residual 220.00 49.63 170.37 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 14672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1771 0.032 - 0.065: 534 0.065 - 0.097: 121 0.097 - 0.130: 64 0.130 - 0.162: 8 Chirality restraints: 2498 Sorted by residual: chirality pdb=" C1' A T 4 " pdb=" O4' A T 4 " pdb=" C2' A T 4 " pdb=" N9 A T 4 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA ILE C 67 " pdb=" N ILE C 67 " pdb=" C ILE C 67 " pdb=" CB ILE C 67 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA ILE B 606 " pdb=" N ILE B 606 " pdb=" C ILE B 606 " pdb=" CB ILE B 606 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 2495 not shown) Planarity restraints: 4265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A T 4 " 0.029 2.00e-02 2.50e+03 1.16e-02 4.38e+00 pdb=" N9 A T 4 " -0.028 2.00e-02 2.50e+03 pdb=" C8 A T 4 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A T 4 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A T 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A T 4 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A T 4 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A T 4 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A T 4 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A T 4 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A T 4 " -0.003 2.00e-02 2.50e+03 pdb=" H8 A T 4 " -0.001 2.00e-02 2.50e+03 pdb=" H2 A T 4 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A T 7 " 0.026 2.00e-02 2.50e+03 1.05e-02 3.57e+00 pdb=" N9 A T 7 " -0.026 2.00e-02 2.50e+03 pdb=" C8 A T 7 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A T 7 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A T 7 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A T 7 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A T 7 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A T 7 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A T 7 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A T 7 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A T 7 " -0.005 2.00e-02 2.50e+03 pdb=" H8 A T 7 " 0.000 2.00e-02 2.50e+03 pdb=" H2 A T 7 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C T 43 " -0.023 2.00e-02 2.50e+03 1.01e-02 2.81e+00 pdb=" N1 C T 43 " 0.023 2.00e-02 2.50e+03 pdb=" C2 C T 43 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C T 43 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C T 43 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C T 43 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C T 43 " -0.005 2.00e-02 2.50e+03 pdb=" C5 C T 43 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C T 43 " 0.004 2.00e-02 2.50e+03 pdb=" H5 C T 43 " -0.004 2.00e-02 2.50e+03 pdb=" H6 C T 43 " 0.005 2.00e-02 2.50e+03 ... (remaining 4262 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 1168 2.15 - 2.76: 57214 2.76 - 3.37: 93755 3.37 - 3.99: 126465 3.99 - 4.60: 192371 Nonbonded interactions: 470973 Sorted by model distance: nonbonded pdb=" N3 C T 29 " pdb=" H1 G T 51 " model vdw 1.532 2.600 nonbonded pdb=" OD1 ASP A 55 " pdb=" H GLU A 59 " model vdw 1.631 2.450 nonbonded pdb=" O2 C T 29 " pdb=" H21 G T 51 " model vdw 1.643 2.450 nonbonded pdb=" OE1 GLU A 166 " pdb="HH12 ARG A 170 " model vdw 1.649 2.450 nonbonded pdb=" HE ARG C 101 " pdb=" OE1 GLU B 575 " model vdw 1.650 2.450 ... (remaining 470968 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.40 max=1.00 mean=0.99 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: 7.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 37.540 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.003 0.108 16178 Z= 0.160 Angle : 0.448 4.537 22248 Z= 0.276 Chirality : 0.036 0.162 2498 Planarity : 0.003 0.034 2559 Dihedral : 18.575 171.592 6760 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.97 % Allowed : 11.50 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.21), residues: 1720 helix: 2.17 (0.18), residues: 828 sheet: -0.09 (0.38), residues: 194 loop : 0.29 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 46 TYR 0.019 0.001 TYR B 557 PHE 0.010 0.001 PHE B 551 TRP 0.013 0.001 TRP C 49 HIS 0.003 0.001 HIS B 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 (16178) covalent geometry : angle 0.44839 / 0.28 (22248) hydrogen bonds : bond 0.13146 / 9.06 ( 796) hydrogen bonds : angle 5.28415 / 3.77 ( 2158) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 273 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7837 (mttt) cc_final: 0.7549 (mtmp) REVERT: A 31 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7334 (mm-30) REVERT: A 33 ASN cc_start: 0.8178 (m-40) cc_final: 0.7892 (m110) REVERT: A 119 GLU cc_start: 0.7911 (tp30) cc_final: 0.7675 (tp30) REVERT: A 179 ARG cc_start: 0.7489 (ttt180) cc_final: 0.7257 (ttt-90) REVERT: A 202 GLU cc_start: 0.7271 (pt0) cc_final: 0.7028 (pp20) REVERT: A 243 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7736 (mp0) REVERT: A 256 ARG cc_start: 0.8352 (ttt180) cc_final: 0.7990 (ttp80) REVERT: A 353 LYS cc_start: 0.6164 (OUTLIER) cc_final: 0.5823 (tppt) REVERT: A 374 MET cc_start: 0.8296 (mmm) cc_final: 0.8095 (mmt) REVERT: A 397 GLU cc_start: 0.7633 (pt0) cc_final: 0.7080 (tt0) REVERT: A 399 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7375 (tm-30) REVERT: A 430 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7735 (pt0) REVERT: A 492 LYS cc_start: 0.8185 (pttt) cc_final: 0.7968 (pttp) REVERT: A 495 ARG cc_start: 0.7850 (ptp-170) cc_final: 0.7404 (ptm160) REVERT: A 497 LYS cc_start: 0.8919 (tttt) cc_final: 0.8666 (tttp) REVERT: A 512 ARG cc_start: 0.6948 (mtt180) cc_final: 0.6454 (mpp80) REVERT: A 551 ARG cc_start: 0.7055 (mtt180) cc_final: 0.6588 (mtp-110) REVERT: A 572 LYS cc_start: 0.8291 (mttt) cc_final: 0.8083 (mmmm) REVERT: C 18 GLU cc_start: 0.7431 (tt0) cc_final: 0.6850 (tp30) REVERT: C 21 THR cc_start: 0.8441 (m) cc_final: 0.8205 (p) REVERT: C 22 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7342 (ttpp) REVERT: C 48 LYS cc_start: 0.8015 (mttt) cc_final: 0.7486 (mmtm) REVERT: C 116 LYS cc_start: 0.8361 (tttt) cc_final: 0.8128 (tttm) REVERT: C 157 LYS cc_start: 0.7769 (mtmt) cc_final: 0.6910 (mmtt) REVERT: C 181 SER cc_start: 0.7965 (p) cc_final: 0.7667 (t) REVERT: C 187 LYS cc_start: 0.7800 (tttt) cc_final: 0.7586 (ttmm) REVERT: C 191 LYS cc_start: 0.7525 (tttt) cc_final: 0.7143 (ttmm) REVERT: B 78 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7945 (mm-30) REVERT: B 104 GLU cc_start: 0.7709 (tt0) cc_final: 0.7195 (tm-30) REVERT: B 208 LYS cc_start: 0.7799 (mttt) cc_final: 0.7180 (tptt) REVERT: B 267 GLU cc_start: 0.8016 (tp30) cc_final: 0.7640 (mm-30) REVERT: B 289 MET cc_start: 0.8471 (mmm) cc_final: 0.8103 (mmm) REVERT: B 290 MET cc_start: 0.7196 (mmm) cc_final: 0.6805 (mtp) REVERT: B 387 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7259 (mp0) REVERT: B 391 LYS cc_start: 0.8458 (tptp) cc_final: 0.7976 (tppt) REVERT: B 414 MET cc_start: 0.8655 (mtm) cc_final: 0.8423 (mtm) REVERT: B 457 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7275 (mp0) REVERT: B 571 ARG cc_start: 0.8430 (ttt-90) cc_final: 0.8043 (ttt-90) REVERT: B 618 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7837 (mm-30) REVERT: B 694 ASN cc_start: 0.8152 (m-40) cc_final: 0.7815 (m-40) REVERT: B 716 GLU cc_start: 0.7499 (tt0) cc_final: 0.7120 (tp30) REVERT: B 734 ARG cc_start: 0.7997 (mtm180) cc_final: 0.7750 (mtm-85) REVERT: B 754 ARG cc_start: 0.7580 (ttp80) cc_final: 0.7320 (ttp-110) outliers start: 15 outliers final: 6 residues processed: 285 average time/residue: 1.5714 time to fit residues: 488.3905 Evaluate side-chains 225 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 218 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 446 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 248 GLN A 388 ASN A 556 GLN B 284 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104414 restraints weight = 90617.544| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.13 r_work: 0.3066 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16178 Z= 0.177 Angle : 0.535 5.140 22248 Z= 0.296 Chirality : 0.039 0.172 2498 Planarity : 0.004 0.039 2559 Dihedral : 17.313 178.225 3217 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.97 % Allowed : 13.32 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1720 helix: 1.97 (0.18), residues: 842 sheet: -0.17 (0.38), residues: 197 loop : 0.12 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 582 TYR 0.026 0.002 TYR B 557 PHE 0.015 0.002 PHE A 381 TRP 0.013 0.002 TRP B 309 HIS 0.004 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (16178) covalent geometry : angle 0.53532 / 0.30 (22248) hydrogen bonds : bond 0.06290 / 4.32 ( 796) hydrogen bonds : angle 4.81171 / 3.46 ( 2158) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 224 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7488 (mm-30) REVERT: A 33 ASN cc_start: 0.8417 (m-40) cc_final: 0.8135 (m110) REVERT: A 49 SER cc_start: 0.8243 (p) cc_final: 0.8031 (t) REVERT: A 353 LYS cc_start: 0.6195 (OUTLIER) cc_final: 0.5970 (tppt) REVERT: A 382 GLU cc_start: 0.7615 (mp0) cc_final: 0.7140 (mm-30) REVERT: A 397 GLU cc_start: 0.7991 (pt0) cc_final: 0.7686 (tt0) REVERT: A 399 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8022 (tm-30) REVERT: A 495 ARG cc_start: 0.8028 (ptp-170) cc_final: 0.7687 (ptm160) REVERT: A 497 LYS cc_start: 0.9075 (tttt) cc_final: 0.8826 (tttt) REVERT: A 512 ARG cc_start: 0.7119 (mtt180) cc_final: 0.6816 (mpp80) REVERT: A 551 ARG cc_start: 0.7105 (mtt180) cc_final: 0.6871 (mtp-110) REVERT: C 11 MET cc_start: 0.8690 (mmm) cc_final: 0.8365 (mmm) REVERT: C 18 GLU cc_start: 0.7469 (tt0) cc_final: 0.7192 (tp30) REVERT: C 22 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7835 (ttpp) REVERT: C 48 LYS cc_start: 0.8231 (mttt) cc_final: 0.8023 (mmtm) REVERT: C 157 LYS cc_start: 0.8168 (mtmt) cc_final: 0.7596 (mmtt) REVERT: C 191 LYS cc_start: 0.7651 (tttt) cc_final: 0.7431 (ttmm) REVERT: C 217 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8862 (m-80) REVERT: B 104 GLU cc_start: 0.7996 (tt0) cc_final: 0.7780 (tm-30) REVERT: B 148 GLU cc_start: 0.8609 (tp30) cc_final: 0.8182 (tp30) REVERT: B 208 LYS cc_start: 0.8034 (mttt) cc_final: 0.7554 (tptt) REVERT: B 228 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8209 (m) REVERT: B 267 GLU cc_start: 0.8222 (tp30) cc_final: 0.8018 (mm-30) REVERT: B 289 MET cc_start: 0.8718 (mmm) cc_final: 0.8396 (mmm) REVERT: B 290 MET cc_start: 0.7222 (mmm) cc_final: 0.6961 (mtp) REVERT: B 387 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7817 (mp0) REVERT: B 391 LYS cc_start: 0.8720 (tptp) cc_final: 0.8170 (tmtt) REVERT: B 414 MET cc_start: 0.8899 (mtm) cc_final: 0.8684 (mtm) REVERT: B 457 GLU cc_start: 0.8234 (mt-10) cc_final: 0.8022 (mp0) REVERT: B 546 MET cc_start: 0.9202 (mtp) cc_final: 0.8969 (mtp) REVERT: B 571 ARG cc_start: 0.8580 (ttt-90) cc_final: 0.8353 (ttt-90) REVERT: B 694 ASN cc_start: 0.8520 (m-40) cc_final: 0.8191 (m-40) REVERT: B 742 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6905 (mm-30) outliers start: 15 outliers final: 5 residues processed: 233 average time/residue: 1.5898 time to fit residues: 405.0214 Evaluate side-chains 212 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 203 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 742 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 40 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 556 GLN B 532 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.148922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.103881 restraints weight = 85601.544| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.12 r_work: 0.3050 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16178 Z= 0.157 Angle : 0.514 4.965 22248 Z= 0.283 Chirality : 0.038 0.158 2498 Planarity : 0.004 0.040 2559 Dihedral : 17.305 179.722 3213 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.04 % Allowed : 14.23 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.20), residues: 1720 helix: 1.90 (0.18), residues: 842 sheet: -0.24 (0.37), residues: 197 loop : 0.06 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 582 TYR 0.025 0.002 TYR B 557 PHE 0.013 0.001 PHE B 551 TRP 0.014 0.002 TRP B 309 HIS 0.004 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (16178) covalent geometry : angle 0.51361 / 0.28 (22248) hydrogen bonds : bond 0.06103 / 4.18 ( 796) hydrogen bonds : angle 4.72432 / 3.39 ( 2158) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7535 (mm-30) REVERT: A 33 ASN cc_start: 0.8408 (m-40) cc_final: 0.8123 (m110) REVERT: A 49 SER cc_start: 0.8237 (p) cc_final: 0.8013 (t) REVERT: A 353 LYS cc_start: 0.6234 (OUTLIER) cc_final: 0.5964 (tppt) REVERT: A 361 LYS cc_start: 0.8849 (mttp) cc_final: 0.8341 (mmtm) REVERT: A 382 GLU cc_start: 0.7673 (mp0) cc_final: 0.7168 (mm-30) REVERT: A 397 GLU cc_start: 0.7979 (pt0) cc_final: 0.7667 (tt0) REVERT: A 399 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7998 (tm-30) REVERT: A 495 ARG cc_start: 0.8023 (ptp-170) cc_final: 0.7690 (ptm160) REVERT: A 512 ARG cc_start: 0.7136 (mtt180) cc_final: 0.6840 (mpp80) REVERT: C 11 MET cc_start: 0.8684 (mmm) cc_final: 0.8445 (mmm) REVERT: C 22 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7856 (ttpp) REVERT: C 48 LYS cc_start: 0.8274 (mttt) cc_final: 0.8044 (mmtm) REVERT: C 157 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7609 (mmtt) REVERT: C 191 LYS cc_start: 0.7677 (tttt) cc_final: 0.7452 (ttmm) REVERT: C 217 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8873 (m-80) REVERT: B 104 GLU cc_start: 0.8027 (tt0) cc_final: 0.7781 (tm-30) REVERT: B 148 GLU cc_start: 0.8618 (tp30) cc_final: 0.8169 (tp30) REVERT: B 208 LYS cc_start: 0.8015 (mttt) cc_final: 0.7536 (tptt) REVERT: B 267 GLU cc_start: 0.8219 (tp30) cc_final: 0.7999 (mm-30) REVERT: B 289 MET cc_start: 0.8729 (mmm) cc_final: 0.8400 (mmm) REVERT: B 290 MET cc_start: 0.7186 (mmm) cc_final: 0.6979 (mtp) REVERT: B 387 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7824 (mp0) REVERT: B 391 LYS cc_start: 0.8726 (tptp) cc_final: 0.8158 (tmtt) REVERT: B 546 MET cc_start: 0.9201 (mtp) cc_final: 0.8974 (mtp) REVERT: B 694 ASN cc_start: 0.8525 (m-40) cc_final: 0.8191 (m-40) outliers start: 16 outliers final: 8 residues processed: 218 average time/residue: 1.6364 time to fit residues: 389.6458 Evaluate side-chains 210 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 200 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain B residue 364 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 388 ASN B 284 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.149182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104371 restraints weight = 81649.946| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.12 r_work: 0.3038 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16178 Z= 0.144 Angle : 0.508 5.008 22248 Z= 0.279 Chirality : 0.038 0.160 2498 Planarity : 0.004 0.040 2559 Dihedral : 17.301 179.124 3213 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.10 % Allowed : 14.49 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1720 helix: 1.92 (0.18), residues: 841 sheet: -0.34 (0.37), residues: 198 loop : 0.04 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 249 TYR 0.024 0.002 TYR B 557 PHE 0.012 0.001 PHE B 551 TRP 0.013 0.002 TRP C 49 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (16178) covalent geometry : angle 0.50841 / 0.28 (22248) hydrogen bonds : bond 0.05842 / 4.01 ( 796) hydrogen bonds : angle 4.67100 / 3.36 ( 2158) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7522 (mm-30) REVERT: A 33 ASN cc_start: 0.8404 (m-40) cc_final: 0.8117 (m110) REVERT: A 353 LYS cc_start: 0.6239 (OUTLIER) cc_final: 0.5956 (tppt) REVERT: A 361 LYS cc_start: 0.8859 (mttp) cc_final: 0.8345 (mmtm) REVERT: A 382 GLU cc_start: 0.7649 (mp0) cc_final: 0.7112 (mm-30) REVERT: A 397 GLU cc_start: 0.7955 (pt0) cc_final: 0.7658 (tt0) REVERT: A 399 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8003 (tm-30) REVERT: A 495 ARG cc_start: 0.8009 (ptp-170) cc_final: 0.7669 (ptm160) REVERT: A 512 ARG cc_start: 0.7144 (mtt180) cc_final: 0.6830 (mpp80) REVERT: C 11 MET cc_start: 0.8660 (mmm) cc_final: 0.8334 (mmm) REVERT: C 22 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7873 (ttpp) REVERT: C 48 LYS cc_start: 0.8279 (mttt) cc_final: 0.8047 (mmtm) REVERT: C 157 LYS cc_start: 0.8201 (mtmt) cc_final: 0.7586 (mmtt) REVERT: C 191 LYS cc_start: 0.7686 (tttt) cc_final: 0.7450 (ttmm) REVERT: C 217 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8881 (m-80) REVERT: B 104 GLU cc_start: 0.8037 (tt0) cc_final: 0.7800 (tm-30) REVERT: B 148 GLU cc_start: 0.8601 (tp30) cc_final: 0.8166 (tp30) REVERT: B 159 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7915 (mt-10) REVERT: B 208 LYS cc_start: 0.7996 (mttt) cc_final: 0.7513 (tptt) REVERT: B 267 GLU cc_start: 0.8223 (tp30) cc_final: 0.8004 (mm-30) REVERT: B 289 MET cc_start: 0.8721 (mmm) cc_final: 0.8378 (mmm) REVERT: B 290 MET cc_start: 0.7175 (mmm) cc_final: 0.6957 (mtp) REVERT: B 363 LYS cc_start: 0.8049 (tttm) cc_final: 0.7779 (tptm) REVERT: B 387 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7812 (mp0) REVERT: B 391 LYS cc_start: 0.8711 (tptp) cc_final: 0.8143 (tmtt) REVERT: B 546 MET cc_start: 0.9188 (mtp) cc_final: 0.8974 (mtp) outliers start: 17 outliers final: 5 residues processed: 210 average time/residue: 1.5993 time to fit residues: 369.6592 Evaluate side-chains 205 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 198 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 166 optimal weight: 0.7980 chunk 118 optimal weight: 0.1980 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.149094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104192 restraints weight = 83453.104| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.08 r_work: 0.3045 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16178 Z= 0.145 Angle : 0.508 5.662 22248 Z= 0.278 Chirality : 0.038 0.156 2498 Planarity : 0.004 0.041 2559 Dihedral : 17.295 178.662 3213 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.17 % Allowed : 14.55 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.20), residues: 1720 helix: 1.90 (0.18), residues: 841 sheet: -0.40 (0.36), residues: 198 loop : 0.03 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 249 TYR 0.024 0.002 TYR B 557 PHE 0.012 0.001 PHE B 551 TRP 0.014 0.002 TRP C 49 HIS 0.004 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (16178) covalent geometry : angle 0.50798 / 0.28 (22248) hydrogen bonds : bond 0.05792 / 3.97 ( 796) hydrogen bonds : angle 4.65165 / 3.34 ( 2158) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.8411 (m-40) cc_final: 0.8113 (m110) REVERT: A 382 GLU cc_start: 0.7661 (mp0) cc_final: 0.7132 (mm-30) REVERT: A 397 GLU cc_start: 0.7967 (pt0) cc_final: 0.7672 (tt0) REVERT: A 399 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8010 (tm-30) REVERT: A 495 ARG cc_start: 0.8027 (ptp-170) cc_final: 0.7691 (ptm160) REVERT: A 512 ARG cc_start: 0.7135 (mtt180) cc_final: 0.6831 (mpp80) REVERT: C 1 MET cc_start: 0.7059 (tpt) cc_final: 0.6807 (tpt) REVERT: C 22 LYS cc_start: 0.8312 (mmtt) cc_final: 0.7913 (ttpp) REVERT: C 48 LYS cc_start: 0.8292 (mttt) cc_final: 0.8070 (mmtm) REVERT: C 157 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7578 (mmtt) REVERT: C 191 LYS cc_start: 0.7687 (tttt) cc_final: 0.7464 (ttmm) REVERT: C 217 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8928 (m-80) REVERT: B 104 GLU cc_start: 0.8051 (tt0) cc_final: 0.7814 (tm-30) REVERT: B 148 GLU cc_start: 0.8603 (tp30) cc_final: 0.8168 (tp30) REVERT: B 208 LYS cc_start: 0.8016 (mttt) cc_final: 0.7551 (tptt) REVERT: B 228 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8220 (m) REVERT: B 267 GLU cc_start: 0.8201 (tp30) cc_final: 0.7976 (mm-30) REVERT: B 289 MET cc_start: 0.8717 (mmm) cc_final: 0.8375 (mmm) REVERT: B 290 MET cc_start: 0.7133 (mmm) cc_final: 0.6916 (mtp) REVERT: B 363 LYS cc_start: 0.8059 (tttm) cc_final: 0.7776 (tptm) REVERT: B 387 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7822 (mp0) REVERT: B 391 LYS cc_start: 0.8719 (tptp) cc_final: 0.8148 (tmtt) REVERT: B 546 MET cc_start: 0.9188 (mtp) cc_final: 0.8977 (mtp) REVERT: B 685 ASP cc_start: 0.7761 (p0) cc_final: 0.7465 (p0) outliers start: 18 outliers final: 8 residues processed: 210 average time/residue: 1.6818 time to fit residues: 385.5133 Evaluate side-chains 206 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 364 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 156 optimal weight: 2.9990 chunk 101 optimal weight: 0.0000 chunk 7 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.148735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107202 restraints weight = 77280.213| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.72 r_work: 0.3085 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16178 Z= 0.140 Angle : 0.504 4.840 22248 Z= 0.276 Chirality : 0.038 0.158 2498 Planarity : 0.004 0.042 2559 Dihedral : 17.282 178.374 3209 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.84 % Allowed : 14.81 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.20), residues: 1720 helix: 1.90 (0.18), residues: 841 sheet: -0.34 (0.36), residues: 196 loop : -0.01 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 249 TYR 0.023 0.002 TYR B 557 PHE 0.012 0.001 PHE B 551 TRP 0.014 0.002 TRP C 49 HIS 0.003 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (16178) covalent geometry : angle 0.50421 / 0.28 (22248) hydrogen bonds : bond 0.05703 / 3.91 ( 796) hydrogen bonds : angle 4.63390 / 3.33 ( 2158) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.8427 (m-40) cc_final: 0.8140 (m110) REVERT: A 397 GLU cc_start: 0.7934 (pt0) cc_final: 0.7685 (tt0) REVERT: A 399 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8021 (tm-30) REVERT: A 495 ARG cc_start: 0.7972 (ptp-170) cc_final: 0.7633 (ptm160) REVERT: A 512 ARG cc_start: 0.7117 (mtt180) cc_final: 0.6826 (mpp80) REVERT: C 11 MET cc_start: 0.8615 (mmm) cc_final: 0.8395 (mmm) REVERT: C 22 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7915 (ttpp) REVERT: C 157 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7572 (mmtt) REVERT: C 191 LYS cc_start: 0.7693 (tttt) cc_final: 0.7469 (ttmm) REVERT: B 104 GLU cc_start: 0.8000 (tt0) cc_final: 0.7789 (tm-30) REVERT: B 148 GLU cc_start: 0.8575 (tp30) cc_final: 0.8140 (tp30) REVERT: B 208 LYS cc_start: 0.8007 (mttt) cc_final: 0.7565 (tptt) REVERT: B 267 GLU cc_start: 0.8161 (tp30) cc_final: 0.7942 (mm-30) REVERT: B 284 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8238 (m110) REVERT: B 289 MET cc_start: 0.8710 (mmm) cc_final: 0.8352 (mmm) REVERT: B 290 MET cc_start: 0.7094 (mmm) cc_final: 0.6842 (mtp) REVERT: B 363 LYS cc_start: 0.8045 (tttm) cc_final: 0.7763 (tptm) REVERT: B 387 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7793 (mp0) REVERT: B 391 LYS cc_start: 0.8706 (tptp) cc_final: 0.8149 (tmtt) REVERT: B 546 MET cc_start: 0.9189 (mtp) cc_final: 0.8978 (mtp) REVERT: B 682 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.7954 (mp) REVERT: B 685 ASP cc_start: 0.7755 (p0) cc_final: 0.7462 (p0) outliers start: 13 outliers final: 5 residues processed: 205 average time/residue: 1.6761 time to fit residues: 376.1229 Evaluate side-chains 202 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 195 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 682 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 120 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 388 ASN B 284 ASN B 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104769 restraints weight = 86403.711| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.02 r_work: 0.3032 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16178 Z= 0.155 Angle : 0.516 4.948 22248 Z= 0.282 Chirality : 0.038 0.154 2498 Planarity : 0.004 0.044 2559 Dihedral : 17.260 178.223 3205 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.78 % Allowed : 15.01 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.20), residues: 1720 helix: 1.85 (0.18), residues: 841 sheet: -0.27 (0.37), residues: 192 loop : 0.01 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 249 TYR 0.024 0.002 TYR B 557 PHE 0.021 0.001 PHE A 46 TRP 0.014 0.002 TRP C 49 HIS 0.004 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (16178) covalent geometry : angle 0.51577 / 0.28 (22248) hydrogen bonds : bond 0.05818 / 3.98 ( 796) hydrogen bonds : angle 4.65222 / 3.35 ( 2158) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.8439 (m-40) cc_final: 0.8146 (m110) REVERT: A 382 GLU cc_start: 0.7679 (mp0) cc_final: 0.7203 (mm-30) REVERT: A 397 GLU cc_start: 0.7992 (pt0) cc_final: 0.7678 (tt0) REVERT: A 399 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7997 (tm-30) REVERT: A 495 ARG cc_start: 0.8026 (ptp-170) cc_final: 0.7688 (ptm160) REVERT: A 512 ARG cc_start: 0.7145 (mtt180) cc_final: 0.6822 (mpp80) REVERT: C 11 MET cc_start: 0.8637 (mmm) cc_final: 0.8395 (mmm) REVERT: C 22 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7924 (ttpp) REVERT: C 157 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7591 (mmtt) REVERT: C 191 LYS cc_start: 0.7701 (tttt) cc_final: 0.7466 (ttmm) REVERT: B 104 GLU cc_start: 0.8058 (tt0) cc_final: 0.7820 (tm-30) REVERT: B 148 GLU cc_start: 0.8607 (tp30) cc_final: 0.8192 (tp30) REVERT: B 208 LYS cc_start: 0.8013 (mttt) cc_final: 0.7546 (tptt) REVERT: B 267 GLU cc_start: 0.8191 (tp30) cc_final: 0.7963 (mm-30) REVERT: B 289 MET cc_start: 0.8718 (mmm) cc_final: 0.8356 (mmm) REVERT: B 290 MET cc_start: 0.7106 (mmm) cc_final: 0.6866 (mtp) REVERT: B 363 LYS cc_start: 0.8057 (tttm) cc_final: 0.7782 (tptm) REVERT: B 387 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7816 (mp0) REVERT: B 391 LYS cc_start: 0.8726 (tptp) cc_final: 0.8157 (tmtt) REVERT: B 546 MET cc_start: 0.9200 (mtp) cc_final: 0.8983 (mtp) REVERT: B 682 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.7961 (mp) REVERT: B 683 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8151 (mt) REVERT: B 685 ASP cc_start: 0.7773 (p0) cc_final: 0.7508 (p0) outliers start: 12 outliers final: 8 residues processed: 200 average time/residue: 1.7090 time to fit residues: 373.5840 Evaluate side-chains 205 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 683 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 142 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.147702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.104801 restraints weight = 80650.335| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.70 r_work: 0.3049 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16178 Z= 0.166 Angle : 0.527 5.090 22248 Z= 0.289 Chirality : 0.038 0.152 2498 Planarity : 0.004 0.048 2559 Dihedral : 17.272 178.035 3204 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.91 % Allowed : 15.01 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.20), residues: 1720 helix: 1.82 (0.18), residues: 840 sheet: -0.47 (0.37), residues: 191 loop : -0.05 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 316 TYR 0.025 0.002 TYR B 557 PHE 0.014 0.002 PHE B 551 TRP 0.015 0.002 TRP C 49 HIS 0.005 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (16178) covalent geometry : angle 0.52743 / 0.29 (22248) hydrogen bonds : bond 0.05950 / 4.06 ( 796) hydrogen bonds : angle 4.68767 / 3.37 ( 2158) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.8417 (m-40) cc_final: 0.8140 (m110) REVERT: A 382 GLU cc_start: 0.7655 (mp0) cc_final: 0.7201 (mm-30) REVERT: A 397 GLU cc_start: 0.7943 (pt0) cc_final: 0.7667 (tt0) REVERT: A 399 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7988 (tm-30) REVERT: A 495 ARG cc_start: 0.7973 (ptp-170) cc_final: 0.7626 (ptm160) REVERT: A 497 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8838 (tttt) REVERT: A 512 ARG cc_start: 0.7092 (mtt180) cc_final: 0.6780 (mpp80) REVERT: C 11 MET cc_start: 0.8624 (mmm) cc_final: 0.8373 (mmm) REVERT: C 22 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7915 (ttpp) REVERT: C 191 LYS cc_start: 0.7704 (tttt) cc_final: 0.7457 (ttmm) REVERT: B 148 GLU cc_start: 0.8565 (tp30) cc_final: 0.8145 (tp30) REVERT: B 208 LYS cc_start: 0.7973 (mttt) cc_final: 0.7500 (tptt) REVERT: B 228 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8224 (m) REVERT: B 267 GLU cc_start: 0.8151 (tp30) cc_final: 0.7925 (mm-30) REVERT: B 289 MET cc_start: 0.8715 (mmm) cc_final: 0.8349 (mmm) REVERT: B 290 MET cc_start: 0.7065 (mmm) cc_final: 0.6844 (mtp) REVERT: B 363 LYS cc_start: 0.8042 (tttm) cc_final: 0.7764 (tptm) REVERT: B 387 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7749 (mp0) REVERT: B 391 LYS cc_start: 0.8693 (tptp) cc_final: 0.8132 (tmtt) REVERT: B 546 MET cc_start: 0.9207 (mtp) cc_final: 0.8984 (mtp) REVERT: B 682 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.7965 (mp) REVERT: B 685 ASP cc_start: 0.7768 (p0) cc_final: 0.7475 (p0) outliers start: 14 outliers final: 7 residues processed: 205 average time/residue: 1.6773 time to fit residues: 375.8824 Evaluate side-chains 204 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 682 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 172 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN B 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103522 restraints weight = 85242.602| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.11 r_work: 0.3022 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16178 Z= 0.157 Angle : 0.522 4.986 22248 Z= 0.286 Chirality : 0.038 0.154 2498 Planarity : 0.004 0.048 2559 Dihedral : 17.268 177.970 3204 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.58 % Allowed : 15.27 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 1720 helix: 1.82 (0.18), residues: 840 sheet: -0.28 (0.37), residues: 192 loop : -0.02 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 269 TYR 0.025 0.002 TYR B 557 PHE 0.024 0.002 PHE A 46 TRP 0.015 0.002 TRP C 49 HIS 0.004 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (16178) covalent geometry : angle 0.52164 / 0.29 (22248) hydrogen bonds : bond 0.05869 / 4.01 ( 796) hydrogen bonds : angle 4.67526 / 3.36 ( 2158) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 193 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.8466 (m-40) cc_final: 0.8185 (m110) REVERT: A 382 GLU cc_start: 0.7710 (mp0) cc_final: 0.7226 (mm-30) REVERT: A 397 GLU cc_start: 0.8001 (pt0) cc_final: 0.7681 (tt0) REVERT: A 399 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7989 (tm-30) REVERT: A 495 ARG cc_start: 0.8015 (ptp-170) cc_final: 0.7675 (ptm160) REVERT: A 512 ARG cc_start: 0.7087 (mtt180) cc_final: 0.6780 (mpp80) REVERT: C 1 MET cc_start: 0.7049 (tpt) cc_final: 0.6837 (tpt) REVERT: C 11 MET cc_start: 0.8632 (mmm) cc_final: 0.8358 (mmm) REVERT: C 22 LYS cc_start: 0.8364 (mmtt) cc_final: 0.7950 (ttpp) REVERT: C 191 LYS cc_start: 0.7711 (tttt) cc_final: 0.7485 (ttmm) REVERT: B 148 GLU cc_start: 0.8610 (tp30) cc_final: 0.8187 (tp30) REVERT: B 208 LYS cc_start: 0.7976 (mttt) cc_final: 0.7495 (tptt) REVERT: B 228 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8218 (m) REVERT: B 267 GLU cc_start: 0.8209 (tp30) cc_final: 0.7973 (mm-30) REVERT: B 289 MET cc_start: 0.8728 (mmm) cc_final: 0.8361 (mmm) REVERT: B 290 MET cc_start: 0.7119 (mmm) cc_final: 0.6899 (mtp) REVERT: B 363 LYS cc_start: 0.8065 (tttm) cc_final: 0.7791 (tptm) REVERT: B 391 LYS cc_start: 0.8730 (tptp) cc_final: 0.8163 (tmtt) REVERT: B 546 MET cc_start: 0.9207 (mtp) cc_final: 0.8987 (mtp) REVERT: B 683 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8130 (mt) REVERT: B 685 ASP cc_start: 0.7783 (p0) cc_final: 0.7516 (p0) outliers start: 9 outliers final: 5 residues processed: 196 average time/residue: 1.5856 time to fit residues: 339.8758 Evaluate side-chains 198 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 191 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 683 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 42 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 85 optimal weight: 0.0570 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 388 ASN B 284 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.106456 restraints weight = 87647.322| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.82 r_work: 0.3046 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16178 Z= 0.141 Angle : 0.510 4.863 22248 Z= 0.279 Chirality : 0.038 0.156 2498 Planarity : 0.004 0.045 2559 Dihedral : 17.254 177.961 3204 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.58 % Allowed : 15.20 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1720 helix: 1.85 (0.18), residues: 841 sheet: -0.30 (0.37), residues: 192 loop : -0.04 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 269 TYR 0.023 0.002 TYR B 557 PHE 0.012 0.001 PHE B 551 TRP 0.014 0.002 TRP C 49 HIS 0.003 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (16178) covalent geometry : angle 0.50975 / 0.28 (22248) hydrogen bonds : bond 0.05699 / 3.90 ( 796) hydrogen bonds : angle 4.63772 / 3.33 ( 2158) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 196 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.8396 (m-40) cc_final: 0.8122 (m110) REVERT: A 382 GLU cc_start: 0.7681 (mp0) cc_final: 0.7188 (mm-30) REVERT: A 397 GLU cc_start: 0.7964 (pt0) cc_final: 0.7692 (tt0) REVERT: A 399 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7980 (tm-30) REVERT: A 495 ARG cc_start: 0.7987 (ptp-170) cc_final: 0.7643 (ptm160) REVERT: A 497 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8824 (tttt) REVERT: A 512 ARG cc_start: 0.7102 (mtt180) cc_final: 0.6749 (mpp80) REVERT: C 11 MET cc_start: 0.8614 (mmm) cc_final: 0.8341 (mmm) REVERT: C 22 LYS cc_start: 0.8347 (mmtt) cc_final: 0.7928 (ttpp) REVERT: C 191 LYS cc_start: 0.7710 (tttt) cc_final: 0.7460 (ttmm) REVERT: B 148 GLU cc_start: 0.8589 (tp30) cc_final: 0.8149 (tp30) REVERT: B 208 LYS cc_start: 0.7969 (mttt) cc_final: 0.7495 (tptt) REVERT: B 228 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8226 (m) REVERT: B 267 GLU cc_start: 0.8171 (tp30) cc_final: 0.7940 (mm-30) REVERT: B 289 MET cc_start: 0.8705 (mmm) cc_final: 0.8327 (mmm) REVERT: B 290 MET cc_start: 0.7071 (mmm) cc_final: 0.6858 (mtp) REVERT: B 363 LYS cc_start: 0.8032 (tttm) cc_final: 0.7751 (tptm) REVERT: B 387 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7777 (mp0) REVERT: B 391 LYS cc_start: 0.8710 (tptp) cc_final: 0.8142 (tmtt) REVERT: B 546 MET cc_start: 0.9196 (mtp) cc_final: 0.8984 (mtp) REVERT: B 635 LYS cc_start: 0.8759 (tttp) cc_final: 0.8529 (tttm) REVERT: B 683 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8097 (mt) REVERT: B 685 ASP cc_start: 0.7786 (p0) cc_final: 0.7523 (p0) outliers start: 9 outliers final: 5 residues processed: 200 average time/residue: 1.5774 time to fit residues: 345.2977 Evaluate side-chains 203 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 683 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 140 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 388 ASN B 284 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.105409 restraints weight = 78892.312| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.68 r_work: 0.3070 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16178 Z= 0.151 Angle : 0.517 5.000 22248 Z= 0.283 Chirality : 0.038 0.154 2498 Planarity : 0.004 0.046 2559 Dihedral : 17.249 177.905 3204 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.52 % Allowed : 15.46 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.20), residues: 1720 helix: 1.84 (0.18), residues: 840 sheet: -0.36 (0.36), residues: 196 loop : -0.06 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.024 0.002 TYR B 557 PHE 0.025 0.001 PHE A 46 TRP 0.015 0.002 TRP C 49 HIS 0.004 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (16178) covalent geometry : angle 0.51707 / 0.28 (22248) hydrogen bonds : bond 0.05785 / 3.95 ( 796) hydrogen bonds : angle 4.65107 / 3.34 ( 2158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14605.26 seconds wall clock time: 247 minutes 27.27 seconds (14847.27 seconds total)