Starting phenix.real_space_refine on Sun Aug 9 02:18:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9raf_53876/08_2026/9raf_53876.cif Found real_map, /net/cci-nas-00/data/ceres_data/9raf_53876/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9raf_53876/08_2026/9raf_53876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9raf_53876/08_2026/9raf_53876.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9raf_53876/08_2026/9raf_53876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9raf_53876/08_2026/9raf_53876.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 7.73, per 1000 atoms: 0.25 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: 2.68 Conformation dependent library (CDL) restraints added in 1.1 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: 4.87 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: 7.36 Time building geometry restraints manager: 3.55 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: 50878 0.91 - 1.81: 4357 1.81 - 2.72: 491 2.72 - 3.63: 148 3.63 - 4.54: 16 Bond angle restraints: 55890 Sorted by residual: angle pdb=" O4' A T 7 " pdb=" C1' A T 7 " pdb=" N9 A T 7 " ideal model delta sigma weight residual 108.20 111.61 -3.41 8.00e-01 1.56e+00 1.81e+01 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 ... (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 - 0.035: 1804 0.035 - 0.070: 452 0.070 - 0.105: 176 0.105 - 0.140: 63 0.140 - 0.176: 3 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 2.47 2.30 0.18 2.00e-01 2.50e+01 7.71e-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: 5.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.260 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 35.440 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.730 ------------------------------------------------------------------------------- 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= 0.166 Angle : 0.493 4.537 22248 Z= 0.333 Chirality : 0.040 0.176 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 0.00288 / 0.17 (16178) covalent geometry : angle 0.49262 / 0.33 (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 : 0.747 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: 0.8127 (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 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: 0.7119 (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: 1.5552 time to fit residues: 484.5158 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 : 0.797 ------------------------------------------------------------------------------- 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: 6.9990 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: 1.9990 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: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.149223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.105524 restraints weight = 90716.500| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.10 r_work: 0.3068 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16178 Z= 0.166 Angle : 0.530 6.905 22248 Z= 0.290 Chirality : 0.039 0.270 2498 Planarity : 0.004 0.037 2559 Dihedral : 17.266 176.834 3217 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.97 % Allowed : 13.52 % Favored : 85.51 % 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: 1.50 (0.20), residues: 1720 helix: 2.02 (0.18), residues: 841 sheet: -0.17 (0.38), residues: 197 loop : 0.14 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 45 TYR 0.025 0.002 TYR B 557 PHE 0.014 0.001 PHE A 381 TRP 0.013 0.002 TRP C 49 HIS 0.004 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (16178) covalent geometry : angle 0.52968 / 0.29 (22248) hydrogen bonds : bond 0.06284 / 4.32 ( 796) hydrogen bonds : angle 4.80654 / 3.45 ( 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 237 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 222 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7490 (mm-30) REVERT: A 33 ASN cc_start: 0.8423 (m-40) cc_final: 0.8137 (m110) REVERT: A 49 SER cc_start: 0.8248 (p) cc_final: 0.8037 (t) REVERT: A 353 LYS cc_start: 0.6202 (OUTLIER) cc_final: 0.5960 (tppt) REVERT: A 382 GLU cc_start: 0.7621 (mp0) cc_final: 0.7145 (mm-30) REVERT: A 397 GLU cc_start: 0.8003 (pt0) cc_final: 0.7690 (tt0) REVERT: A 399 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8015 (tm-30) REVERT: A 495 ARG cc_start: 0.8048 (ptp-170) cc_final: 0.7708 (ptm160) REVERT: A 497 LYS cc_start: 0.9083 (tttt) cc_final: 0.8843 (tttt) REVERT: A 512 ARG cc_start: 0.7126 (mtt180) cc_final: 0.6807 (mpp80) REVERT: A 551 ARG cc_start: 0.7144 (mtt180) cc_final: 0.6889 (mtp-110) REVERT: C 11 MET cc_start: 0.8687 (mmm) cc_final: 0.8358 (mmm) REVERT: C 18 GLU cc_start: 0.7484 (tt0) cc_final: 0.7192 (tp30) REVERT: C 22 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7828 (ttpp) REVERT: C 157 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7601 (mmtt) REVERT: C 191 LYS cc_start: 0.7662 (tttt) cc_final: 0.7426 (ttmm) REVERT: C 217 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8861 (m-80) REVERT: B 104 GLU cc_start: 0.8012 (tt0) cc_final: 0.7781 (tm-30) REVERT: B 208 LYS cc_start: 0.8020 (mttt) cc_final: 0.7538 (tptt) REVERT: B 228 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8195 (m) REVERT: B 267 GLU cc_start: 0.8243 (tp30) cc_final: 0.8037 (mm-30) REVERT: B 289 MET cc_start: 0.8708 (mmm) cc_final: 0.8386 (mmm) REVERT: B 290 MET cc_start: 0.7208 (mmm) cc_final: 0.6944 (mtp) REVERT: B 387 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7813 (mp0) REVERT: B 391 LYS cc_start: 0.8727 (tptp) cc_final: 0.8178 (tmtt) REVERT: B 457 GLU cc_start: 0.8244 (mt-10) cc_final: 0.8029 (mp0) REVERT: B 571 ARG cc_start: 0.8583 (ttt-90) cc_final: 0.8357 (ttt-90) REVERT: B 694 ASN cc_start: 0.8522 (m-40) cc_final: 0.8193 (m-40) outliers start: 15 outliers final: 5 residues processed: 231 average time/residue: 1.5498 time to fit residues: 393.2734 Evaluate side-chains 207 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 40 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 248 GLN A 556 GLN B 532 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.103589 restraints weight = 85660.145| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.13 r_work: 0.3033 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 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 = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1202 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= 0.167 Angle : 0.529 6.607 22248 Z= 0.289 Chirality : 0.039 0.260 2498 Planarity : 0.004 0.041 2559 Dihedral : 17.274 178.528 3213 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.10 % Allowed : 13.97 % Favored : 84.93 % 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: 1.32 (0.20), residues: 1720 helix: 1.87 (0.18), residues: 842 sheet: -0.24 (0.37), residues: 197 loop : 0.05 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 583 TYR 0.026 0.002 TYR B 557 PHE 0.014 0.002 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 0.00362 / 0.17 (16178) covalent geometry : angle 0.52874 / 0.29 (22248) hydrogen bonds : bond 0.06206 / 4.25 ( 796) hydrogen bonds : angle 4.74134 / 3.41 ( 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 228 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7542 (mm-30) REVERT: A 33 ASN cc_start: 0.8406 (m-40) cc_final: 0.8119 (m110) REVERT: A 49 SER cc_start: 0.8229 (p) cc_final: 0.8000 (t) REVERT: A 353 LYS cc_start: 0.6211 (OUTLIER) cc_final: 0.5981 (tppt) REVERT: A 361 LYS cc_start: 0.8845 (mttp) cc_final: 0.8356 (mmtm) REVERT: A 382 GLU cc_start: 0.7709 (mp0) cc_final: 0.7214 (mm-30) REVERT: A 397 GLU cc_start: 0.8002 (pt0) cc_final: 0.7680 (tt0) REVERT: A 399 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8018 (tm-30) REVERT: A 495 ARG cc_start: 0.8014 (ptp-170) cc_final: 0.7685 (ptm160) REVERT: A 512 ARG cc_start: 0.7143 (mtt180) cc_final: 0.6877 (mpp80) REVERT: C 11 MET cc_start: 0.8683 (mmm) cc_final: 0.8441 (mmm) REVERT: C 22 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7852 (ttpp) REVERT: C 157 LYS cc_start: 0.8192 (mtmt) cc_final: 0.7607 (mmtt) REVERT: C 217 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8880 (m-80) REVERT: B 104 GLU cc_start: 0.8033 (tt0) cc_final: 0.7789 (tm-30) REVERT: B 148 GLU cc_start: 0.8633 (tp30) cc_final: 0.8252 (tp30) REVERT: B 208 LYS cc_start: 0.8030 (mttt) cc_final: 0.7546 (tptt) REVERT: B 267 GLU cc_start: 0.8215 (tp30) cc_final: 0.7996 (mm-30) REVERT: B 289 MET cc_start: 0.8747 (mmm) cc_final: 0.8423 (mmm) REVERT: B 387 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7836 (mp0) REVERT: B 391 LYS cc_start: 0.8724 (tptp) cc_final: 0.8171 (tmtt) REVERT: B 546 MET cc_start: 0.9203 (mtp) cc_final: 0.8974 (mtp) REVERT: B 694 ASN cc_start: 0.8513 (m-40) cc_final: 0.8185 (m-40) REVERT: B 742 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6869 (mm-30) outliers start: 17 outliers final: 8 residues processed: 219 average time/residue: 1.4992 time to fit residues: 360.2772 Evaluate side-chains 209 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 742 GLU 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: 3.9990 chunk 24 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.149280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104620 restraints weight = 81868.085| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.08 r_work: 0.3041 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1313 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= 0.138 Angle : 0.511 6.559 22248 Z= 0.278 Chirality : 0.038 0.262 2498 Planarity : 0.004 0.040 2559 Dihedral : 17.272 179.033 3213 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.17 % Allowed : 14.42 % 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: 1.91 (0.18), residues: 842 sheet: -0.32 (0.37), residues: 197 loop : 0.04 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 0.00294 / 0.14 (16178) covalent geometry : angle 0.51071 / 0.28 (22248) hydrogen bonds : bond 0.05835 / 4.01 ( 796) hydrogen bonds : angle 4.67805 / 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 215 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7523 (mm-30) REVERT: A 33 ASN cc_start: 0.8412 (m-40) cc_final: 0.8125 (m110) REVERT: A 353 LYS cc_start: 0.6224 (OUTLIER) cc_final: 0.5970 (tppt) REVERT: A 361 LYS cc_start: 0.8868 (mttp) cc_final: 0.8360 (mmtm) REVERT: A 382 GLU cc_start: 0.7663 (mp0) cc_final: 0.7137 (mm-30) REVERT: A 397 GLU cc_start: 0.7957 (pt0) cc_final: 0.7660 (tt0) REVERT: A 399 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8014 (tm-30) REVERT: A 495 ARG cc_start: 0.8018 (ptp-170) cc_final: 0.7684 (ptm160) REVERT: A 512 ARG cc_start: 0.7144 (mtt180) cc_final: 0.6859 (mpp80) REVERT: C 11 MET cc_start: 0.8666 (mmm) cc_final: 0.8340 (mmm) REVERT: C 22 LYS cc_start: 0.8279 (mmtt) cc_final: 0.7884 (ttpp) REVERT: C 157 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7599 (mmtt) REVERT: C 217 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8879 (m-80) REVERT: B 104 GLU cc_start: 0.8057 (tt0) cc_final: 0.7810 (tm-30) REVERT: B 208 LYS cc_start: 0.8016 (mttt) cc_final: 0.7543 (tptt) REVERT: B 267 GLU cc_start: 0.8219 (tp30) cc_final: 0.8001 (mm-30) REVERT: B 289 MET cc_start: 0.8722 (mmm) cc_final: 0.8396 (mmm) REVERT: B 363 LYS cc_start: 0.8055 (tttm) cc_final: 0.7777 (tptm) REVERT: B 387 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7819 (mp0) REVERT: B 391 LYS cc_start: 0.8719 (tptp) cc_final: 0.8154 (tmtt) REVERT: B 546 MET cc_start: 0.9189 (mtp) cc_final: 0.8973 (mtp) outliers start: 18 outliers final: 4 residues processed: 208 average time/residue: 1.3932 time to fit residues: 316.5376 Evaluate side-chains 203 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 197 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 353 LYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 166 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 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: 2.9990 chunk 50 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 388 ASN B 425 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 = 0.148303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103390 restraints weight = 83360.995| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.09 r_work: 0.3025 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 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: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16178 Z= 0.167 Angle : 0.533 6.544 22248 Z= 0.290 Chirality : 0.039 0.263 2498 Planarity : 0.004 0.045 2559 Dihedral : 17.301 179.588 3211 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.04 % Allowed : 14.42 % Favored : 84.54 % 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: 1.25 (0.20), residues: 1720 helix: 1.84 (0.18), residues: 840 sheet: -0.39 (0.36), residues: 198 loop : 0.03 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 583 TYR 0.025 0.002 TYR B 557 PHE 0.014 0.002 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 0.00363 / 0.17 (16178) covalent geometry : angle 0.53322 / 0.29 (22248) hydrogen bonds : bond 0.06047 / 4.14 ( 796) hydrogen bonds : angle 4.69886 / 3.38 ( 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 213 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.8410 (m-40) cc_final: 0.8133 (m110) REVERT: A 382 GLU cc_start: 0.7647 (mp0) cc_final: 0.7115 (mm-30) REVERT: A 397 GLU cc_start: 0.7958 (pt0) cc_final: 0.7674 (tt0) REVERT: A 399 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8016 (tm-30) REVERT: A 495 ARG cc_start: 0.8024 (ptp-170) cc_final: 0.7682 (ptm160) REVERT: A 512 ARG cc_start: 0.7108 (mtt180) cc_final: 0.6797 (mpp80) REVERT: C 1 MET cc_start: 0.7062 (tpt) cc_final: 0.6812 (tpt) REVERT: C 22 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7897 (ttpp) REVERT: C 157 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7569 (mmtt) REVERT: C 217 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8893 (m-80) REVERT: B 104 GLU cc_start: 0.8057 (tt0) cc_final: 0.7831 (tm-30) REVERT: B 208 LYS cc_start: 0.7995 (mttt) cc_final: 0.7509 (tptt) REVERT: B 228 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8217 (m) REVERT: B 267 GLU cc_start: 0.8189 (tp30) cc_final: 0.7955 (mm-30) REVERT: B 289 MET cc_start: 0.8752 (mmm) cc_final: 0.8432 (mmm) REVERT: B 363 LYS cc_start: 0.8059 (tttm) cc_final: 0.7772 (tptm) REVERT: B 387 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7800 (mp0) REVERT: B 391 LYS cc_start: 0.8716 (tptp) cc_final: 0.8150 (tmtt) REVERT: B 546 MET cc_start: 0.9209 (mtp) cc_final: 0.8984 (mtp) REVERT: B 682 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.7944 (mp) REVERT: B 685 ASP cc_start: 0.7741 (p0) cc_final: 0.7458 (p0) outliers start: 16 outliers final: 7 residues processed: 205 average time/residue: 1.5387 time to fit residues: 344.6189 Evaluate side-chains 202 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 682 ILE 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: 1.9990 chunk 7 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.149364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105317 restraints weight = 77204.745| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.00 r_work: 0.3062 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 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 = 0.2935 r_free = 0.2935 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: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16178 Z= 0.127 Angle : 0.502 6.443 22248 Z= 0.272 Chirality : 0.038 0.260 2498 Planarity : 0.004 0.042 2559 Dihedral : 17.282 179.731 3207 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.71 % Allowed : 14.75 % Favored : 84.54 % 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: 1.91 (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 45 TYR 0.022 0.001 TYR B 557 PHE 0.012 0.001 PHE B 551 TRP 0.014 0.001 TRP C 49 HIS 0.003 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (16178) covalent geometry : angle 0.50209 / 0.27 (22248) hydrogen bonds : bond 0.05653 / 3.88 ( 796) hydrogen bonds : angle 4.63203 / 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 210 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 199 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.8419 (m-40) cc_final: 0.8124 (m110) REVERT: A 382 GLU cc_start: 0.7663 (mp0) cc_final: 0.7149 (mm-30) REVERT: A 397 GLU cc_start: 0.7943 (pt0) cc_final: 0.7673 (tt0) REVERT: A 399 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8006 (tm-30) REVERT: A 495 ARG cc_start: 0.7997 (ptp-170) cc_final: 0.7663 (ptm160) REVERT: A 512 ARG cc_start: 0.7079 (mtt180) cc_final: 0.6788 (mpp80) REVERT: C 11 MET cc_start: 0.8627 (mmm) cc_final: 0.8380 (mmm) REVERT: C 22 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7920 (ttpp) REVERT: C 157 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7583 (mmtt) REVERT: C 217 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8886 (m-80) REVERT: B 104 GLU cc_start: 0.8038 (tt0) cc_final: 0.7799 (tm-30) REVERT: B 159 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7897 (mt-10) REVERT: B 208 LYS cc_start: 0.8020 (mttt) cc_final: 0.7565 (tptt) REVERT: B 230 ASP cc_start: 0.7961 (m-30) cc_final: 0.7755 (m-30) REVERT: B 267 GLU cc_start: 0.8178 (tp30) cc_final: 0.7960 (mm-30) REVERT: B 289 MET cc_start: 0.8702 (mmm) cc_final: 0.8363 (mmm) REVERT: B 363 LYS cc_start: 0.8058 (tttm) cc_final: 0.7771 (tptm) REVERT: B 387 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7799 (mp0) REVERT: B 391 LYS cc_start: 0.8711 (tptp) cc_final: 0.8148 (tmtt) REVERT: B 546 MET cc_start: 0.9187 (mtp) cc_final: 0.8979 (mtp) REVERT: B 683 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8138 (mt) REVERT: B 685 ASP cc_start: 0.7758 (p0) cc_final: 0.7462 (p0) outliers start: 11 outliers final: 5 residues processed: 205 average time/residue: 1.5087 time to fit residues: 339.4411 Evaluate side-chains 200 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 193 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 C residue 16 THR Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain B residue 683 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 120 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 85 optimal weight: 0.0370 chunk 165 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.5264 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.148048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104607 restraints weight = 86404.654| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.02 r_work: 0.3043 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 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 = 0.2904 r_free = 0.2904 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: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1507 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= 0.153 Angle : 0.519 6.422 22248 Z= 0.281 Chirality : 0.039 0.262 2498 Planarity : 0.004 0.044 2559 Dihedral : 17.285 179.999 3207 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.65 % Allowed : 14.75 % Favored : 84.60 % 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: 1.27 (0.20), residues: 1720 helix: 1.87 (0.18), residues: 841 sheet: -0.38 (0.37), residues: 194 loop : 0.01 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 45 TYR 0.024 0.002 TYR B 557 PHE 0.020 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 0.00331 / 0.15 (16178) covalent geometry : angle 0.51914 / 0.28 (22248) hydrogen bonds : bond 0.05826 / 3.98 ( 796) hydrogen bonds : angle 4.64630 / 3.34 ( 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 206 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.8429 (m-40) cc_final: 0.8153 (m110) REVERT: A 382 GLU cc_start: 0.7667 (mp0) cc_final: 0.7466 (mp0) REVERT: A 397 GLU cc_start: 0.8008 (pt0) cc_final: 0.7686 (tt0) REVERT: A 399 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8009 (tm-30) REVERT: A 495 ARG cc_start: 0.8039 (ptp-170) cc_final: 0.7702 (ptm160) REVERT: A 512 ARG cc_start: 0.7099 (mtt180) cc_final: 0.6766 (mpp80) REVERT: C 11 MET cc_start: 0.8638 (mmm) cc_final: 0.8397 (mmm) REVERT: C 22 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7915 (ttpp) REVERT: C 157 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7590 (mmtt) REVERT: C 217 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8894 (m-80) REVERT: B 104 GLU cc_start: 0.8073 (tt0) cc_final: 0.7828 (tm-30) REVERT: B 208 LYS cc_start: 0.8029 (mttt) cc_final: 0.7555 (tptt) REVERT: B 230 ASP cc_start: 0.7981 (m-30) cc_final: 0.7770 (m-30) REVERT: B 267 GLU cc_start: 0.8200 (tp30) cc_final: 0.7966 (mm-30) REVERT: B 289 MET cc_start: 0.8720 (mmm) cc_final: 0.8377 (mmm) REVERT: B 363 LYS cc_start: 0.8057 (tttm) cc_final: 0.7771 (tptm) REVERT: B 387 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7800 (mp0) REVERT: B 391 LYS cc_start: 0.8733 (tptp) cc_final: 0.8164 (tmtt) REVERT: B 546 MET cc_start: 0.9202 (mtp) cc_final: 0.8987 (mtp) REVERT: B 683 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8157 (mt) REVERT: B 685 ASP cc_start: 0.7761 (p0) cc_final: 0.7470 (p0) outliers start: 10 outliers final: 7 residues processed: 198 average time/residue: 1.5570 time to fit residues: 336.9844 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 : 0.581 ------------------------------------------------------------------------------- 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 683 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 142 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.148653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104016 restraints weight = 80321.651| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.06 r_work: 0.3057 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 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 = 0.2905 r_free = 0.2905 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: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16178 Z= 0.151 Angle : 0.521 6.477 22248 Z= 0.283 Chirality : 0.039 0.263 2498 Planarity : 0.004 0.047 2559 Dihedral : 17.286 179.799 3206 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.78 % Allowed : 14.94 % 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: 1.24 (0.20), residues: 1720 helix: 1.87 (0.18), residues: 840 sheet: -0.36 (0.36), residues: 196 loop : -0.03 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 15 TYR 0.024 0.002 TYR B 557 PHE 0.013 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 0.00326 / 0.15 (16178) covalent geometry : angle 0.52073 / 0.28 (22248) hydrogen bonds : bond 0.05834 / 3.99 ( 796) hydrogen bonds : angle 4.65694 / 3.35 ( 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 208 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.8420 (m-40) cc_final: 0.8136 (m110) REVERT: A 382 GLU cc_start: 0.7659 (mp0) cc_final: 0.7146 (mm-30) REVERT: A 397 GLU cc_start: 0.7996 (pt0) cc_final: 0.7691 (tt0) REVERT: A 399 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7986 (tm-30) REVERT: A 495 ARG cc_start: 0.8023 (ptp-170) cc_final: 0.7680 (ptm160) REVERT: A 512 ARG cc_start: 0.7101 (mtt180) cc_final: 0.6777 (mpp80) REVERT: C 11 MET cc_start: 0.8625 (mmm) cc_final: 0.8368 (mmm) REVERT: C 22 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7912 (ttpp) REVERT: C 217 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8890 (m-80) REVERT: B 104 GLU cc_start: 0.8042 (tt0) cc_final: 0.7809 (tm-30) REVERT: B 208 LYS cc_start: 0.8004 (mttt) cc_final: 0.7532 (tptt) REVERT: B 228 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8217 (m) REVERT: B 230 ASP cc_start: 0.7962 (m-30) cc_final: 0.7740 (m-30) REVERT: B 267 GLU cc_start: 0.8188 (tp30) cc_final: 0.7955 (mm-30) REVERT: B 289 MET cc_start: 0.8697 (mmm) cc_final: 0.8347 (mmm) REVERT: B 363 LYS cc_start: 0.8047 (tttm) cc_final: 0.7754 (tptm) REVERT: B 387 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7787 (mp0) REVERT: B 391 LYS cc_start: 0.8717 (tptp) cc_final: 0.8146 (tmtt) REVERT: B 546 MET cc_start: 0.9204 (mtp) cc_final: 0.8986 (mtp) REVERT: B 683 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8145 (mt) REVERT: B 685 ASP cc_start: 0.7767 (p0) cc_final: 0.7475 (p0) outliers start: 12 outliers final: 6 residues processed: 201 average time/residue: 1.4144 time to fit residues: 311.6702 Evaluate side-chains 204 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 172 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.147656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.105884 restraints weight = 85581.966| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.83 r_work: 0.3030 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 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 = 0.2904 r_free = 0.2904 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: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16178 Z= 0.161 Angle : 0.531 6.463 22248 Z= 0.288 Chirality : 0.039 0.264 2498 Planarity : 0.004 0.049 2559 Dihedral : 17.291 179.613 3206 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.71 % Allowed : 14.88 % 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: 1.20 (0.20), residues: 1720 helix: 1.83 (0.18), residues: 840 sheet: -0.46 (0.36), residues: 198 loop : -0.02 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 249 TYR 0.025 0.002 TYR B 557 PHE 0.025 0.002 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 0.00351 / 0.16 (16178) covalent geometry : angle 0.53080 / 0.29 (22248) hydrogen bonds : bond 0.05922 / 4.04 ( 796) hydrogen bonds : angle 4.67424 / 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 205 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.8466 (m-40) cc_final: 0.8197 (m110) REVERT: A 397 GLU cc_start: 0.7960 (pt0) cc_final: 0.7680 (tt0) REVERT: A 399 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7994 (tm-30) REVERT: A 495 ARG cc_start: 0.8016 (ptp-170) cc_final: 0.7669 (ptm160) REVERT: A 497 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8855 (tttt) REVERT: A 512 ARG cc_start: 0.7054 (mtt180) cc_final: 0.6747 (mpp80) REVERT: C 1 MET cc_start: 0.7043 (tpt) cc_final: 0.6827 (tpt) REVERT: C 11 MET cc_start: 0.8636 (mmm) cc_final: 0.8391 (mmm) REVERT: C 22 LYS cc_start: 0.8332 (mmtt) cc_final: 0.7932 (ttpp) REVERT: C 217 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8895 (m-80) REVERT: B 104 GLU cc_start: 0.8020 (tt0) cc_final: 0.7809 (tm-30) REVERT: B 208 LYS cc_start: 0.7996 (mttt) cc_final: 0.7552 (tptt) REVERT: B 228 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8220 (m) REVERT: B 230 ASP cc_start: 0.7954 (m-30) cc_final: 0.7740 (m-30) REVERT: B 267 GLU cc_start: 0.8178 (tp30) cc_final: 0.7949 (mm-30) REVERT: B 289 MET cc_start: 0.8703 (mmm) cc_final: 0.8353 (mmm) REVERT: B 363 LYS cc_start: 0.8047 (tttm) cc_final: 0.7763 (tptm) REVERT: B 391 LYS cc_start: 0.8716 (tptp) cc_final: 0.8152 (tmtt) REVERT: B 546 MET cc_start: 0.9207 (mtp) cc_final: 0.8989 (mtp) REVERT: B 683 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8150 (mt) REVERT: B 685 ASP cc_start: 0.7770 (p0) cc_final: 0.7482 (p0) outliers start: 11 outliers final: 7 residues processed: 198 average time/residue: 1.4639 time to fit residues: 318.4283 Evaluate side-chains 203 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 103 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.149177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.104795 restraints weight = 87418.108| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.04 r_work: 0.3045 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 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 = 0.2915 r_free = 0.2915 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: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16178 Z= 0.136 Angle : 0.511 6.371 22248 Z= 0.277 Chirality : 0.038 0.262 2498 Planarity : 0.004 0.045 2559 Dihedral : 17.274 179.647 3206 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.58 % Allowed : 15.07 % 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: 1.27 (0.20), residues: 1720 helix: 1.88 (0.18), residues: 841 sheet: -0.32 (0.36), residues: 192 loop : -0.03 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 45 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 0.00292 / 0.14 (16178) covalent geometry : angle 0.51129 / 0.28 (22248) hydrogen bonds : bond 0.05673 / 3.88 ( 796) hydrogen bonds : angle 4.62453 / 3.32 ( 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 204 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.8398 (m-40) cc_final: 0.8120 (m110) REVERT: A 104 LYS cc_start: 0.8727 (mptp) cc_final: 0.8360 (mttp) REVERT: A 382 GLU cc_start: 0.7637 (mp0) cc_final: 0.7165 (mm-30) REVERT: A 397 GLU cc_start: 0.7990 (pt0) cc_final: 0.7688 (tt0) REVERT: A 399 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7975 (tm-30) REVERT: A 495 ARG cc_start: 0.8013 (ptp-170) cc_final: 0.7668 (ptm160) REVERT: A 512 ARG cc_start: 0.7063 (mtt180) cc_final: 0.6741 (mpp80) REVERT: C 11 MET cc_start: 0.8617 (mmm) cc_final: 0.8334 (mmm) REVERT: C 22 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7927 (ttpp) REVERT: C 217 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8898 (m-80) REVERT: B 104 GLU cc_start: 0.8035 (tt0) cc_final: 0.7800 (tm-30) REVERT: B 208 LYS cc_start: 0.8014 (mttt) cc_final: 0.7548 (tptt) REVERT: B 228 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8229 (m) REVERT: B 230 ASP cc_start: 0.7969 (m-30) cc_final: 0.7769 (m-30) REVERT: B 267 GLU cc_start: 0.8192 (tp30) cc_final: 0.7950 (mm-30) REVERT: B 289 MET cc_start: 0.8682 (mmm) cc_final: 0.8323 (mmm) REVERT: B 363 LYS cc_start: 0.8044 (tttm) cc_final: 0.7759 (tptm) REVERT: B 387 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7795 (mp0) REVERT: B 391 LYS cc_start: 0.8717 (tptp) cc_final: 0.8146 (tmtt) REVERT: B 546 MET cc_start: 0.9193 (mtp) cc_final: 0.8983 (mtp) REVERT: B 683 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8156 (mt) REVERT: B 685 ASP cc_start: 0.7778 (p0) cc_final: 0.7484 (p0) outliers start: 9 outliers final: 5 residues processed: 197 average time/residue: 1.7015 time to fit residues: 367.1856 Evaluate side-chains 202 residues out of total 1514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 120 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 51 optimal weight: 0.0870 chunk 125 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.148849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106238 restraints weight = 79132.968| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.68 r_work: 0.3095 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16178 Z= 0.129 Angle : 0.504 6.275 22248 Z= 0.273 Chirality : 0.038 0.261 2498 Planarity : 0.004 0.042 2559 Dihedral : 17.257 179.607 3206 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.58 % Allowed : 15.07 % 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: 1.28 (0.20), residues: 1720 helix: 1.87 (0.18), residues: 847 sheet: -0.33 (0.36), residues: 192 loop : -0.00 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.022 0.002 TYR B 557 PHE 0.025 0.001 PHE A 46 TRP 0.014 0.001 TRP C 49 HIS 0.003 0.001 HIS C 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (16178) covalent geometry : angle 0.50431 / 0.27 (22248) hydrogen bonds : bond 0.05565 / 3.81 ( 796) hydrogen bonds : angle 4.59651 / 3.30 ( 2158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13667.58 seconds wall clock time: 231 minutes 28.03 seconds (13888.03 seconds total)