Starting phenix.real_space_refine on Fri Jul 3 15:33:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pnq_17783/07_2026/8pnq_17783.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pnq_17783/07_2026/8pnq_17783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pnq_17783/07_2026/8pnq_17783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pnq_17783/07_2026/8pnq_17783.map" model { file = "/net/cci-nas-00/data/ceres_data/8pnq_17783/07_2026/8pnq_17783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pnq_17783/07_2026/8pnq_17783.cif" } resolution = 2.88 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= 0.002 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: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 2 5.21 5 S 104 5.16 5 C 9214 2.51 5 N 2587 2.21 5 O 2956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14913 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 5748 Classifications: {'peptide': 708} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 Chain: "B" Number of atoms: 5958 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 744, 5950 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 713} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 744, 5950 Classifications: {'peptide': 744} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 713} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 6054 Chain: "C" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2024 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain: "V" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 758 Classifications: {'RNA': 36} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 9, 'rna3p_pyr': 14} Link IDs: {'rna2p': 13, 'rna3p': 22} Chain breaks: 1 Chain: "M" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 202 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 9} Link IDs: {'rna3p': 8} Chain: "G" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 192 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 7, 'TRANS': 17} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, '2KH': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALEU B 218 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU B 218 " occ=0.50 Time building chain proxies: 3.93, per 1000 atoms: 0.26 Number of scatterers: 14913 At special positions: 0 Unit cell: (96.6, 100.8, 141.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 50 15.00 Mg 2 11.99 O 2956 8.00 N 2587 7.00 C 9214 6.00 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: 1.28 Conformation dependent library (CDL) restraints added in 786.3 milliseconds 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3268 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 16 sheets defined 52.0% alpha, 13.4% beta 11 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 23 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 removed outlier: 3.695A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 185 removed outlier: 3.685A pdb=" N ARG A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 195 through 198 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 313 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.586A 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 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.534A pdb=" N SER A 409 " --> pdb=" O CYS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.992A 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 533 through 538 removed outlier: 3.736A 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: 4.011A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 4.096A 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: 4.136A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 4.192A 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 716 removed outlier: 3.950A pdb=" N ARG A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 5.447A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (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 160 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.510A pdb=" N PHE B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.567A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 293 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.522A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN B 313 " --> pdb=" O ASN B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 309 through 313' Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.685A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.597A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 376 removed outlier: 4.205A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (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 474 Processing helix chain 'B' and resid 505 through 512 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 536 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 removed outlier: 3.829A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 679 through 700 removed outlier: 3.782A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ASP B 685 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU B 686 " --> pdb=" O ILE B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.297A 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 733 Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.827A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 24 through 33 removed outlier: 4.194A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.689A pdb=" N MET C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.742A 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: 3.886A 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 194 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 236 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 removed outlier: 3.758A pdb=" N LYS A 73 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 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: 7.404A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU A 549 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLU A 544 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 11.026A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 11.484A 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: 5.319A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 380 removed outlier: 5.779A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL A 379 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.268A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 181 Processing sheet with id=AB2, first strand: chain 'B' and resid 184 through 192 removed outlier: 8.061A pdb=" N SER B 678 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG B 203 " --> pdb=" O SER B 678 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.855A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.633A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.582A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.695A pdb=" N LYS C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 2011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2393 1.31 - 1.44: 4242 1.44 - 1.57: 8393 1.57 - 1.69: 101 1.69 - 1.82: 180 Bond restraints: 15309 Sorted by residual: bond pdb=" N3A 2KH B 801 " pdb=" PA 2KH B 801 " ideal model delta sigma weight residual 1.933 1.670 0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C2' 2KH B 801 " pdb=" C3' 2KH B 801 " ideal model delta sigma weight residual 1.548 1.310 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" N3A 2KH B 801 " pdb=" PB 2KH B 801 " ideal model delta sigma weight residual 1.890 1.697 0.193 2.00e-02 2.50e+03 9.33e+01 bond pdb=" O3G 2KH B 801 " pdb=" PG 2KH B 801 " ideal model delta sigma weight residual 1.669 1.497 0.172 2.00e-02 2.50e+03 7.39e+01 bond pdb=" O2G 2KH B 801 " pdb=" PG 2KH B 801 " ideal model delta sigma weight residual 1.682 1.528 0.154 2.00e-02 2.50e+03 5.91e+01 ... (remaining 15304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.35: 20864 12.35 - 24.70: 7 24.70 - 37.05: 0 37.05 - 49.40: 0 49.40 - 61.75: 2 Bond angle restraints: 20873 Sorted by residual: angle pdb=" N3A 2KH B 801 " pdb=" PA 2KH B 801 " pdb=" O2A 2KH B 801 " ideal model delta sigma weight residual 48.17 109.92 -61.75 3.00e+00 1.11e-01 4.24e+02 angle pdb=" O2G 2KH B 801 " pdb=" PG 2KH B 801 " pdb=" O3G 2KH B 801 " ideal model delta sigma weight residual 53.94 109.50 -55.56 3.00e+00 1.11e-01 3.43e+02 angle pdb=" O1A 2KH B 801 " pdb=" PA 2KH B 801 " pdb=" O2A 2KH B 801 " ideal model delta sigma weight residual 130.82 109.28 21.54 3.00e+00 1.11e-01 5.16e+01 angle pdb=" O1G 2KH B 801 " pdb=" PG 2KH B 801 " pdb=" O2G 2KH B 801 " ideal model delta sigma weight residual 130.21 109.42 20.79 3.00e+00 1.11e-01 4.80e+01 angle pdb=" O1B 2KH B 801 " pdb=" PB 2KH B 801 " pdb=" O2B 2KH B 801 " ideal model delta sigma weight residual 130.56 109.91 20.65 3.00e+00 1.11e-01 4.74e+01 ... (remaining 20868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 8780 32.09 - 64.18: 617 64.18 - 96.26: 47 96.26 - 128.35: 1 128.35 - 160.44: 2 Dihedral angle restraints: 9447 sinusoidal: 4401 harmonic: 5046 Sorted by residual: dihedral pdb=" C5' 2KH B 801 " pdb=" O5' 2KH B 801 " pdb=" PA 2KH B 801 " pdb=" O2A 2KH B 801 " ideal model delta sinusoidal sigma weight residual 16.44 -144.00 160.44 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" O1A 2KH B 801 " pdb=" N3A 2KH B 801 " pdb=" PA 2KH B 801 " pdb=" PB 2KH B 801 " ideal model delta sinusoidal sigma weight residual 154.31 -46.11 -159.58 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" C5' 2KH B 801 " pdb=" O5' 2KH B 801 " pdb=" PA 2KH B 801 " pdb=" O1A 2KH B 801 " ideal model delta sinusoidal sigma weight residual -149.66 -24.13 -125.53 1 3.00e+01 1.11e-03 1.69e+01 ... (remaining 9444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2205 0.083 - 0.165: 107 0.165 - 0.248: 2 0.248 - 0.330: 0 0.330 - 0.413: 1 Chirality restraints: 2315 Sorted by residual: chirality pdb=" C2' 2KH B 801 " pdb=" C1' 2KH B 801 " pdb=" C3' 2KH B 801 " pdb=" O2' 2KH B 801 " both_signs ideal model delta sigma weight residual False -2.85 -2.43 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" C3' 2KH B 801 " pdb=" C2' 2KH B 801 " pdb=" C4' 2KH B 801 " pdb=" O3' 2KH B 801 " both_signs ideal model delta sigma weight residual False -2.66 -2.43 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C1' 2KH B 801 " pdb=" C2' 2KH B 801 " pdb=" N1 2KH B 801 " pdb=" O4' 2KH B 801 " both_signs ideal model delta sigma weight residual False 2.59 2.39 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 2312 not shown) Planarity restraints: 2515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 584 " 0.221 9.50e-02 1.11e+02 9.92e-02 6.73e+00 pdb=" NE ARG B 584 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 584 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 584 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 584 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.024 2.00e-02 2.50e+03 1.04e-02 2.95e+00 pdb=" N9 A V 4 " 0.023 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.020 2.00e-02 2.50e+03 9.34e-03 2.40e+00 pdb=" N9 A V 7 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A V 7 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A V 7 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.002 2.00e-02 2.50e+03 ... (remaining 2512 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 64 2.46 - 3.07: 10025 3.07 - 3.68: 22963 3.68 - 4.29: 35357 4.29 - 4.90: 58414 Nonbonded interactions: 126823 Sorted by model distance: nonbonded pdb=" OD1 ASP B 305 " pdb="MG MG B 803 " model vdw 1.845 2.170 nonbonded pdb=" OD2 ASP B 305 " pdb="MG MG B 802 " model vdw 1.922 2.170 nonbonded pdb=" O1B 2KH B 801 " pdb="MG MG B 803 " model vdw 1.923 2.170 nonbonded pdb=" OG1 THR B 226 " pdb=" O ARG B 350 " model vdw 2.054 3.040 nonbonded pdb=" O1A 2KH B 801 " pdb="MG MG B 803 " model vdw 2.084 2.170 ... (remaining 126818 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.470 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 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 : 0.005 0.263 15309 Z= 0.267 Angle : 0.829 61.746 20873 Z= 0.344 Chirality : 0.037 0.413 2315 Planarity : 0.003 0.099 2515 Dihedral : 19.332 160.439 6179 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.01 % Allowed : 25.28 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1711 helix: 2.41 (0.19), residues: 811 sheet: 0.26 (0.36), residues: 193 loop : -0.13 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 584 TYR 0.014 0.001 TYR B 555 PHE 0.010 0.001 PHE A 53 TRP 0.014 0.001 TRP C 49 HIS 0.003 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.27 (15309) covalent geometry : angle 0.82868 / 0.34 (20873) hydrogen bonds : bond 0.12412 / 7.67 ( 746) hydrogen bonds : angle 5.28249 / 3.68 ( 2065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6787 (mp0) cc_final: 0.6483 (pm20) REVERT: A 168 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7139 (mtm110) REVERT: A 201 ILE cc_start: 0.8780 (mm) cc_final: 0.8544 (mm) REVERT: A 348 ILE cc_start: 0.8747 (tp) cc_final: 0.8476 (tp) REVERT: C 243 MET cc_start: 0.8660 (mtp) cc_final: 0.8452 (mtp) outliers start: 30 outliers final: 25 residues processed: 218 average time/residue: 0.6274 time to fit residues: 149.7466 Evaluate side-chains 206 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 GLN B 158 ASN B 184 HIS C 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.075638 restraints weight = 49147.409| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.03 r_work: 0.2702 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15309 Z= 0.205 Angle : 0.550 8.932 20873 Z= 0.291 Chirality : 0.042 0.179 2315 Planarity : 0.004 0.043 2515 Dihedral : 13.554 136.207 2649 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.89 % Allowed : 23.20 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1711 helix: 2.06 (0.18), residues: 831 sheet: 0.29 (0.36), residues: 196 loop : -0.18 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 584 TYR 0.015 0.002 TYR B 557 PHE 0.012 0.001 PHE B 185 TRP 0.016 0.001 TRP C 49 HIS 0.007 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (15309) covalent geometry : angle 0.54970 / 0.29 (20873) hydrogen bonds : bond 0.04949 / 3.26 ( 746) hydrogen bonds : angle 4.54914 / 3.17 ( 2065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 200 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6592 (pm20) REVERT: A 168 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7092 (mtm110) REVERT: A 191 PHE cc_start: 0.8230 (t80) cc_final: 0.7922 (t80) REVERT: A 201 ILE cc_start: 0.8731 (mm) cc_final: 0.8509 (mm) REVERT: A 348 ILE cc_start: 0.8696 (tp) cc_final: 0.8459 (tp) REVERT: B 1 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.6881 (tpp) REVERT: B 566 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8644 (t) REVERT: B 669 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7758 (ttmm) REVERT: C 53 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7360 (mpt) REVERT: G 11 SER cc_start: 0.4754 (OUTLIER) cc_final: 0.4430 (p) outliers start: 59 outliers final: 21 residues processed: 239 average time/residue: 0.6452 time to fit residues: 169.0353 Evaluate side-chains 209 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 669 LYS Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 167 optimal weight: 0.0370 chunk 131 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.4664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 GLN B 158 ASN C 100 ASN C 182 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.105973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.078319 restraints weight = 27958.678| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.28 r_work: 0.2774 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15309 Z= 0.138 Angle : 0.491 9.007 20873 Z= 0.262 Chirality : 0.039 0.187 2315 Planarity : 0.004 0.041 2515 Dihedral : 13.383 136.192 2635 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.69 % Allowed : 23.53 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.38 (0.20), residues: 1711 helix: 2.02 (0.18), residues: 826 sheet: 0.28 (0.36), residues: 196 loop : -0.20 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 584 TYR 0.017 0.001 TYR B 557 PHE 0.010 0.001 PHE A 520 TRP 0.017 0.001 TRP C 49 HIS 0.004 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (15309) covalent geometry : angle 0.49134 / 0.26 (20873) hydrogen bonds : bond 0.04397 / 2.91 ( 746) hydrogen bonds : angle 4.37723 / 3.05 ( 2065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 199 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6531 (pm20) REVERT: A 78 ILE cc_start: 0.8948 (mm) cc_final: 0.8680 (mm) REVERT: A 168 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7102 (mtm110) REVERT: A 201 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8524 (mm) REVERT: A 348 ILE cc_start: 0.8721 (tp) cc_final: 0.8480 (tp) REVERT: A 551 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7666 (ttp80) REVERT: B 208 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7664 (pttp) REVERT: B 348 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8339 (mmm) REVERT: B 566 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8641 (t) REVERT: B 731 GLU cc_start: 0.8254 (tp30) cc_final: 0.7927 (mm-30) REVERT: B 754 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7620 (ptt180) REVERT: C 53 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7442 (mpt) REVERT: G 20 THR cc_start: 0.9345 (m) cc_final: 0.9040 (p) outliers start: 56 outliers final: 25 residues processed: 234 average time/residue: 0.6208 time to fit residues: 158.9106 Evaluate side-chains 218 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 18 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 7 optimal weight: 0.0870 chunk 154 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 41 optimal weight: 0.0070 chunk 117 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 ASN B 124 GLN B 134 ASN C 233 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.079358 restraints weight = 49203.510| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.71 r_work: 0.2771 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15309 Z= 0.101 Angle : 0.454 7.468 20873 Z= 0.244 Chirality : 0.038 0.149 2315 Planarity : 0.003 0.040 2515 Dihedral : 13.209 132.536 2629 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.76 % Allowed : 23.78 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.37 (0.20), residues: 1711 helix: 2.02 (0.18), residues: 833 sheet: 0.52 (0.37), residues: 177 loop : -0.31 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 584 TYR 0.017 0.001 TYR B 557 PHE 0.013 0.001 PHE B 185 TRP 0.016 0.001 TRP C 49 HIS 0.003 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (15309) covalent geometry : angle 0.45387 / 0.24 (20873) hydrogen bonds : bond 0.03764 / 2.50 ( 746) hydrogen bonds : angle 4.18093 / 2.91 ( 2065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6446 (pm20) REVERT: A 147 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8197 (tt) REVERT: A 168 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.7014 (mtm110) REVERT: A 195 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6411 (tm-30) REVERT: A 348 ILE cc_start: 0.8688 (tp) cc_final: 0.8464 (tp) REVERT: A 551 ARG cc_start: 0.7846 (mtm180) cc_final: 0.7630 (ttp80) REVERT: B 174 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8739 (mtp) REVERT: B 208 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7682 (pttp) REVERT: B 566 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8582 (t) REVERT: B 731 GLU cc_start: 0.8164 (tp30) cc_final: 0.7875 (mm-30) REVERT: B 751 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8164 (tm-30) REVERT: B 754 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7520 (ptt180) REVERT: C 53 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7249 (mpt) REVERT: G 11 SER cc_start: 0.4755 (OUTLIER) cc_final: 0.4468 (p) REVERT: G 20 THR cc_start: 0.9321 (m) cc_final: 0.9018 (p) outliers start: 56 outliers final: 22 residues processed: 240 average time/residue: 0.5593 time to fit residues: 147.8201 Evaluate side-chains 216 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 6 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 ASN B 116 GLN B 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.077937 restraints weight = 37692.386| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.52 r_work: 0.2746 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15309 Z= 0.151 Angle : 0.491 10.512 20873 Z= 0.261 Chirality : 0.039 0.163 2315 Planarity : 0.004 0.042 2515 Dihedral : 13.165 131.894 2629 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.15 % Allowed : 23.78 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1711 helix: 1.91 (0.18), residues: 839 sheet: 0.30 (0.37), residues: 186 loop : -0.30 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 287 TYR 0.016 0.001 TYR B 557 PHE 0.011 0.001 PHE A 520 TRP 0.018 0.001 TRP C 49 HIS 0.005 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (15309) covalent geometry : angle 0.49140 / 0.26 (20873) hydrogen bonds : bond 0.04234 / 2.82 ( 746) hydrogen bonds : angle 4.23680 / 2.95 ( 2065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 198 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6516 (pm20) REVERT: A 138 ILE cc_start: 0.8235 (mp) cc_final: 0.8032 (mp) REVERT: A 147 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8257 (tt) REVERT: A 168 ARG cc_start: 0.7702 (mtm-85) cc_final: 0.7069 (mtm110) REVERT: A 195 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6309 (tm-30) REVERT: A 348 ILE cc_start: 0.8691 (tp) cc_final: 0.8471 (tp) REVERT: A 551 ARG cc_start: 0.7925 (mtm180) cc_final: 0.7697 (ttp80) REVERT: A 559 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8215 (mtp85) REVERT: B 1 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.6842 (tpt) REVERT: B 208 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7680 (pttp) REVERT: B 566 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8624 (t) REVERT: B 655 MET cc_start: 0.7340 (mmm) cc_final: 0.7113 (mmp) REVERT: B 731 GLU cc_start: 0.8283 (tp30) cc_final: 0.7949 (mm-30) REVERT: C 53 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7317 (mpt) REVERT: C 202 MET cc_start: 0.8517 (mtp) cc_final: 0.8239 (mmt) REVERT: G 11 SER cc_start: 0.4724 (OUTLIER) cc_final: 0.4413 (p) REVERT: G 20 THR cc_start: 0.9382 (m) cc_final: 0.9068 (p) outliers start: 62 outliers final: 33 residues processed: 240 average time/residue: 0.6327 time to fit residues: 166.6514 Evaluate side-chains 226 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 118 optimal weight: 1.9990 chunk 11 optimal weight: 0.0050 chunk 161 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 41 optimal weight: 0.0670 overall best weight: 0.5134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 481 GLN A 499 ASN B 582 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.108316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.081701 restraints weight = 28503.875| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.18 r_work: 0.2822 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15309 Z= 0.098 Angle : 0.461 8.259 20873 Z= 0.245 Chirality : 0.037 0.154 2315 Planarity : 0.003 0.041 2515 Dihedral : 13.067 130.627 2628 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.37 % Allowed : 24.24 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.36 (0.20), residues: 1711 helix: 2.00 (0.18), residues: 834 sheet: 0.40 (0.38), residues: 178 loop : -0.27 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 287 TYR 0.014 0.001 TYR B 557 PHE 0.015 0.001 PHE A 53 TRP 0.018 0.001 TRP C 49 HIS 0.003 0.000 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (15309) covalent geometry : angle 0.46065 / 0.24 (20873) hydrogen bonds : bond 0.03650 / 2.43 ( 746) hydrogen bonds : angle 4.10430 / 2.85 ( 2065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6430 (pm20) REVERT: A 138 ILE cc_start: 0.8303 (mp) cc_final: 0.8053 (mp) REVERT: A 168 ARG cc_start: 0.7699 (mtm-85) cc_final: 0.7102 (mtm110) REVERT: A 195 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6300 (tm-30) REVERT: A 348 ILE cc_start: 0.8673 (tp) cc_final: 0.8442 (tp) REVERT: A 551 ARG cc_start: 0.7872 (mtm180) cc_final: 0.7670 (ttp80) REVERT: A 559 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8166 (mtp85) REVERT: B 1 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.6868 (tpt) REVERT: B 208 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7683 (pttp) REVERT: B 566 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8595 (t) REVERT: B 731 GLU cc_start: 0.8232 (tp30) cc_final: 0.7950 (mm-30) REVERT: B 754 ARG cc_start: 0.8041 (ttt180) cc_final: 0.7519 (ptt180) REVERT: C 53 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7255 (mpt) REVERT: G 11 SER cc_start: 0.4627 (OUTLIER) cc_final: 0.4345 (p) REVERT: G 20 THR cc_start: 0.9335 (m) cc_final: 0.9058 (p) outliers start: 50 outliers final: 23 residues processed: 232 average time/residue: 0.6166 time to fit residues: 156.9477 Evaluate side-chains 218 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 121 optimal weight: 0.8980 chunk 152 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 26 optimal weight: 0.0870 chunk 154 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 ASN C 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.108459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.080346 restraints weight = 41086.311| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.71 r_work: 0.2778 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15309 Z= 0.100 Angle : 0.455 8.149 20873 Z= 0.242 Chirality : 0.038 0.217 2315 Planarity : 0.003 0.042 2515 Dihedral : 12.986 128.269 2627 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.24 % Allowed : 24.37 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.38 (0.20), residues: 1711 helix: 1.98 (0.18), residues: 834 sheet: 0.46 (0.38), residues: 178 loop : -0.22 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 287 TYR 0.015 0.001 TYR B 557 PHE 0.013 0.001 PHE A 191 TRP 0.015 0.001 TRP C 49 HIS 0.002 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (15309) covalent geometry : angle 0.45499 / 0.24 (20873) hydrogen bonds : bond 0.03581 / 2.39 ( 746) hydrogen bonds : angle 4.05780 / 2.81 ( 2065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6489 (pm20) REVERT: A 138 ILE cc_start: 0.8303 (mp) cc_final: 0.8089 (mp) REVERT: A 168 ARG cc_start: 0.7644 (mtm-85) cc_final: 0.7028 (mtm110) REVERT: B 1 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.6753 (tpt) REVERT: B 208 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7692 (pttp) REVERT: B 566 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8567 (t) REVERT: B 731 GLU cc_start: 0.8176 (tp30) cc_final: 0.7945 (mm-30) REVERT: B 754 ARG cc_start: 0.7994 (ttt180) cc_final: 0.7555 (ptt180) REVERT: C 53 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7116 (mpt) REVERT: G 11 SER cc_start: 0.4679 (OUTLIER) cc_final: 0.4407 (p) REVERT: G 20 THR cc_start: 0.9327 (m) cc_final: 0.9042 (p) outliers start: 48 outliers final: 25 residues processed: 229 average time/residue: 0.6382 time to fit residues: 160.0554 Evaluate side-chains 220 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 208 LYS Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 124 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 77 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 131 optimal weight: 0.0470 overall best weight: 0.4882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 ASN C 100 ASN C 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.109526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.082596 restraints weight = 30924.154| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.27 r_work: 0.2829 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15309 Z= 0.093 Angle : 0.462 14.183 20873 Z= 0.242 Chirality : 0.037 0.176 2315 Planarity : 0.003 0.042 2515 Dihedral : 12.932 126.685 2627 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.59 % Allowed : 25.02 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1711 helix: 2.01 (0.18), residues: 834 sheet: 0.71 (0.39), residues: 169 loop : -0.23 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 551 TYR 0.018 0.001 TYR B 557 PHE 0.018 0.001 PHE A 53 TRP 0.016 0.001 TRP C 49 HIS 0.002 0.000 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (15309) covalent geometry : angle 0.46204 / 0.24 (20873) hydrogen bonds : bond 0.03409 / 2.27 ( 746) hydrogen bonds : angle 4.00722 / 2.77 ( 2065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6439 (pm20) REVERT: A 168 ARG cc_start: 0.7656 (mtm-85) cc_final: 0.7444 (mtm180) REVERT: A 356 ARG cc_start: 0.7995 (tpp80) cc_final: 0.7672 (mmt90) REVERT: B 566 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8607 (p) REVERT: B 684 GLU cc_start: 0.7844 (tt0) cc_final: 0.7494 (tt0) REVERT: B 731 GLU cc_start: 0.8278 (tp30) cc_final: 0.8038 (mm-30) REVERT: B 754 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7596 (ptt180) REVERT: G 11 SER cc_start: 0.4684 (OUTLIER) cc_final: 0.4404 (p) REVERT: G 20 THR cc_start: 0.9327 (m) cc_final: 0.9040 (p) outliers start: 38 outliers final: 21 residues processed: 217 average time/residue: 0.6395 time to fit residues: 152.5891 Evaluate side-chains 210 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain B residue 754 ARG Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 90 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 26 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.080353 restraints weight = 36908.643| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.65 r_work: 0.2788 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15309 Z= 0.104 Angle : 0.466 8.241 20873 Z= 0.247 Chirality : 0.037 0.170 2315 Planarity : 0.003 0.039 2515 Dihedral : 12.892 125.544 2625 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.27 % Allowed : 25.47 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.42 (0.20), residues: 1711 helix: 2.00 (0.18), residues: 834 sheet: 0.51 (0.38), residues: 178 loop : -0.21 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 287 TYR 0.019 0.001 TYR G 17 PHE 0.008 0.001 PHE A 520 TRP 0.016 0.001 TRP C 49 HIS 0.002 0.000 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (15309) covalent geometry : angle 0.46584 / 0.25 (20873) hydrogen bonds : bond 0.03480 / 2.32 ( 746) hydrogen bonds : angle 4.02913 / 2.79 ( 2065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6451 (pm20) REVERT: A 134 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7870 (tptm) REVERT: A 168 ARG cc_start: 0.7625 (mtm-85) cc_final: 0.7368 (mtm110) REVERT: A 356 ARG cc_start: 0.8025 (tpp80) cc_final: 0.7816 (mmt90) REVERT: B 731 GLU cc_start: 0.8280 (tp30) cc_final: 0.8047 (mm-30) REVERT: C 15 ARG cc_start: 0.7689 (mmm160) cc_final: 0.7435 (tpt170) REVERT: C 53 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7247 (mpt) REVERT: G 11 SER cc_start: 0.4674 (OUTLIER) cc_final: 0.4388 (p) REVERT: G 20 THR cc_start: 0.9346 (m) cc_final: 0.9056 (p) outliers start: 33 outliers final: 21 residues processed: 209 average time/residue: 0.6180 time to fit residues: 141.4106 Evaluate side-chains 204 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 110 optimal weight: 0.7980 chunk 134 optimal weight: 0.0060 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 70 optimal weight: 0.0470 chunk 129 optimal weight: 0.4980 chunk 26 optimal weight: 0.0010 chunk 73 optimal weight: 5.9990 overall best weight: 0.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 ASN B 582 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.082412 restraints weight = 38221.738| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.70 r_work: 0.2832 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15309 Z= 0.093 Angle : 0.474 13.868 20873 Z= 0.248 Chirality : 0.037 0.162 2315 Planarity : 0.003 0.041 2515 Dihedral : 12.860 123.396 2625 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.01 % Allowed : 25.41 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.46 (0.20), residues: 1711 helix: 2.02 (0.18), residues: 835 sheet: 0.74 (0.40), residues: 165 loop : -0.22 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 495 TYR 0.017 0.001 TYR B 557 PHE 0.016 0.001 PHE A 53 TRP 0.017 0.001 TRP C 49 HIS 0.002 0.000 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (15309) covalent geometry : angle 0.47353 / 0.25 (20873) hydrogen bonds : bond 0.03194 / 2.12 ( 746) hydrogen bonds : angle 3.98191 / 2.76 ( 2065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6474 (pm20) REVERT: A 130 TYR cc_start: 0.7617 (t80) cc_final: 0.7302 (t80) REVERT: A 168 ARG cc_start: 0.7611 (mtm-85) cc_final: 0.7346 (mtm110) REVERT: A 356 ARG cc_start: 0.7930 (tpp80) cc_final: 0.7689 (mmt90) REVERT: B 159 GLU cc_start: 0.7355 (mp0) cc_final: 0.7105 (mp0) REVERT: C 53 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7076 (mpt) REVERT: G 11 SER cc_start: 0.4703 (OUTLIER) cc_final: 0.4449 (p) REVERT: G 20 THR cc_start: 0.9306 (m) cc_final: 0.9033 (p) outliers start: 29 outliers final: 15 residues processed: 217 average time/residue: 0.6350 time to fit residues: 150.7771 Evaluate side-chains 209 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 CYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 728 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 134 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 chunk 137 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 ASN B 582 GLN C 236 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.109473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.082578 restraints weight = 25579.787| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.18 r_work: 0.2850 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15309 Z= 0.103 Angle : 0.469 8.669 20873 Z= 0.248 Chirality : 0.037 0.162 2315 Planarity : 0.004 0.044 2515 Dihedral : 12.792 121.919 2623 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.62 % Allowed : 25.99 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 1.46 (0.20), residues: 1711 helix: 2.02 (0.18), residues: 835 sheet: 0.75 (0.40), residues: 169 loop : -0.21 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 495 TYR 0.018 0.001 TYR B 557 PHE 0.016 0.001 PHE A 105 TRP 0.016 0.001 TRP C 49 HIS 0.002 0.000 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (15309) covalent geometry : angle 0.46938 / 0.25 (20873) hydrogen bonds : bond 0.03368 / 2.25 ( 746) hydrogen bonds : angle 3.98884 / 2.77 ( 2065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5370.23 seconds wall clock time: 92 minutes 14.12 seconds (5534.12 seconds total)