Starting phenix.real_space_refine on Sat Aug 8 21:53:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rag_53877/08_2026/9rag_53877.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rag_53877/08_2026/9rag_53877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rag_53877/08_2026/9rag_53877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rag_53877/08_2026/9rag_53877.map" model { file = "/net/cci-nas-00/data/ceres_data/9rag_53877/08_2026/9rag_53877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rag_53877/08_2026/9rag_53877.cif" } resolution = 1.99 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= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 49 5.49 5 Mg 3 5.21 5 S 103 5.16 5 C 9186 2.51 5 N 2590 2.21 5 O 3600 1.98 5 H 14344 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29875 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 11590 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 716, 11546 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 33, 'TRANS': 682} Conformer: "B" Number of residues, atoms: 716, 11546 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 33, 'TRANS': 682} bond proxies already assigned to first conformer: 11624 Chain: "C" Number of atoms: 4140 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 4084 Classifications: {'peptide': 248} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 235} Conformer: "B" Number of residues, atoms: 248, 4084 Classifications: {'peptide': 248} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 235} bond proxies already assigned to first conformer: 4065 Chain: "G" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 351 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 7, 'TRANS': 17} Chain: "M" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 361 Classifications: {'RNA': 11} Modifications used: {'3*END': 1, 'rna3p_pur': 7, 'rna3p_pyr': 4} Link IDs: {'rna3p': 10} Chain: "B" Number of atoms: 11688 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 726, 11598 Classifications: {'peptide': 726} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 695} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 726, 11598 Classifications: {'peptide': 726} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 695} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 11615 Chain: "T" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1066 Classifications: {'RNA': 33} Modifications used: {'3*END': 1, 'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 12, 'rna3p_pyr': 9} Link IDs: {'rna2p': 11, 'rna3p': 21} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {' MG': 2, 'POP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 229 Classifications: {'water': 229} Link IDs: {None: 228} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "G" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 261 Classifications: {'water': 261} Link IDs: {None: 260} Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ALYS A 378 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS A 378 " occ=0.50 residue: pdb=" N AILE A 465 " occ=0.50 ... (36 atoms not shown) pdb="HD13BILE A 465 " occ=0.50 residue: pdb=" N AARG C 46 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG C 46 " occ=0.50 residue: pdb=" N AMET C 50 " occ=0.50 ... (32 atoms not shown) pdb=" HE3BMET C 50 " occ=0.50 residue: pdb=" N AASN C 148 " occ=0.40 ... (26 atoms not shown) pdb="HD22BASN C 148 " occ=0.60 residue: pdb=" N AILE B 322 " occ=0.50 ... (36 atoms not shown) pdb="HD13BILE B 322 " occ=0.50 residue: pdb=" N AARG B 334 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG B 334 " occ=0.50 residue: pdb=" N ALEU B 337 " occ=0.50 ... (36 atoms not shown) pdb="HD23BLEU B 337 " occ=0.50 residue: pdb=" N AARG B 350 " occ=0.60 ... (46 atoms not shown) pdb="HH22BARG B 350 " occ=0.40 Time building chain proxies: 8.22, per 1000 atoms: 0.28 Number of scatterers: 29875 At special positions: 0 Unit cell: (95.63, 102.2, 142.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 103 16.00 P 49 15.00 Mg 3 11.99 O 3600 8.00 N 2590 7.00 C 9186 6.00 H 14344 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.5 seconds 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3262 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 16 sheets defined 53.8% alpha, 12.9% beta 12 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 5.82 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 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.786A pdb=" N GLU A 199 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.759A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.593A pdb=" N GLU A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.632A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 582 through 604 removed outlier: 3.981A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.868A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 697 through 715 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 24 through 37 removed outlier: 3.827A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.747A 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: 3.660A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 13 through 22 removed outlier: 5.683A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.512A pdb=" N SER B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 265 removed outlier: 4.101A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 293 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.558A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.113A pdb=" N TYR B 380 " --> pdb=" O ASP B 377 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 381' Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 removed outlier: 3.527A pdb=" N SER B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 473 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.537A pdb=" N MET B 507 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.865A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 685 through 700 removed outlier: 3.647A pdb=" N TYR B 689 " --> pdb=" O ASP B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.300A 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 sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.407A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.293A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLY A 555 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG A 551 " --> pdb=" O GLY A 555 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU A 549 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A 542 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY A 546 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N GLU A 319 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N MET A 548 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N TRP A 317 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.291A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.843A 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 378 removed outlier: 5.822A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.128A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 80 removed outlier: 4.474A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.702A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.513A pdb=" N LYS C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AB3, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AB5, first strand: chain 'B' and resid 187 through 188 Processing sheet with id=AB6, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.891A pdb=" N LEU B 224 " --> pdb=" O AARG B 350 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 489 through 492 742 hydrogen bonds defined for protein. 2053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 7.46 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14315 1.03 - 1.23: 45 1.23 - 1.42: 6422 1.42 - 1.62: 8649 1.62 - 1.81: 177 Bond restraints: 29608 Sorted by residual: bond pdb=" O POP B 803 " pdb=" P2 POP B 803 " ideal model delta sigma weight residual 1.661 1.611 0.050 2.00e-02 2.50e+03 6.32e+00 bond pdb=" O POP B 803 " pdb=" P1 POP B 803 " ideal model delta sigma weight residual 1.660 1.612 0.048 2.00e-02 2.50e+03 5.67e+00 bond pdb=" N9 G T 2 " pdb=" C4 G T 2 " ideal model delta sigma weight residual 1.375 1.365 0.010 8.00e-03 1.56e+04 1.59e+00 bond pdb=" O1 POP B 803 " pdb=" P1 POP B 803 " ideal model delta sigma weight residual 1.531 1.507 0.024 2.00e-02 2.50e+03 1.42e+00 bond pdb=" N9 A T 8 " pdb=" C4 A T 8 " ideal model delta sigma weight residual 1.374 1.367 0.007 6.00e-03 2.78e+04 1.40e+00 ... (remaining 29603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 53471 3.59 - 7.18: 23 7.18 - 10.77: 1 10.77 - 14.36: 0 14.36 - 17.94: 1 Bond angle restraints: 53496 Sorted by residual: angle pdb=" P1 POP B 803 " pdb=" O POP B 803 " pdb=" P2 POP B 803 " ideal model delta sigma weight residual 139.66 121.72 17.94 3.00e+00 1.11e-01 3.58e+01 angle pdb=" O4' A T 7 " pdb=" C1' A T 7 " pdb=" N9 A T 7 " ideal model delta sigma weight residual 108.20 111.95 -3.75 8.00e-01 1.56e+00 2.20e+01 angle pdb=" O5' C T 69 " pdb=" C5' C T 69 " pdb=" C4' C T 69 " ideal model delta sigma weight residual 109.40 112.08 -2.68 8.00e-01 1.56e+00 1.13e+01 angle pdb=" O5' U T 70 " pdb=" C5' U T 70 " pdb=" C4' U T 70 " ideal model delta sigma weight residual 109.40 112.08 -2.68 8.00e-01 1.56e+00 1.13e+01 angle pdb=" O5' U T 65 " pdb=" C5' U T 65 " pdb=" C4' U T 65 " ideal model delta sigma weight residual 109.40 112.06 -2.66 8.00e-01 1.56e+00 1.10e+01 ... (remaining 53491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 12395 17.76 - 35.51: 1009 35.51 - 53.27: 380 53.27 - 71.03: 140 71.03 - 88.79: 44 Dihedral angle restraints: 13968 sinusoidal: 8089 harmonic: 5879 Sorted by residual: dihedral pdb=" CA ILE B 302 " pdb=" C ILE B 302 " pdb=" N THR B 303 " pdb=" CA THR B 303 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ARG B 602 " pdb=" C ARG B 602 " pdb=" N ASN B 603 " pdb=" CA ASN B 603 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA TYR A 540 " pdb=" C TYR A 540 " pdb=" N CYS A 541 " pdb=" CA CYS A 541 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 13965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1656 0.035 - 0.070: 442 0.070 - 0.104: 143 0.104 - 0.139: 54 0.139 - 0.174: 6 Chirality restraints: 2301 Sorted by residual: chirality pdb=" C1' A T 4 " pdb=" O4' A T 4 " pdb=" C2' A T 4 " pdb=" N9 A T 4 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" C1' A T 7 " pdb=" O4' A T 7 " pdb=" C2' A T 7 " pdb=" N9 A T 7 " both_signs ideal model delta sigma weight residual False 2.44 2.29 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE A 302 " pdb=" N ILE A 302 " pdb=" C ILE A 302 " pdb=" CB ILE A 302 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 2298 not shown) Planarity restraints: 4198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A T 4 " 0.033 2.00e-02 2.50e+03 1.31e-02 5.55e+00 pdb=" N9 A T 4 " -0.031 2.00e-02 2.50e+03 pdb=" C8 A T 4 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A T 4 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A T 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A T 4 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A T 4 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A T 4 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A T 4 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A T 4 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A T 4 " -0.004 2.00e-02 2.50e+03 pdb=" H8 A T 4 " -0.001 2.00e-02 2.50e+03 pdb=" H2 A T 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A T 7 " 0.027 2.00e-02 2.50e+03 1.12e-02 4.06e+00 pdb=" N9 A T 7 " -0.027 2.00e-02 2.50e+03 pdb=" C8 A T 7 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A T 7 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A T 7 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A T 7 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A T 7 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A T 7 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A T 7 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A T 7 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A T 7 " -0.006 2.00e-02 2.50e+03 pdb=" H8 A T 7 " -0.001 2.00e-02 2.50e+03 pdb=" H2 A T 7 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 594 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C SER A 594 " -0.027 2.00e-02 2.50e+03 pdb=" O SER A 594 " 0.010 2.00e-02 2.50e+03 pdb=" N MET A 595 " 0.009 2.00e-02 2.50e+03 ... (remaining 4195 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2129 2.20 - 2.80: 60893 2.80 - 3.40: 89618 3.40 - 4.00: 121528 4.00 - 4.60: 182220 Nonbonded interactions: 456388 Sorted by model distance: nonbonded pdb=" OE1 GLU A 427 " pdb=" H GLU A 427 " model vdw 1.600 2.450 nonbonded pdb=" OE2 GLU B 519 " pdb="HH12 ARG B 572 " model vdw 1.650 2.450 nonbonded pdb=" H HIS A 326 " pdb=" OD1 ASN A 331 " model vdw 1.655 2.450 nonbonded pdb=" HZ2 LYS A 362 " pdb=" O ASP A 478 " model vdw 1.655 2.450 nonbonded pdb=" HE ARG A 583 " pdb=" O PHE B 512 " model vdw 1.660 2.450 ... (remaining 456383 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.240 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 36.610 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15264 Z= 0.139 Angle : 0.518 17.945 20821 Z= 0.313 Chirality : 0.039 0.174 2301 Planarity : 0.003 0.035 2519 Dihedral : 17.616 88.787 6146 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.78 % Allowed : 11.25 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.20), residues: 1719 helix: 1.87 (0.18), residues: 846 sheet: -0.27 (0.36), residues: 189 loop : 0.30 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 144 TYR 0.023 0.001 TYR B 557 PHE 0.013 0.001 PHE B 551 TRP 0.015 0.002 TRP C 49 HIS 0.003 0.001 HIS B 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (15264) covalent geometry : angle 0.51780 / 0.31 (20821) hydrogen bonds : bond 0.12388 / 8.05 ( 771) hydrogen bonds : angle 5.53299 / 4.07 ( 2119) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 238 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7371 (mt-10) REVERT: A 84 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7602 (ttt90) REVERT: A 394 ASP cc_start: 0.8181 (t70) cc_final: 0.7971 (t0) REVERT: C 11 MET cc_start: 0.8251 (mmm) cc_final: 0.7700 (mmm) REVERT: C 17 ARG cc_start: 0.7786 (ttp-110) cc_final: 0.7577 (ttp80) REVERT: C 146 ASP cc_start: 0.8176 (m-30) cc_final: 0.7894 (m-30) REVERT: C 160 GLN cc_start: 0.7932 (mt0) cc_final: 0.7004 (tp-100) REVERT: C 176 ILE cc_start: 0.8099 (tt) cc_final: 0.7812 (pp) REVERT: C 191 LYS cc_start: 0.8066 (tttt) cc_final: 0.7694 (tmtt) REVERT: B 104 GLU cc_start: 0.8141 (tt0) cc_final: 0.7897 (mp0) REVERT: B 116 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8261 (mp10) REVERT: B 120 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8565 (p0) REVERT: B 159 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7419 (mm-30) REVERT: B 179 MET cc_start: 0.8584 (tpt) cc_final: 0.8296 (mmm) REVERT: B 227 MET cc_start: 0.8243 (mpp) cc_final: 0.8025 (mpp) REVERT: B 287 ARG cc_start: 0.7954 (ttm110) cc_final: 0.7724 (ttm-80) REVERT: B 445 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8613 (p0) REVERT: B 569 GLN cc_start: 0.8609 (mm110) cc_final: 0.8388 (mm110) REVERT: B 602 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7915 (ttp-110) REVERT: B 691 LYS cc_start: 0.7679 (mtpt) cc_final: 0.7295 (mttp) REVERT: B 707 ARG cc_start: 0.8024 (tmm160) cc_final: 0.7746 (ttp80) outliers start: 12 outliers final: 2 residues processed: 250 average time/residue: 1.6806 time to fit residues: 455.4497 Evaluate side-chains 209 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 204 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 602 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 614 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.160213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117909 restraints weight = 67882.933| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.93 r_work: 0.3103 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15264 Z= 0.200 Angle : 0.577 5.903 20821 Z= 0.317 Chirality : 0.040 0.175 2301 Planarity : 0.005 0.046 2519 Dihedral : 13.444 82.714 2603 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.91 % Allowed : 11.70 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.20), residues: 1719 helix: 1.63 (0.17), residues: 851 sheet: -0.37 (0.37), residues: 188 loop : 0.25 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 279 TYR 0.030 0.002 TYR B 557 PHE 0.017 0.002 PHE B 551 TRP 0.019 0.002 TRP B 309 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (15264) covalent geometry : angle 0.57721 / 0.32 (20821) hydrogen bonds : bond 0.06727 / 4.51 ( 771) hydrogen bonds : angle 5.06790 / 3.74 ( 2119) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7336 (mt-10) REVERT: A 84 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7681 (ttt90) REVERT: A 119 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6895 (tt0) REVERT: A 204 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7841 (ttm170) REVERT: A 386 ASP cc_start: 0.7397 (m-30) cc_final: 0.7193 (m-30) REVERT: A 394 ASP cc_start: 0.8182 (t70) cc_final: 0.7970 (t0) REVERT: C 11 MET cc_start: 0.8233 (mmm) cc_final: 0.7736 (mmm) REVERT: C 146 ASP cc_start: 0.8288 (m-30) cc_final: 0.7987 (m-30) REVERT: C 160 GLN cc_start: 0.7861 (mt0) cc_final: 0.6992 (tp-100) REVERT: C 176 ILE cc_start: 0.8096 (tt) cc_final: 0.7829 (pp) REVERT: C 191 LYS cc_start: 0.8081 (tttt) cc_final: 0.7658 (tmtt) REVERT: B 159 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7419 (mm-30) REVERT: B 179 MET cc_start: 0.8593 (tpt) cc_final: 0.8251 (mmm) REVERT: B 430 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8323 (pttp) REVERT: B 569 GLN cc_start: 0.8601 (mm110) cc_final: 0.8399 (mm110) REVERT: B 691 LYS cc_start: 0.7666 (mtpt) cc_final: 0.7266 (mttp) REVERT: B 707 ARG cc_start: 0.8022 (tmm160) cc_final: 0.7741 (ttp80) outliers start: 14 outliers final: 5 residues processed: 212 average time/residue: 1.9145 time to fit residues: 439.4452 Evaluate side-chains 201 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 193 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 614 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 38 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 614 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.161980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.119093 restraints weight = 63490.020| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.90 r_work: 0.3158 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15264 Z= 0.128 Angle : 0.512 5.041 20821 Z= 0.278 Chirality : 0.038 0.159 2301 Planarity : 0.004 0.040 2519 Dihedral : 13.289 83.272 2592 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.65 % Allowed : 12.22 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.20), residues: 1719 helix: 1.69 (0.18), residues: 856 sheet: -0.38 (0.37), residues: 186 loop : 0.24 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 721 TYR 0.023 0.002 TYR B 557 PHE 0.014 0.001 PHE B 551 TRP 0.015 0.002 TRP B 309 HIS 0.004 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (15264) covalent geometry : angle 0.51168 / 0.28 (20821) hydrogen bonds : bond 0.05694 / 3.83 ( 771) hydrogen bonds : angle 4.85608 / 3.59 ( 2119) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7307 (mt-10) REVERT: A 84 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7622 (ttt90) REVERT: A 386 ASP cc_start: 0.7385 (m-30) cc_final: 0.7184 (m-30) REVERT: C 11 MET cc_start: 0.8165 (mmm) cc_final: 0.7596 (mmm) REVERT: C 146 ASP cc_start: 0.8195 (m-30) cc_final: 0.7898 (m-30) REVERT: C 160 GLN cc_start: 0.7845 (mt0) cc_final: 0.6911 (tp-100) REVERT: C 176 ILE cc_start: 0.8080 (tt) cc_final: 0.7815 (pp) REVERT: C 191 LYS cc_start: 0.8067 (tttt) cc_final: 0.7693 (tmtt) REVERT: B 159 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7418 (mm-30) REVERT: B 179 MET cc_start: 0.8582 (tpt) cc_final: 0.8291 (mmm) REVERT: B 430 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8306 (pttp) REVERT: B 569 GLN cc_start: 0.8614 (mm110) cc_final: 0.8404 (mm110) REVERT: B 691 LYS cc_start: 0.7634 (mtpt) cc_final: 0.7243 (mttp) REVERT: B 707 ARG cc_start: 0.8036 (tmm160) cc_final: 0.7739 (ttp80) outliers start: 10 outliers final: 3 residues processed: 203 average time/residue: 1.7213 time to fit residues: 379.8469 Evaluate side-chains 193 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 189 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 430 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 614 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.159485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.116907 restraints weight = 63547.125| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.90 r_work: 0.3121 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15264 Z= 0.204 Angle : 0.580 5.807 20821 Z= 0.318 Chirality : 0.040 0.170 2301 Planarity : 0.004 0.050 2519 Dihedral : 13.383 83.741 2592 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.72 % Allowed : 11.77 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.20), residues: 1719 helix: 1.50 (0.17), residues: 855 sheet: -0.39 (0.37), residues: 188 loop : 0.18 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 401 TYR 0.030 0.002 TYR B 557 PHE 0.018 0.002 PHE B 551 TRP 0.019 0.002 TRP B 309 HIS 0.006 0.001 HIS B 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (15264) covalent geometry : angle 0.58016 / 0.32 (20821) hydrogen bonds : bond 0.06659 / 4.47 ( 771) hydrogen bonds : angle 5.01430 / 3.70 ( 2119) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7337 (mt-10) REVERT: A 84 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7641 (ttt90) REVERT: C 11 MET cc_start: 0.8191 (mmm) cc_final: 0.7604 (mmm) REVERT: C 146 ASP cc_start: 0.8280 (m-30) cc_final: 0.7990 (m-30) REVERT: C 160 GLN cc_start: 0.7861 (mt0) cc_final: 0.7031 (tp-100) REVERT: C 176 ILE cc_start: 0.8115 (tt) cc_final: 0.7898 (pp) REVERT: C 191 LYS cc_start: 0.8064 (tttt) cc_final: 0.7715 (tmtt) REVERT: C 192 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: B 159 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7459 (mm-30) REVERT: B 179 MET cc_start: 0.8612 (tpt) cc_final: 0.8228 (mmm) REVERT: B 430 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8340 (pttp) REVERT: B 691 LYS cc_start: 0.7687 (mtpt) cc_final: 0.7281 (mttp) REVERT: B 707 ARG cc_start: 0.8052 (tmm160) cc_final: 0.7774 (ttp80) outliers start: 11 outliers final: 4 residues processed: 199 average time/residue: 1.7386 time to fit residues: 375.3650 Evaluate side-chains 198 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 192 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 430 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 67 optimal weight: 0.0010 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 614 ASN B 569 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.161481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119228 restraints weight = 62320.680| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.82 r_work: 0.3152 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15264 Z= 0.130 Angle : 0.519 5.441 20821 Z= 0.281 Chirality : 0.038 0.158 2301 Planarity : 0.004 0.040 2519 Dihedral : 13.321 84.805 2592 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.52 % Allowed : 12.09 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.20), residues: 1719 helix: 1.64 (0.17), residues: 855 sheet: -0.41 (0.38), residues: 186 loop : 0.15 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 721 TYR 0.023 0.002 TYR B 557 PHE 0.014 0.001 PHE B 551 TRP 0.016 0.002 TRP B 309 HIS 0.004 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (15264) covalent geometry : angle 0.51861 / 0.28 (20821) hydrogen bonds : bond 0.05626 / 3.79 ( 771) hydrogen bonds : angle 4.81744 / 3.56 ( 2119) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7307 (mt-10) REVERT: A 84 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7648 (ttt90) REVERT: C 18 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7150 (mm-30) REVERT: C 146 ASP cc_start: 0.8212 (m-30) cc_final: 0.7909 (m-30) REVERT: C 160 GLN cc_start: 0.7815 (mt0) cc_final: 0.6939 (tp-100) REVERT: C 176 ILE cc_start: 0.8102 (tt) cc_final: 0.7859 (pp) REVERT: C 191 LYS cc_start: 0.8067 (tttt) cc_final: 0.7719 (tmtt) REVERT: B 120 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8572 (p0) REVERT: B 159 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7490 (mm-30) REVERT: B 179 MET cc_start: 0.8594 (tpt) cc_final: 0.8270 (mmm) REVERT: B 372 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7998 (ptm) REVERT: B 430 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8370 (pttp) REVERT: B 553 LYS cc_start: 0.8599 (tttt) cc_final: 0.8382 (ttpt) REVERT: B 691 LYS cc_start: 0.7689 (mtpt) cc_final: 0.7288 (mttp) REVERT: B 707 ARG cc_start: 0.8055 (tmm160) cc_final: 0.7765 (ttp80) outliers start: 8 outliers final: 4 residues processed: 200 average time/residue: 1.8274 time to fit residues: 396.8218 Evaluate side-chains 197 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 190 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 430 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 39 optimal weight: 0.0170 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 614 ASN B 569 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.160154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118436 restraints weight = 70670.987| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.05 r_work: 0.3114 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15264 Z= 0.168 Angle : 0.553 5.520 20821 Z= 0.301 Chirality : 0.039 0.166 2301 Planarity : 0.004 0.042 2519 Dihedral : 13.342 85.057 2592 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.52 % Allowed : 12.16 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.20), residues: 1719 helix: 1.56 (0.17), residues: 855 sheet: -0.42 (0.38), residues: 188 loop : 0.14 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 144 TYR 0.027 0.002 TYR B 557 PHE 0.016 0.002 PHE B 551 TRP 0.017 0.002 TRP B 309 HIS 0.005 0.001 HIS B 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (15264) covalent geometry : angle 0.55261 / 0.30 (20821) hydrogen bonds : bond 0.06155 / 4.14 ( 771) hydrogen bonds : angle 4.90123 / 3.62 ( 2119) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 190 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7343 (mt-10) REVERT: A 84 ARG cc_start: 0.8125 (ttp80) cc_final: 0.7672 (ttt90) REVERT: C 18 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7205 (mm-30) REVERT: C 146 ASP cc_start: 0.8273 (m-30) cc_final: 0.7975 (m-30) REVERT: C 160 GLN cc_start: 0.7872 (mt0) cc_final: 0.6973 (tp-100) REVERT: C 176 ILE cc_start: 0.8116 (tt) cc_final: 0.7900 (pp) REVERT: C 191 LYS cc_start: 0.8088 (tttt) cc_final: 0.7722 (tmtt) REVERT: B 120 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8601 (p0) REVERT: B 159 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7512 (mm-30) REVERT: B 179 MET cc_start: 0.8618 (tpt) cc_final: 0.8270 (mmm) REVERT: B 372 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8019 (ptm) REVERT: B 430 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8396 (pttp) REVERT: B 553 LYS cc_start: 0.8632 (tttt) cc_final: 0.8408 (ttpt) REVERT: B 691 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7301 (mttp) REVERT: B 707 ARG cc_start: 0.8081 (tmm160) cc_final: 0.7793 (ttp80) outliers start: 8 outliers final: 4 residues processed: 196 average time/residue: 1.7084 time to fit residues: 364.5088 Evaluate side-chains 196 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 189 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 430 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 137 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 167 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 614 ASN B 569 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.160638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117989 restraints weight = 66673.473| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.00 r_work: 0.3138 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15264 Z= 0.151 Angle : 0.536 5.357 20821 Z= 0.292 Chirality : 0.038 0.161 2301 Planarity : 0.004 0.038 2519 Dihedral : 13.336 85.757 2592 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.46 % Allowed : 12.29 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.20), residues: 1719 helix: 1.62 (0.17), residues: 849 sheet: -0.41 (0.38), residues: 186 loop : 0.11 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 17 TYR 0.026 0.002 TYR B 557 PHE 0.015 0.001 PHE B 551 TRP 0.016 0.002 TRP B 309 HIS 0.004 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (15264) covalent geometry : angle 0.53559 / 0.29 (20821) hydrogen bonds : bond 0.05894 / 3.97 ( 771) hydrogen bonds : angle 4.85042 / 3.59 ( 2119) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 191 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7328 (mt-10) REVERT: A 84 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7655 (ttt90) REVERT: C 18 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7177 (mm-30) REVERT: C 146 ASP cc_start: 0.8227 (m-30) cc_final: 0.7926 (m-30) REVERT: C 160 GLN cc_start: 0.7830 (mt0) cc_final: 0.6939 (tp-100) REVERT: C 176 ILE cc_start: 0.8124 (tt) cc_final: 0.7919 (pp) REVERT: C 191 LYS cc_start: 0.8071 (tttt) cc_final: 0.7722 (tmtt) REVERT: B 120 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8558 (p0) REVERT: B 159 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7467 (mm-30) REVERT: B 179 MET cc_start: 0.8605 (tpt) cc_final: 0.8270 (mmm) REVERT: B 372 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7970 (ptm) REVERT: B 430 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8376 (pttp) REVERT: B 691 LYS cc_start: 0.7730 (mtpt) cc_final: 0.7323 (mttp) REVERT: B 707 ARG cc_start: 0.8075 (tmm160) cc_final: 0.7786 (ttp80) outliers start: 7 outliers final: 4 residues processed: 195 average time/residue: 1.7378 time to fit residues: 367.9503 Evaluate side-chains 196 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 189 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 430 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 130 optimal weight: 0.3980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 614 ASN B 569 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.161097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118905 restraints weight = 64205.803| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.17 r_work: 0.3142 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15264 Z= 0.138 Angle : 0.521 5.384 20821 Z= 0.283 Chirality : 0.038 0.155 2301 Planarity : 0.004 0.033 2519 Dihedral : 13.298 85.918 2592 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.59 % Allowed : 12.03 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.20), residues: 1719 helix: 1.69 (0.17), residues: 849 sheet: -0.44 (0.38), residues: 186 loop : 0.14 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 496 TYR 0.025 0.002 TYR B 557 PHE 0.014 0.001 PHE B 551 TRP 0.015 0.002 TRP B 309 HIS 0.004 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (15264) covalent geometry : angle 0.52127 / 0.28 (20821) hydrogen bonds : bond 0.05653 / 3.81 ( 771) hydrogen bonds : angle 4.78729 / 3.54 ( 2119) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 194 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7337 (mt-10) REVERT: A 84 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7681 (ttt90) REVERT: C 18 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7171 (mm-30) REVERT: C 146 ASP cc_start: 0.8228 (m-30) cc_final: 0.7924 (m-30) REVERT: C 160 GLN cc_start: 0.7860 (mt0) cc_final: 0.6956 (tp-100) REVERT: C 176 ILE cc_start: 0.8122 (tt) cc_final: 0.7898 (pp) REVERT: C 191 LYS cc_start: 0.8086 (tttt) cc_final: 0.7731 (tmtt) REVERT: B 120 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8582 (p0) REVERT: B 159 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7509 (mm-30) REVERT: B 179 MET cc_start: 0.8607 (tpt) cc_final: 0.8277 (mmm) REVERT: B 372 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8004 (ptm) REVERT: B 430 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8382 (pttp) REVERT: B 691 LYS cc_start: 0.7721 (mtpt) cc_final: 0.7310 (mttp) REVERT: B 707 ARG cc_start: 0.8077 (tmm160) cc_final: 0.7783 (ttp80) outliers start: 9 outliers final: 4 residues processed: 201 average time/residue: 1.6551 time to fit residues: 360.9650 Evaluate side-chains 197 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 190 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 430 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 130 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 614 ASN B 569 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.160057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.117873 restraints weight = 62034.078| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.65 r_work: 0.3123 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15264 Z= 0.168 Angle : 0.553 5.809 20821 Z= 0.301 Chirality : 0.039 0.161 2301 Planarity : 0.004 0.042 2519 Dihedral : 13.338 86.255 2592 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.59 % Allowed : 12.09 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.20), residues: 1719 helix: 1.60 (0.17), residues: 849 sheet: -0.46 (0.38), residues: 188 loop : 0.11 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 706 TYR 0.027 0.002 TYR B 557 PHE 0.016 0.002 PHE B 551 TRP 0.017 0.002 TRP B 309 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (15264) covalent geometry : angle 0.55341 / 0.30 (20821) hydrogen bonds : bond 0.06122 / 4.13 ( 771) hydrogen bonds : angle 4.88057 / 3.61 ( 2119) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7355 (mt-10) REVERT: A 84 ARG cc_start: 0.8071 (ttp80) cc_final: 0.7647 (ttt90) REVERT: C 18 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7171 (mm-30) REVERT: C 146 ASP cc_start: 0.8234 (m-30) cc_final: 0.7930 (m-30) REVERT: C 160 GLN cc_start: 0.7835 (mt0) cc_final: 0.6941 (tp-100) REVERT: C 191 LYS cc_start: 0.8081 (tttt) cc_final: 0.7734 (tmtt) REVERT: B 120 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8553 (p0) REVERT: B 159 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7535 (mm-30) REVERT: B 179 MET cc_start: 0.8624 (tpt) cc_final: 0.8268 (mmm) REVERT: B 372 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8011 (ptm) REVERT: B 430 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8373 (pttp) REVERT: B 691 LYS cc_start: 0.7724 (mtpt) cc_final: 0.7322 (mttp) REVERT: B 707 ARG cc_start: 0.8079 (tmm160) cc_final: 0.7792 (ttp80) outliers start: 9 outliers final: 6 residues processed: 198 average time/residue: 1.7231 time to fit residues: 371.0009 Evaluate side-chains 200 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 430 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 127 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 614 ASN B 569 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.161776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.120040 restraints weight = 70861.721| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.00 r_work: 0.3154 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15264 Z= 0.122 Angle : 0.509 6.061 20821 Z= 0.276 Chirality : 0.038 0.150 2301 Planarity : 0.003 0.030 2519 Dihedral : 13.280 87.453 2592 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.39 % Allowed : 12.35 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1719 helix: 1.75 (0.18), residues: 849 sheet: -0.48 (0.38), residues: 186 loop : 0.13 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 706 TYR 0.022 0.002 TYR B 557 PHE 0.013 0.001 PHE B 551 TRP 0.016 0.002 TRP C 49 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (15264) covalent geometry : angle 0.50881 / 0.28 (20821) hydrogen bonds : bond 0.05346 / 3.61 ( 771) hydrogen bonds : angle 4.72325 / 3.50 ( 2119) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 194 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7340 (mt-10) REVERT: A 84 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7657 (ttt90) REVERT: A 113 LYS cc_start: 0.7932 (tttm) cc_final: 0.7695 (ttpp) REVERT: C 18 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7149 (mm-30) REVERT: C 146 ASP cc_start: 0.8193 (m-30) cc_final: 0.7888 (m-30) REVERT: C 160 GLN cc_start: 0.7842 (mt0) cc_final: 0.6932 (tp-100) REVERT: C 191 LYS cc_start: 0.8071 (tttt) cc_final: 0.7721 (tmtt) REVERT: B 159 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7537 (mm-30) REVERT: B 179 MET cc_start: 0.8596 (tpt) cc_final: 0.8278 (mmm) REVERT: B 430 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8376 (pttp) REVERT: B 691 LYS cc_start: 0.7683 (mtpt) cc_final: 0.7274 (mttp) REVERT: B 707 ARG cc_start: 0.8067 (tmm160) cc_final: 0.7757 (ttp80) outliers start: 6 outliers final: 4 residues processed: 198 average time/residue: 1.5889 time to fit residues: 341.7455 Evaluate side-chains 195 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 190 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain B residue 430 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 77 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 166 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN B 284 ASN B 569 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.161018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.118980 restraints weight = 65933.403| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.80 r_work: 0.3153 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15264 Z= 0.141 Angle : 0.528 6.487 20821 Z= 0.286 Chirality : 0.038 0.156 2301 Planarity : 0.004 0.034 2519 Dihedral : 13.279 87.818 2592 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.33 % Allowed : 12.48 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.20), residues: 1719 helix: 1.72 (0.17), residues: 849 sheet: -0.49 (0.38), residues: 186 loop : 0.12 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 706 TYR 0.025 0.002 TYR B 557 PHE 0.015 0.001 PHE B 551 TRP 0.015 0.002 TRP C 49 HIS 0.004 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (15264) covalent geometry : angle 0.52758 / 0.29 (20821) hydrogen bonds : bond 0.05640 / 3.81 ( 771) hydrogen bonds : angle 4.76805 / 3.53 ( 2119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14572.33 seconds wall clock time: 246 minutes 44.09 seconds (14804.09 seconds total)