Starting phenix.real_space_refine on Sun Jul 5 22:03:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rag_53877/07_2026/9rag_53877.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rag_53877/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9rag_53877/07_2026/9rag_53877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rag_53877/07_2026/9rag_53877.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rag_53877/07_2026/9rag_53877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rag_53877/07_2026/9rag_53877.map" } 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-dev-6108/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: 8.52, per 1000 atoms: 0.29 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: 2.96 Conformation dependent library (CDL) restraints added in 1.3 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: 5.42 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: 8.05 Time building geometry restraints manager: 4.18 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=" N ILE A 323 " pdb=" CA ILE A 323 " pdb=" C ILE A 323 " ideal model delta sigma weight residual 113.53 110.32 3.21 9.80e-01 1.04e+00 1.07e+01 angle pdb=" N1 C T 9 " pdb=" C2 C T 9 " pdb=" O2 C T 9 " ideal model delta sigma weight residual 118.90 117.11 1.79 6.00e-01 2.78e+00 8.87e+00 angle pdb=" N1 C T 40 " pdb=" C2 C T 40 " pdb=" O2 C T 40 " ideal model delta sigma weight residual 118.90 117.29 1.61 6.00e-01 2.78e+00 7.17e+00 angle pdb=" CA TYR B 557 " pdb=" CB TYR B 557 " pdb=" CG TYR B 557 " ideal model delta sigma weight residual 113.90 109.09 4.81 1.80e+00 3.09e-01 7.15e+00 ... (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 - 0.032: 1603 0.032 - 0.064: 505 0.064 - 0.096: 127 0.096 - 0.129: 57 0.129 - 0.161: 9 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 2.46 2.30 0.16 2.00e-01 2.50e+01 6.45e-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 5.50e-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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.300 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 39.600 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.110 ------------------------------------------------------------------------------- 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 : 0.002 0.050 15264 Z= 0.135 Angle : 0.496 17.945 20821 Z= 0.281 Chirality : 0.037 0.161 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 0.00247 / 0.13 (15264) covalent geometry : angle 0.49608 / 0.28 (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 : 0.628 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: 1.5684 time to fit residues: 424.9976 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 : 0.542 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.161112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119276 restraints weight = 68058.169| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.98 r_work: 0.3124 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- 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 = 0.31 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: 0.8669 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15264 Z= 0.202 Angle : 0.571 5.893 20821 Z= 0.316 Chirality : 0.040 0.195 2301 Planarity : 0.005 0.045 2519 Dihedral : 13.482 84.142 2603 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.91 % Allowed : 11.77 % 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: 1.24 (0.20), residues: 1719 helix: 1.64 (0.17), residues: 851 sheet: -0.31 (0.36), residues: 193 loop : 0.24 (0.24), residues: 675 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 0.018 0.002 TRP B 309 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (15264) covalent geometry : angle 0.57137 / 0.32 (20821) hydrogen bonds : bond 0.06735 / 4.51 ( 771) hydrogen bonds : angle 5.07420 / 3.75 ( 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 216 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7346 (mt-10) REVERT: A 84 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7694 (ttt90) REVERT: A 119 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6856 (tt0) REVERT: A 204 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7844 (ttm170) REVERT: A 386 ASP cc_start: 0.7403 (m-30) cc_final: 0.7197 (m-30) REVERT: A 394 ASP cc_start: 0.8177 (t70) cc_final: 0.7966 (t0) REVERT: C 11 MET cc_start: 0.8241 (mmm) cc_final: 0.7747 (mmm) REVERT: C 17 ARG cc_start: 0.7773 (ttp-110) cc_final: 0.7554 (ttp80) REVERT: C 146 ASP cc_start: 0.8281 (m-30) cc_final: 0.7982 (m-30) REVERT: C 160 GLN cc_start: 0.7874 (mt0) cc_final: 0.7012 (tp-100) REVERT: C 176 ILE cc_start: 0.8094 (tt) cc_final: 0.7830 (pp) REVERT: C 191 LYS cc_start: 0.8079 (tttt) cc_final: 0.7660 (tmtt) REVERT: B 104 GLU cc_start: 0.8116 (tt0) cc_final: 0.7911 (mp0) REVERT: B 159 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7424 (mm-30) REVERT: B 179 MET cc_start: 0.8591 (tpt) cc_final: 0.8252 (mmm) REVERT: B 430 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8356 (pttp) REVERT: B 569 GLN cc_start: 0.8608 (mm110) cc_final: 0.8404 (mm110) REVERT: B 691 LYS cc_start: 0.7671 (mtpt) cc_final: 0.7273 (mttp) REVERT: B 707 ARG cc_start: 0.8026 (tmm160) cc_final: 0.7744 (ttp80) outliers start: 14 outliers final: 5 residues processed: 210 average time/residue: 1.6325 time to fit residues: 370.3249 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 : 2.199 ------------------------------------------------------------------------------- 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: 0.2980 chunk 21 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 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: 0.8980 chunk 59 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 165 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.162693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121157 restraints weight = 63616.918| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.91 r_work: 0.3173 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15264 Z= 0.119 Angle : 0.498 4.912 20821 Z= 0.270 Chirality : 0.038 0.186 2301 Planarity : 0.003 0.031 2519 Dihedral : 13.317 85.054 2592 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.72 % Allowed : 11.96 % 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: 1.33 (0.20), residues: 1719 helix: 1.77 (0.18), residues: 852 sheet: -0.39 (0.37), residues: 186 loop : 0.23 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 721 TYR 0.021 0.001 TYR B 557 PHE 0.012 0.001 PHE B 551 TRP 0.015 0.001 TRP B 309 HIS 0.004 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (15264) covalent geometry : angle 0.49785 / 0.27 (20821) hydrogen bonds : bond 0.05443 / 3.66 ( 771) hydrogen bonds : angle 4.80701 / 3.56 ( 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 211 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7327 (mt-10) REVERT: A 84 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7645 (ttt90) REVERT: C 11 MET cc_start: 0.8204 (mmm) cc_final: 0.7620 (mmm) REVERT: C 146 ASP cc_start: 0.8186 (m-30) cc_final: 0.7889 (m-30) REVERT: C 160 GLN cc_start: 0.7833 (mt0) cc_final: 0.6914 (tp-100) REVERT: C 176 ILE cc_start: 0.8071 (tt) cc_final: 0.7809 (pp) REVERT: C 191 LYS cc_start: 0.8076 (tttt) cc_final: 0.7698 (tmtt) REVERT: B 104 GLU cc_start: 0.8110 (tt0) cc_final: 0.7894 (mp0) REVERT: B 159 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7441 (mm-30) REVERT: B 179 MET cc_start: 0.8566 (tpt) cc_final: 0.8295 (mmm) REVERT: B 430 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8297 (pttp) REVERT: B 445 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8599 (p0) REVERT: B 569 GLN cc_start: 0.8632 (mm110) cc_final: 0.8421 (mm110) REVERT: B 691 LYS cc_start: 0.7631 (mtpt) cc_final: 0.7246 (mttp) REVERT: B 707 ARG cc_start: 0.8031 (tmm160) cc_final: 0.7728 (ttp80) outliers start: 11 outliers final: 3 residues processed: 208 average time/residue: 1.6038 time to fit residues: 360.7293 Evaluate side-chains 196 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 191 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 445 ASP 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: 2.9990 chunk 86 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 614 ASN B 284 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.159934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.117020 restraints weight = 63149.200| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.91 r_work: 0.3130 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- 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 = 0.25 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 = 0.25 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: 0.8653 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15264 Z= 0.186 Angle : 0.561 5.643 20821 Z= 0.308 Chirality : 0.040 0.189 2301 Planarity : 0.004 0.046 2519 Dihedral : 13.379 85.260 2592 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.59 % Allowed : 11.77 % Favored : 87.65 % 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: 1.59 (0.17), residues: 855 sheet: -0.38 (0.38), residues: 186 loop : 0.22 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 144 TYR 0.028 0.002 TYR B 557 PHE 0.017 0.002 PHE B 551 TRP 0.018 0.002 TRP B 309 HIS 0.006 0.001 HIS B 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 (15264) covalent geometry : angle 0.56082 / 0.31 (20821) hydrogen bonds : bond 0.06417 / 4.32 ( 771) hydrogen bonds : angle 4.95119 / 3.66 ( 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 201 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7301 (mt-10) REVERT: A 84 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7644 (ttt90) REVERT: C 11 MET cc_start: 0.8189 (mmm) cc_final: 0.7612 (mmm) REVERT: C 146 ASP cc_start: 0.8252 (m-30) cc_final: 0.7945 (m-30) REVERT: C 160 GLN cc_start: 0.7849 (mt0) cc_final: 0.7013 (tp-100) REVERT: C 176 ILE cc_start: 0.8107 (tt) cc_final: 0.7883 (pp) REVERT: C 191 LYS cc_start: 0.8057 (tttt) cc_final: 0.7706 (tmtt) REVERT: B 104 GLU cc_start: 0.8091 (tt0) cc_final: 0.7884 (mp0) REVERT: B 159 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7462 (mm-30) REVERT: B 179 MET cc_start: 0.8602 (tpt) cc_final: 0.8270 (mmm) REVERT: B 430 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8352 (pttp) REVERT: B 569 GLN cc_start: 0.8602 (mm110) cc_final: 0.8400 (mm110) REVERT: B 691 LYS cc_start: 0.7661 (mtpt) cc_final: 0.7259 (mttp) REVERT: B 707 ARG cc_start: 0.8036 (tmm160) cc_final: 0.7751 (ttp80) outliers start: 9 outliers final: 4 residues processed: 197 average time/residue: 1.5881 time to fit residues: 338.8797 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 : 0.834 ------------------------------------------------------------------------------- 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 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: 0.2980 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.160704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118355 restraints weight = 61859.372| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.79 r_work: 0.3145 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 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 = 0.3026 r_free = 0.3026 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: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15264 Z= 0.151 Angle : 0.531 5.394 20821 Z= 0.290 Chirality : 0.039 0.173 2301 Planarity : 0.004 0.038 2519 Dihedral : 13.376 86.014 2592 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: 1.17 (0.20), residues: 1719 helix: 1.61 (0.17), residues: 855 sheet: -0.39 (0.38), residues: 186 loop : 0.17 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 721 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 0.00306 / 0.15 (15264) covalent geometry : angle 0.53147 / 0.29 (20821) hydrogen bonds : bond 0.05965 / 4.02 ( 771) hydrogen bonds : angle 4.86828 / 3.60 ( 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 199 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 191 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7301 (mt-10) REVERT: A 84 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7672 (ttt90) REVERT: C 11 MET cc_start: 0.8187 (mmm) cc_final: 0.7638 (mmm) REVERT: C 18 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7154 (mm-30) REVERT: C 146 ASP cc_start: 0.8222 (m-30) cc_final: 0.7916 (m-30) REVERT: C 160 GLN cc_start: 0.7831 (mt0) cc_final: 0.7005 (tp-100) REVERT: C 176 ILE cc_start: 0.8105 (tt) cc_final: 0.7869 (pp) REVERT: C 191 LYS cc_start: 0.8070 (tttt) cc_final: 0.7721 (tmtt) REVERT: B 120 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8559 (p0) REVERT: B 159 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7490 (mm-30) REVERT: B 179 MET cc_start: 0.8595 (tpt) cc_final: 0.8269 (mmm) REVERT: B 372 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7965 (ptm) REVERT: B 430 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8360 (pttp) REVERT: B 691 LYS cc_start: 0.7682 (mtpt) cc_final: 0.7278 (mttp) REVERT: B 707 ARG cc_start: 0.8056 (tmm160) cc_final: 0.7767 (ttp80) outliers start: 8 outliers final: 4 residues processed: 196 average time/residue: 1.5397 time to fit residues: 327.3620 Evaluate side-chains 195 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 188 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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: 2.9990 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 171 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.160471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118734 restraints weight = 70633.898| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.07 r_work: 0.3102 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15264 Z= 0.162 Angle : 0.545 5.545 20821 Z= 0.298 Chirality : 0.039 0.178 2301 Planarity : 0.004 0.040 2519 Dihedral : 13.383 86.455 2592 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.72 % Allowed : 12.03 % 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: 1.58 (0.17), residues: 855 sheet: -0.40 (0.38), residues: 186 loop : 0.15 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 287 TYR 0.026 0.002 TYR B 557 PHE 0.016 0.002 PHE B 551 TRP 0.016 0.002 TRP B 309 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (15264) covalent geometry : angle 0.54488 / 0.30 (20821) hydrogen bonds : bond 0.06070 / 4.09 ( 771) hydrogen bonds : angle 4.88179 / 3.61 ( 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 202 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7339 (mt-10) REVERT: A 84 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7665 (ttt90) REVERT: C 11 MET cc_start: 0.8188 (mmm) cc_final: 0.7635 (mmm) REVERT: C 18 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7172 (mm-30) REVERT: C 146 ASP cc_start: 0.8244 (m-30) cc_final: 0.7948 (m-30) REVERT: C 160 GLN cc_start: 0.7851 (mt0) cc_final: 0.7013 (tp-100) REVERT: C 176 ILE cc_start: 0.8106 (tt) cc_final: 0.7865 (pp) REVERT: C 191 LYS cc_start: 0.8088 (tttt) cc_final: 0.7719 (tmtt) REVERT: B 120 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8578 (p0) REVERT: B 159 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7501 (mm-30) REVERT: B 179 MET cc_start: 0.8599 (tpt) cc_final: 0.8270 (mmm) REVERT: B 372 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8010 (ptm) REVERT: B 430 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8394 (pttp) REVERT: B 691 LYS cc_start: 0.7704 (mtpt) cc_final: 0.7299 (mttp) REVERT: B 707 ARG cc_start: 0.8072 (tmm160) cc_final: 0.7784 (ttp80) outliers start: 11 outliers final: 4 residues processed: 198 average time/residue: 1.5915 time to fit residues: 341.8571 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 : 0.773 ------------------------------------------------------------------------------- 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: 3.9990 chunk 170 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 614 ASN C 151 HIS B 569 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.158836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116275 restraints weight = 65986.767| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.91 r_work: 0.3108 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15264 Z= 0.226 Angle : 0.614 6.349 20821 Z= 0.338 Chirality : 0.041 0.205 2301 Planarity : 0.005 0.055 2519 Dihedral : 13.494 87.470 2592 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.65 % Allowed : 11.83 % 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: 0.91 (0.20), residues: 1719 helix: 1.37 (0.17), residues: 849 sheet: -0.42 (0.37), residues: 188 loop : 0.06 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 498 TYR 0.031 0.003 TYR B 557 PHE 0.020 0.002 PHE B 551 TRP 0.022 0.003 TRP B 309 HIS 0.007 0.002 HIS B 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.23 (15264) covalent geometry : angle 0.61428 / 0.34 (20821) hydrogen bonds : bond 0.07014 / 4.71 ( 771) hydrogen bonds : angle 5.08425 / 3.75 ( 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 206 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7338 (mt-10) REVERT: A 84 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7653 (ttt90) REVERT: C 11 MET cc_start: 0.8226 (mmm) cc_final: 0.7671 (mmm) REVERT: C 146 ASP cc_start: 0.8332 (m-30) cc_final: 0.8039 (m-30) REVERT: C 160 GLN cc_start: 0.7887 (mt0) cc_final: 0.7056 (tp-100) REVERT: C 191 LYS cc_start: 0.8076 (tttt) cc_final: 0.7713 (tmtt) REVERT: B 120 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8575 (p0) REVERT: B 159 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7504 (mm-30) REVERT: B 179 MET cc_start: 0.8658 (tpt) cc_final: 0.8281 (mmm) REVERT: B 372 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8004 (ptm) REVERT: B 414 MET cc_start: 0.8969 (mtm) cc_final: 0.8743 (mtm) REVERT: B 430 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8373 (pttp) REVERT: B 691 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7315 (mttp) REVERT: B 707 ARG cc_start: 0.8088 (tmm160) cc_final: 0.7808 (ttp80) outliers start: 10 outliers final: 5 residues processed: 202 average time/residue: 1.6785 time to fit residues: 367.5650 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 : 0.712 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 698 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 22 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 130 optimal weight: 0.0970 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.161939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.119153 restraints weight = 64219.962| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.94 r_work: 0.3148 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1437 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= 0.118 Angle : 0.510 5.578 20821 Z= 0.277 Chirality : 0.038 0.176 2301 Planarity : 0.004 0.044 2519 Dihedral : 13.393 88.337 2592 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.39 % Allowed : 12.29 % 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: 1.16 (0.20), residues: 1719 helix: 1.68 (0.17), residues: 849 sheet: -0.46 (0.38), residues: 186 loop : 0.10 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 721 TYR 0.021 0.002 TYR B 557 PHE 0.013 0.001 PHE B 551 TRP 0.017 0.002 TRP B 309 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (15264) covalent geometry : angle 0.51000 / 0.28 (20821) hydrogen bonds : bond 0.05382 / 3.64 ( 771) hydrogen bonds : angle 4.77698 / 3.53 ( 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 200 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 194 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7306 (mt-10) REVERT: A 84 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7646 (ttt90) REVERT: C 18 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7121 (mm-30) REVERT: C 146 ASP cc_start: 0.8172 (m-30) cc_final: 0.7871 (m-30) REVERT: C 160 GLN cc_start: 0.7795 (mt0) cc_final: 0.6911 (tp-100) REVERT: C 191 LYS cc_start: 0.8072 (tttt) cc_final: 0.7723 (tmtt) REVERT: B 120 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8529 (p0) REVERT: B 159 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7447 (mm-30) REVERT: B 179 MET cc_start: 0.8587 (tpt) cc_final: 0.8292 (mmm) REVERT: B 430 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8344 (pttp) REVERT: B 691 LYS cc_start: 0.7671 (mtpt) cc_final: 0.7254 (mttp) REVERT: B 707 ARG cc_start: 0.8050 (tmm160) cc_final: 0.7755 (ttp80) outliers start: 6 outliers final: 4 residues processed: 198 average time/residue: 1.5942 time to fit residues: 342.3781 Evaluate side-chains 194 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 188 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 120 ASP 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: 6.9990 chunk 87 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN B 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.159987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116437 restraints weight = 61948.222| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.98 r_work: 0.3123 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15264 Z= 0.179 Angle : 0.559 5.924 20821 Z= 0.306 Chirality : 0.039 0.185 2301 Planarity : 0.004 0.043 2519 Dihedral : 13.411 88.418 2592 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: 1.08 (0.20), residues: 1719 helix: 1.58 (0.17), residues: 849 sheet: -0.49 (0.37), residues: 188 loop : 0.10 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 706 TYR 0.027 0.002 TYR B 557 PHE 0.016 0.002 PHE B 551 TRP 0.018 0.002 TRP B 309 HIS 0.005 0.001 HIS B 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (15264) covalent geometry : angle 0.55944 / 0.31 (20821) hydrogen bonds : bond 0.06247 / 4.21 ( 771) hydrogen bonds : angle 4.90628 / 3.63 ( 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 199 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 192 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7689 (ttt90) REVERT: C 18 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7181 (mm-30) REVERT: C 146 ASP cc_start: 0.8277 (m-30) cc_final: 0.7980 (m-30) REVERT: C 160 GLN cc_start: 0.7844 (mt0) cc_final: 0.7038 (tp-100) REVERT: C 191 LYS cc_start: 0.8077 (tttt) cc_final: 0.7730 (tmtt) REVERT: B 120 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8572 (p0) REVERT: B 159 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7502 (mm-30) REVERT: B 179 MET cc_start: 0.8634 (tpt) cc_final: 0.8286 (mmm) REVERT: B 430 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8408 (pttp) REVERT: B 691 LYS cc_start: 0.7726 (mtpt) cc_final: 0.7322 (mttp) REVERT: B 707 ARG cc_start: 0.8084 (tmm160) cc_final: 0.7797 (ttp80) outliers start: 7 outliers final: 5 residues processed: 197 average time/residue: 1.5264 time to fit residues: 326.4436 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 : 0.864 ------------------------------------------------------------------------------- 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 120 ASP Chi-restraints excluded: chain B residue 291 THR 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: 0.8980 chunk 10 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 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: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.162399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120420 restraints weight = 70876.171| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.96 r_work: 0.3168 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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= 0.115 Angle : 0.502 6.147 20821 Z= 0.272 Chirality : 0.038 0.178 2301 Planarity : 0.003 0.034 2519 Dihedral : 13.337 89.724 2592 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.33 % Allowed : 12.42 % 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: 1.23 (0.20), residues: 1719 helix: 1.77 (0.18), residues: 849 sheet: -0.51 (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 B 706 TYR 0.021 0.001 TYR B 557 PHE 0.012 0.001 PHE B 551 TRP 0.017 0.002 TRP C 49 HIS 0.003 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (15264) covalent geometry : angle 0.50244 / 0.27 (20821) hydrogen bonds : bond 0.05200 / 3.51 ( 771) hydrogen bonds : angle 4.70064 / 3.48 ( 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: 5 poor density : 195 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7673 (ttt90) REVERT: C 18 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7131 (mm-30) REVERT: C 146 ASP cc_start: 0.8171 (m-30) cc_final: 0.7870 (m-30) REVERT: C 160 GLN cc_start: 0.7833 (mt0) cc_final: 0.6937 (tp-100) REVERT: C 191 LYS cc_start: 0.8091 (tttt) cc_final: 0.7736 (tmtt) REVERT: B 104 GLU cc_start: 0.8272 (tt0) cc_final: 0.8003 (mp0) REVERT: B 120 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8565 (p0) REVERT: B 159 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7518 (mm-30) REVERT: B 179 MET cc_start: 0.8576 (tpt) cc_final: 0.8290 (mmm) REVERT: B 691 LYS cc_start: 0.7676 (mtpt) cc_final: 0.7271 (mttp) REVERT: B 707 ARG cc_start: 0.8066 (tmm160) cc_final: 0.7768 (ttp80) outliers start: 5 outliers final: 4 residues processed: 199 average time/residue: 1.5811 time to fit residues: 341.1870 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 : 0.684 ------------------------------------------------------------------------------- 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 2 SER Chi-restraints excluded: chain B residue 120 ASP 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: 0.7980 chunk 67 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 614 ASN B 284 ASN B 569 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.161373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118888 restraints weight = 65635.713| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.77 r_work: 0.3136 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 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 = 0.3035 r_free = 0.3035 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: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1485 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= 0.137 Angle : 0.523 7.140 20821 Z= 0.283 Chirality : 0.038 0.169 2301 Planarity : 0.004 0.033 2519 Dihedral : 13.326 90.193 2592 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.39 % Allowed : 12.48 % 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: 1.22 (0.20), residues: 1719 helix: 1.74 (0.18), residues: 849 sheet: -0.51 (0.38), residues: 186 loop : 0.12 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 706 TYR 0.024 0.002 TYR B 557 PHE 0.014 0.001 PHE B 551 TRP 0.016 0.002 TRP C 49 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 0.52349 / 0.28 (20821) hydrogen bonds : bond 0.05556 / 3.75 ( 771) hydrogen bonds : angle 4.74745 / 3.51 ( 2119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13411.78 seconds wall clock time: 227 minutes 1.05 seconds (13621.05 seconds total)