Starting phenix.real_space_refine on Sat Sep 12 10:46:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pik_13439/09_2026/7pik_13439.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pik_13439/09_2026/7pik_13439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pik_13439/09_2026/7pik_13439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pik_13439/09_2026/7pik_13439.map" model { file = "/net/cci-nas-00/data/ceres_data/7pik_13439/09_2026/7pik_13439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pik_13439/09_2026/7pik_13439.cif" } resolution = 2.68 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= 0.001 sd= 0.045 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: 5 Type Number sf(0) Gaussians P 125 5.49 5 S 33 5.16 5 C 9497 2.51 5 N 2741 2.21 5 O 3079 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15475 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1240 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 141} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 4272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4272 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 29, 'TRANS': 511} Chain breaks: 4 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 10, 'ASN:plan1': 1, 'ARG:plan': 4, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 106 Chain: "C" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4513 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 28, 'TRANS': 528} Chain breaks: 4 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2602 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 15, 'TRANS': 319} Chain breaks: 2 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 5, 'HIS:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "K" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1282 Classifications: {'DNA': 63} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 62} Chain: "L" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1298 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "E" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 268 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 3.28, per 1000 atoms: 0.21 Number of scatterers: 15475 At special positions: 0 Unit cell: (129.86, 168.56, 169.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 125 15.00 O 3079 8.00 N 2741 7.00 C 9497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 530.6 milliseconds 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3092 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 14 sheets defined 47.2% alpha, 15.2% beta 50 base pairs and 116 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 42 through 51 removed outlier: 3.648A pdb=" N GLU A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 73 through 91 removed outlier: 3.593A pdb=" N ILE A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 97 through 113 Processing helix chain 'A' and resid 115 through 129 Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.530A pdb=" N ILE A 137 " --> pdb=" O ASN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'B' and resid 42 through 52 Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.892A pdb=" N ASP B 65 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 84 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 97 through 113 Processing helix chain 'B' and resid 115 through 129 removed outlier: 3.576A pdb=" N VAL B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.529A pdb=" N ILE B 137 " --> pdb=" O ASN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 173 through 188 Processing helix chain 'B' and resid 195 through 211 removed outlier: 3.562A pdb=" N ALA B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP B 205 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 Processing helix chain 'B' and resid 221 through 232 Processing helix chain 'B' and resid 318 through 330 removed outlier: 4.525A pdb=" N GLN B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS B 330 " --> pdb=" O PHE B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 340 Processing helix chain 'B' and resid 366 through 376 Processing helix chain 'B' and resid 389 through 396 removed outlier: 3.536A pdb=" N GLY B 393 " --> pdb=" O GLY B 389 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 394 " --> pdb=" O ASP B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 452 Processing helix chain 'B' and resid 471 through 483 Processing helix chain 'B' and resid 491 through 499 removed outlier: 3.519A pdb=" N LEU B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 528 removed outlier: 4.097A pdb=" N ARG B 526 " --> pdb=" O SER B 522 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU B 527 " --> pdb=" O GLU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 578 removed outlier: 3.760A pdb=" N PHE B 577 " --> pdb=" O SER B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 596 Processing helix chain 'C' and resid 41 through 52 removed outlier: 3.665A pdb=" N LEU C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 67 removed outlier: 3.642A pdb=" N LEU C 64 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU C 67 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 92 Proline residue: C 88 - end of helix removed outlier: 3.793A pdb=" N SER C 92 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 113 removed outlier: 3.603A pdb=" N GLU C 111 " --> pdb=" O HIS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 130 removed outlier: 3.562A pdb=" N VAL C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY C 130 " --> pdb=" O TYR C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 removed outlier: 4.041A pdb=" N ILE C 137 " --> pdb=" O ASN C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 173 through 188 Processing helix chain 'C' and resid 195 through 211 removed outlier: 3.625A pdb=" N ALA C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.621A pdb=" N ASP C 218 " --> pdb=" O PRO C 215 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR C 219 " --> pdb=" O GLN C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 219' Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 321 through 330 removed outlier: 4.078A pdb=" N ALA C 325 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS C 330 " --> pdb=" O PHE C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 340 Processing helix chain 'C' and resid 361 through 365 removed outlier: 3.555A pdb=" N GLU C 364 " --> pdb=" O ASP C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 375 Processing helix chain 'C' and resid 389 through 396 Processing helix chain 'C' and resid 434 through 452 Processing helix chain 'C' and resid 471 through 483 Processing helix chain 'C' and resid 491 through 499 removed outlier: 3.648A pdb=" N LEU C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 527 removed outlier: 3.847A pdb=" N LEU C 525 " --> pdb=" O GLY C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 533 removed outlier: 3.964A pdb=" N ARG C 532 " --> pdb=" O GLY C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 578 removed outlier: 3.565A pdb=" N ARG C 575 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLN C 576 " --> pdb=" O ARG C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 624 removed outlier: 5.501A pdb=" N LYS C 600 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLN C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C 605 " --> pdb=" O GLN C 601 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 624 " --> pdb=" O LYS C 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 330 removed outlier: 4.784A pdb=" N GLN D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA D 325 " --> pdb=" O VAL D 321 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS D 330 " --> pdb=" O PHE D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 340 Processing helix chain 'D' and resid 361 through 365 removed outlier: 3.659A pdb=" N LEU D 365 " --> pdb=" O ARG D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 376 Processing helix chain 'D' and resid 389 through 396 Processing helix chain 'D' and resid 435 through 452 Processing helix chain 'D' and resid 471 through 483 Processing helix chain 'D' and resid 491 through 499 removed outlier: 3.545A pdb=" N LEU D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 578 removed outlier: 5.731A pdb=" N GLN D 576 " --> pdb=" O ARG D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 595 Processing helix chain 'D' and resid 598 through 625 Processing helix chain 'E' and resid 588 through 599 removed outlier: 4.267A pdb=" N ALA E 599 " --> pdb=" O ASN E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 625 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.834A pdb=" N GLN A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 20 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL A 26 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.659A pdb=" N ALA B 19 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N MET B 28 " --> pdb=" O ILE B 17 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE B 17 " --> pdb=" O MET B 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 307 through 313 removed outlier: 6.673A pdb=" N VAL B 299 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE B 310 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR B 297 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE B 312 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR B 295 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TYR B 270 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 382 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 307 through 313 removed outlier: 6.673A pdb=" N VAL B 299 " --> pdb=" O THR B 308 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE B 310 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR B 297 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE B 312 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR B 295 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE B 276 " --> pdb=" O LEU B 402 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 281 through 282 removed outlier: 3.657A pdb=" N GLY B 292 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 502 through 504 removed outlier: 4.434A pdb=" N GLU B 543 " --> pdb=" O PHE B 557 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 38 through 40 removed outlier: 7.166A pdb=" N GLN C 24 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE C 20 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C 26 " --> pdb=" O LEU C 18 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 307 through 313 removed outlier: 6.328A pdb=" N ILE C 307 " --> pdb=" O ASP C 301 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASP C 301 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY C 309 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE C 276 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 402 " --> pdb=" O ILE C 276 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 359 Processing sheet with id=AB1, first strand: chain 'C' and resid 502 through 508 removed outlier: 4.395A pdb=" N GLU C 543 " --> pdb=" O PHE C 557 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU C 542 " --> pdb=" O VAL C 505 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 306 through 313 removed outlier: 3.593A pdb=" N MET D 306 " --> pdb=" O ASP D 301 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL D 299 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE D 310 " --> pdb=" O TYR D 297 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR D 297 " --> pdb=" O PHE D 310 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE D 312 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR D 295 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR D 270 " --> pdb=" O LEU D 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 306 through 313 removed outlier: 3.593A pdb=" N MET D 306 " --> pdb=" O ASP D 301 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL D 299 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE D 310 " --> pdb=" O TYR D 297 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR D 297 " --> pdb=" O PHE D 310 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE D 312 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR D 295 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE D 276 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D 402 " --> pdb=" O ILE D 276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 281 through 282 Processing sheet with id=AB5, first strand: chain 'D' and resid 502 through 504 removed outlier: 4.432A pdb=" N GLU D 543 " --> pdb=" O PHE D 557 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 110 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 116 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2455 1.32 - 1.44: 4927 1.44 - 1.57: 8403 1.57 - 1.69: 249 1.69 - 1.81: 54 Bond restraints: 16088 Sorted by residual: bond pdb=" C3' DG K 25 " pdb=" C2' DG K 25 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C3' DA K 50 " pdb=" C2' DA K 50 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DT K 14 " pdb=" C2' DT K 14 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DC L 46 " pdb=" C2' DC L 46 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DA L 44 " pdb=" C2' DA L 44 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 ... (remaining 16083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 22100 2.44 - 4.87: 266 4.87 - 7.31: 17 7.31 - 9.75: 3 9.75 - 12.19: 1 Bond angle restraints: 22387 Sorted by residual: angle pdb=" N3 DT K 26 " pdb=" C4 DT K 26 " pdb=" O4 DT K 26 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT L 49 " pdb=" C4 DT L 49 " pdb=" O4 DT L 49 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT K 14 " pdb=" C4 DT K 14 " pdb=" O4 DT K 14 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT K 41 " pdb=" C4 DT K 41 " pdb=" O4 DT K 41 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT L 40 " pdb=" C4 DT L 40 " pdb=" O4 DT L 40 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 22382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 7768 17.82 - 35.64: 951 35.64 - 53.46: 515 53.46 - 71.28: 89 71.28 - 89.10: 15 Dihedral angle restraints: 9338 sinusoidal: 4574 harmonic: 4764 Sorted by residual: dihedral pdb=" CA LYS D 407 " pdb=" C LYS D 407 " pdb=" N SER D 408 " pdb=" CA SER D 408 " ideal model delta harmonic sigma weight residual -180.00 -157.32 -22.68 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA GLU B 232 " pdb=" C GLU B 232 " pdb=" N TYR B 233 " pdb=" CA TYR B 233 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLU D 491 " pdb=" C GLU D 491 " pdb=" N GLN D 492 " pdb=" CA GLN D 492 " ideal model delta harmonic sigma weight residual -180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 9335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1916 0.051 - 0.102: 453 0.102 - 0.154: 109 0.154 - 0.205: 7 0.205 - 0.256: 3 Chirality restraints: 2488 Sorted by residual: chirality pdb=" CA TRP C 27 " pdb=" N TRP C 27 " pdb=" C TRP C 27 " pdb=" CB TRP C 27 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA TRP B 27 " pdb=" N TRP B 27 " pdb=" C TRP B 27 " pdb=" CB TRP B 27 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASP D 348 " pdb=" N ASP D 348 " pdb=" C ASP D 348 " pdb=" CB ASP D 348 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2485 not shown) Planarity restraints: 2445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 347 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.48e+00 pdb=" C SER B 347 " -0.044 2.00e-02 2.50e+03 pdb=" O SER B 347 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP B 348 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 527 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C GLU C 527 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU C 527 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY C 528 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 173 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.54e+00 pdb=" N PRO C 174 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 174 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 174 " 0.033 5.00e-02 4.00e+02 ... (remaining 2442 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3724 2.81 - 3.33: 12753 3.33 - 3.85: 24689 3.85 - 4.38: 30405 4.38 - 4.90: 48936 Nonbonded interactions: 120507 Sorted by model distance: nonbonded pdb=" N2 DG K 60 " pdb=" O2 DC L 11 " model vdw 2.284 3.120 nonbonded pdb=" NH1 ARG B 460 " pdb=" O LEU B 468 " model vdw 2.288 3.120 nonbonded pdb=" O PHE B 303 " pdb=" OH TYR B 458 " model vdw 2.294 3.040 nonbonded pdb=" OD1 ASN C 5 " pdb=" NE2 GLN C 131 " model vdw 2.322 3.120 nonbonded pdb=" NE2 GLN C 47 " pdb=" OE2 GLU C 51 " model vdw 2.322 3.120 ... (remaining 120502 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 93 or (resid 94 and (name N or name CA or name C \ or name O or name CB )) or resid 95 through 150 or resid 169 through 177 or (re \ sid 178 and (name N or name CA or name C or name O or name CB )) or resid 179 th \ rough 184 or (resid 185 and (name N or name CA or name C or name O or name CB )) \ or resid 186 through 234 or (resid 235 through 236 and (name N or name CA or na \ me C or name O or name CB )) or resid 264 through 315 or (resid 316 and (name N \ or name CA or name C or name O or name CB )) or resid 317 through 529 or resid 5 \ 40 through 597)) selection = (chain 'C' and (resid 1 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB )) or resid 51 through 102 or (resid 103 and (name N or na \ me CA or name C or name O or name CB )) or resid 104 through 172 or (resid 173 a \ nd (name N or name CA or name C or name O or name CB )) or resid 174 through 185 \ or (resid 186 and (name N or name CA or name C or name O or name CB or name CG \ or name CD )) or resid 187 through 189 or (resid 190 and (name N or name CA or n \ ame C or name O or name CB )) or resid 191 through 216 or (resid 217 through 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 through 2 \ 81 or (resid 282 through 283 and (name N or name CA or name C or name O or name \ CB )) or resid 284 through 285 or (resid 286 through 290 and (name N or name CA \ or name C or name O or name CB )) or resid 291 through 314 or (resid 315 through \ 316 and (name N or name CA or name C or name O or name CB )) or resid 317 throu \ gh 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) or \ resid 342 through 387 or (resid 388 and (name N or name CA or name C or name O \ or name CB )) or resid 389 through 399 or (resid 400 and (name N or name CA or n \ ame C or name O or name CB )) or resid 401 or (resid 402 and (name N or name CA \ or name C or name O or name CB )) or resid 403 through 412 or resid 431 through \ 458 or (resid 459 and (name N or name CA or name C or name O or name CB )) or re \ sid 460 or (resid 461 through 463 and (name N or name CA or name C or name O or \ name CB )) or resid 464 through 492 or (resid 493 and (name N or name CA or name \ C or name O or name CB )) or resid 494 through 526 or (resid 527 and (name N or \ name CA or name C or name O or name CB )) or resid 528 through 529 or (resid 53 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 541 through \ 571 or (resid 572 and (name N or name CA or name C or name O or name CB )) or re \ sid 573 through 586 or (resid 587 and (name N or name CA or name C or name O or \ name CB )) or resid 588 through 592 or (resid 593 through 594 and (name N or nam \ e CA or name C or name O or name CB )) or resid 595 or (resid 596 through 597 an \ d (name N or name CA or name C or name O or name CB )))) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 16.140 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 : 0.004 0.042 16088 Z= 0.374 Angle : 0.676 12.186 22387 Z= 0.505 Chirality : 0.047 0.256 2488 Planarity : 0.005 0.059 2445 Dihedral : 19.276 89.096 6246 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.08 % Allowed : 1.28 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.21), residues: 1594 helix: 1.30 (0.21), residues: 629 sheet: 0.30 (0.41), residues: 144 loop : -1.03 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.020 0.001 TYR C 48 PHE 0.024 0.001 PHE B 228 TRP 0.017 0.001 TRP B 586 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.37 (16088) covalent geometry : angle 0.67604 / 0.50 (22387) hydrogen bonds : bond 0.16949 / 11.68 ( 699) hydrogen bonds : angle 5.77647 / 4.11 ( 1893) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8132 (pttp) cc_final: 0.7719 (tmtt) REVERT: D 323 MET cc_start: 0.8598 (mmp) cc_final: 0.8363 (mmp) outliers start: 1 outliers final: 2 residues processed: 199 average time/residue: 0.7134 time to fit residues: 153.5785 Evaluate side-chains 148 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain D residue 615 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN C 128 GLN C 368 HIS ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.192040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.159266 restraints weight = 12823.808| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.16 r_work: 0.3650 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16088 Z= 0.153 Angle : 0.626 9.833 22387 Z= 0.360 Chirality : 0.047 0.256 2488 Planarity : 0.005 0.064 2445 Dihedral : 21.171 73.001 3236 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.58 % Allowed : 8.87 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.21), residues: 1594 helix: 1.54 (0.21), residues: 639 sheet: 0.47 (0.41), residues: 142 loop : -0.92 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 607 TYR 0.037 0.001 TYR C 48 PHE 0.023 0.001 PHE B 228 TRP 0.010 0.001 TRP B 586 HIS 0.006 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (16088) covalent geometry : angle 0.62556 / 0.36 (22387) hydrogen bonds : bond 0.06099 / 4.11 ( 699) hydrogen bonds : angle 4.38499 / 3.11 ( 1893) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8360 (pttp) cc_final: 0.7600 (tmtt) REVERT: B 13 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: B 28 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.6940 (tpp) REVERT: B 366 MET cc_start: 0.7391 (mmm) cc_final: 0.7124 (mmm) REVERT: C 177 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7612 (tm-30) REVERT: C 529 TRP cc_start: 0.7593 (OUTLIER) cc_final: 0.6548 (m100) REVERT: C 592 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6960 (pt0) REVERT: C 616 GLN cc_start: 0.7502 (tm-30) cc_final: 0.7189 (tm-30) REVERT: D 289 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7125 (mtmt) REVERT: D 323 MET cc_start: 0.8724 (mmp) cc_final: 0.8508 (mmp) REVERT: D 592 GLU cc_start: 0.7252 (mm-30) cc_final: 0.7011 (mm-30) outliers start: 21 outliers final: 7 residues processed: 165 average time/residue: 0.7238 time to fit residues: 129.7057 Evaluate side-chains 160 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 559 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.5980 chunk 78 optimal weight: 0.0670 chunk 148 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 2 optimal weight: 0.0770 chunk 40 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 101 optimal weight: 0.0030 chunk 170 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.3086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 ASN C 368 HIS ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.194372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.166516 restraints weight = 13117.783| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 0.91 r_work: 0.3716 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16088 Z= 0.124 Angle : 0.554 7.416 22387 Z= 0.322 Chirality : 0.043 0.214 2488 Planarity : 0.004 0.064 2445 Dihedral : 21.483 73.941 3232 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.25 % Allowed : 10.07 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.61 (0.21), residues: 1594 helix: 1.79 (0.21), residues: 638 sheet: 0.58 (0.41), residues: 148 loop : -0.79 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 575 TYR 0.052 0.001 TYR C 48 PHE 0.021 0.001 PHE B 228 TRP 0.010 0.001 TRP B 586 HIS 0.006 0.001 HIS C 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.12 (16088) covalent geometry : angle 0.55434 / 0.32 (22387) hydrogen bonds : bond 0.04700 / 3.10 ( 699) hydrogen bonds : angle 4.10287 / 2.89 ( 1893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: A 93 LYS cc_start: 0.8302 (pttp) cc_final: 0.7592 (tmtt) REVERT: B 13 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7771 (m-30) REVERT: B 306 MET cc_start: 0.8298 (ttt) cc_final: 0.7871 (ttt) REVERT: B 366 MET cc_start: 0.7032 (mmm) cc_final: 0.6647 (mmm) REVERT: B 449 ARG cc_start: 0.7475 (tmt170) cc_final: 0.7246 (tmt170) REVERT: C 293 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6734 (ptp90) REVERT: C 453 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8567 (tt) REVERT: C 529 TRP cc_start: 0.7533 (OUTLIER) cc_final: 0.6472 (m100) REVERT: C 592 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6862 (pt0) REVERT: C 616 GLN cc_start: 0.7545 (tm-30) cc_final: 0.7227 (tm-30) REVERT: D 323 MET cc_start: 0.8705 (mmp) cc_final: 0.8482 (mmp) outliers start: 30 outliers final: 7 residues processed: 169 average time/residue: 0.7044 time to fit residues: 129.2372 Evaluate side-chains 150 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain D residue 559 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 44 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 HIS C 368 HIS ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.189177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.166308 restraints weight = 12858.033| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 0.62 r_work: 0.3640 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16088 Z= 0.210 Angle : 0.696 7.893 22387 Z= 0.391 Chirality : 0.052 0.322 2488 Planarity : 0.006 0.064 2445 Dihedral : 21.605 71.515 3232 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.18 % Allowed : 12.25 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.21), residues: 1594 helix: 1.46 (0.21), residues: 639 sheet: 0.18 (0.41), residues: 137 loop : -0.96 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 575 TYR 0.044 0.002 TYR C 48 PHE 0.026 0.002 PHE B 228 TRP 0.013 0.002 TRP C 529 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.21 (16088) covalent geometry : angle 0.69583 / 0.39 (22387) hydrogen bonds : bond 0.06741 / 4.57 ( 699) hydrogen bonds : angle 4.22309 / 2.99 ( 1893) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7663 (mp10) REVERT: A 84 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7696 (mtp180) REVERT: A 93 LYS cc_start: 0.8335 (pttp) cc_final: 0.7665 (tmtt) REVERT: B 13 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: B 366 MET cc_start: 0.7314 (mmm) cc_final: 0.7023 (mmm) REVERT: B 449 ARG cc_start: 0.7607 (tmt170) cc_final: 0.7390 (tmt170) REVERT: C 306 MET cc_start: 0.8449 (ttt) cc_final: 0.8199 (mtp) REVERT: C 529 TRP cc_start: 0.7720 (OUTLIER) cc_final: 0.6701 (m100) REVERT: C 592 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6944 (pt0) REVERT: C 611 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6615 (mp0) REVERT: C 616 GLN cc_start: 0.7525 (tm-30) cc_final: 0.7197 (tm-30) REVERT: D 289 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7005 (mtmt) REVERT: D 323 MET cc_start: 0.8708 (mmp) cc_final: 0.8374 (mmp) outliers start: 29 outliers final: 10 residues processed: 163 average time/residue: 0.7086 time to fit residues: 125.4871 Evaluate side-chains 158 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 526 ARG Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 593 LYS Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 395 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 19 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 53 optimal weight: 0.0670 chunk 114 optimal weight: 0.7980 chunk 170 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN B 482 HIS ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.190731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.161607 restraints weight = 12970.716| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 0.91 r_work: 0.3663 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16088 Z= 0.164 Angle : 0.628 7.713 22387 Z= 0.358 Chirality : 0.047 0.272 2488 Planarity : 0.005 0.066 2445 Dihedral : 21.602 71.031 3232 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.55 % Allowed : 12.92 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.21), residues: 1594 helix: 1.54 (0.21), residues: 640 sheet: 0.30 (0.42), residues: 129 loop : -0.95 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 526 TYR 0.053 0.002 TYR C 48 PHE 0.025 0.002 PHE B 228 TRP 0.011 0.001 TRP B 586 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (16088) covalent geometry : angle 0.62830 / 0.36 (22387) hydrogen bonds : bond 0.05673 / 3.80 ( 699) hydrogen bonds : angle 4.13971 / 2.92 ( 1893) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: A 77 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7537 (mp-120) REVERT: A 93 LYS cc_start: 0.8305 (pttp) cc_final: 0.7604 (tmtt) REVERT: B 13 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: B 28 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.7174 (tpp) REVERT: B 306 MET cc_start: 0.8371 (ttt) cc_final: 0.7979 (ttt) REVERT: B 366 MET cc_start: 0.7212 (mmm) cc_final: 0.6906 (mmm) REVERT: C 306 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8194 (mtp) REVERT: C 529 TRP cc_start: 0.7694 (OUTLIER) cc_final: 0.6682 (m100) REVERT: C 592 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6928 (pt0) REVERT: C 611 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6517 (mp0) REVERT: C 616 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7205 (tm-30) REVERT: D 289 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6959 (mtmt) REVERT: D 323 MET cc_start: 0.8695 (mmp) cc_final: 0.8417 (mmp) outliers start: 34 outliers final: 12 residues processed: 165 average time/residue: 0.6683 time to fit residues: 120.0658 Evaluate side-chains 163 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 395 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 58 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 141 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN B 482 HIS C 77 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.189744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.164648 restraints weight = 12814.451| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 0.74 r_work: 0.3672 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16088 Z= 0.174 Angle : 0.638 7.043 22387 Z= 0.363 Chirality : 0.048 0.280 2488 Planarity : 0.005 0.066 2445 Dihedral : 21.619 70.781 3232 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.70 % Allowed : 13.37 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.21), residues: 1594 helix: 1.54 (0.21), residues: 640 sheet: 0.27 (0.42), residues: 129 loop : -0.97 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 526 TYR 0.028 0.002 TYR C 48 PHE 0.024 0.002 PHE B 228 TRP 0.015 0.001 TRP B 586 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (16088) covalent geometry : angle 0.63782 / 0.36 (22387) hydrogen bonds : bond 0.05838 / 3.92 ( 699) hydrogen bonds : angle 4.15410 / 2.94 ( 1893) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7593 (mp10) REVERT: A 77 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7520 (mp10) REVERT: A 93 LYS cc_start: 0.8311 (pttp) cc_final: 0.7641 (tmtt) REVERT: B 13 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: B 366 MET cc_start: 0.7239 (mmm) cc_final: 0.6819 (mmm) REVERT: C 106 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: C 186 LYS cc_start: 0.8008 (ptmm) cc_final: 0.7760 (ttpt) REVERT: C 306 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8214 (mtp) REVERT: C 529 TRP cc_start: 0.7706 (OUTLIER) cc_final: 0.6693 (m100) REVERT: C 592 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6886 (pt0) REVERT: C 611 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6585 (mp0) REVERT: C 616 GLN cc_start: 0.7551 (tm-30) cc_final: 0.7217 (tm-30) REVERT: D 289 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6963 (mtmt) REVERT: D 407 LYS cc_start: 0.7763 (pttp) cc_final: 0.7547 (pttm) outliers start: 36 outliers final: 15 residues processed: 159 average time/residue: 0.7018 time to fit residues: 121.5669 Evaluate side-chains 162 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 466 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 143 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN B 482 HIS C 12 ASN C 77 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.189941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.168206 restraints weight = 12696.415| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 0.55 r_work: 0.3649 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16088 Z= 0.170 Angle : 0.636 10.247 22387 Z= 0.361 Chirality : 0.048 0.276 2488 Planarity : 0.005 0.067 2445 Dihedral : 21.621 70.569 3232 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.78 % Allowed : 13.90 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.21), residues: 1594 helix: 1.52 (0.21), residues: 645 sheet: 0.42 (0.42), residues: 134 loop : -1.02 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 526 TYR 0.016 0.002 TYR C 48 PHE 0.023 0.002 PHE B 228 TRP 0.018 0.001 TRP B 586 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (16088) covalent geometry : angle 0.63588 / 0.36 (22387) hydrogen bonds : bond 0.05731 / 3.85 ( 699) hydrogen bonds : angle 4.13778 / 2.93 ( 1893) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7624 (mp10) REVERT: A 77 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7488 (mp10) REVERT: A 93 LYS cc_start: 0.8317 (pttp) cc_final: 0.7624 (tmtt) REVERT: B 13 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7879 (m-30) REVERT: B 366 MET cc_start: 0.7262 (mmm) cc_final: 0.6855 (mmm) REVERT: C 106 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6600 (mp0) REVERT: C 186 LYS cc_start: 0.8028 (ptmm) cc_final: 0.7778 (ttpt) REVERT: C 306 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8259 (mtp) REVERT: C 529 TRP cc_start: 0.7711 (OUTLIER) cc_final: 0.6688 (m100) REVERT: C 592 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6873 (pt0) REVERT: C 611 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6568 (mp0) REVERT: C 616 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7225 (tm-30) REVERT: D 289 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6985 (mtmt) outliers start: 37 outliers final: 16 residues processed: 164 average time/residue: 0.6501 time to fit residues: 116.1885 Evaluate side-chains 166 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 480 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 71 optimal weight: 0.0570 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 0.0060 chunk 99 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 overall best weight: 0.5514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN B 482 HIS C 12 ASN C 77 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.191844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.160220 restraints weight = 12931.239| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.10 r_work: 0.3666 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16088 Z= 0.138 Angle : 0.595 10.932 22387 Z= 0.340 Chirality : 0.045 0.249 2488 Planarity : 0.005 0.066 2445 Dihedral : 21.576 70.095 3232 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.33 % Allowed : 14.73 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.21), residues: 1594 helix: 1.69 (0.21), residues: 645 sheet: 0.53 (0.42), residues: 139 loop : -0.94 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 575 TYR 0.016 0.001 TYR C 48 PHE 0.023 0.001 PHE A 76 TRP 0.021 0.001 TRP B 586 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (16088) covalent geometry : angle 0.59518 / 0.34 (22387) hydrogen bonds : bond 0.04942 / 3.29 ( 699) hydrogen bonds : angle 4.05801 / 2.87 ( 1893) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7653 (mp10) REVERT: A 77 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7350 (mp10) REVERT: A 93 LYS cc_start: 0.8323 (pttp) cc_final: 0.7577 (tmtt) REVERT: B 13 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7853 (m-30) REVERT: B 366 MET cc_start: 0.7101 (mmm) cc_final: 0.6690 (mmm) REVERT: C 106 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: C 186 LYS cc_start: 0.8048 (ptmm) cc_final: 0.7767 (ttpt) REVERT: C 269 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6621 (ptm-80) REVERT: C 306 MET cc_start: 0.8438 (ttt) cc_final: 0.8219 (mtp) REVERT: C 529 TRP cc_start: 0.7631 (OUTLIER) cc_final: 0.6589 (m100) REVERT: C 592 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6870 (pt0) REVERT: C 607 ARG cc_start: 0.7690 (ttm110) cc_final: 0.7358 (ttm110) REVERT: C 611 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6480 (mp0) REVERT: C 616 GLN cc_start: 0.7523 (tm-30) cc_final: 0.7186 (tm-30) REVERT: D 289 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7092 (mtmt) outliers start: 31 outliers final: 11 residues processed: 162 average time/residue: 0.6912 time to fit residues: 121.7385 Evaluate side-chains 159 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 480 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 83 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 0.0970 chunk 37 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN B 482 HIS C 12 ASN C 77 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.191017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.166227 restraints weight = 12810.593| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 0.68 r_work: 0.3692 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 : 0.003 0.044 16088 Z= 0.150 Angle : 0.613 11.792 22387 Z= 0.348 Chirality : 0.046 0.264 2488 Planarity : 0.005 0.066 2445 Dihedral : 21.566 69.958 3232 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.18 % Allowed : 14.95 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.21), residues: 1594 helix: 1.66 (0.21), residues: 645 sheet: 0.45 (0.42), residues: 134 loop : -0.92 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 575 TYR 0.014 0.001 TYR D 297 PHE 0.024 0.002 PHE B 228 TRP 0.026 0.001 TRP B 586 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (16088) covalent geometry : angle 0.61267 / 0.35 (22387) hydrogen bonds : bond 0.05174 / 3.47 ( 699) hydrogen bonds : angle 4.07467 / 2.88 ( 1893) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7593 (mp10) REVERT: A 77 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7325 (mp10) REVERT: A 93 LYS cc_start: 0.8314 (pttp) cc_final: 0.7572 (tppt) REVERT: B 13 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7838 (m-30) REVERT: B 366 MET cc_start: 0.7112 (mmm) cc_final: 0.6703 (mmm) REVERT: C 186 LYS cc_start: 0.7983 (ptmm) cc_final: 0.7729 (ttpt) REVERT: C 269 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.6652 (ptm-80) REVERT: C 306 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8242 (mtp) REVERT: C 529 TRP cc_start: 0.7629 (OUTLIER) cc_final: 0.6601 (m100) REVERT: C 592 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6926 (pt0) REVERT: C 607 ARG cc_start: 0.7729 (ttm110) cc_final: 0.7406 (ttm110) REVERT: C 611 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: C 616 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7250 (tm-30) REVERT: D 289 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7054 (mtmt) outliers start: 29 outliers final: 14 residues processed: 157 average time/residue: 0.6969 time to fit residues: 119.3519 Evaluate side-chains 160 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 480 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 122 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 482 HIS C 12 ASN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.191397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.160292 restraints weight = 12888.362| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.06 r_work: 0.3663 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 16088 Z= 0.186 Angle : 0.842 59.149 22387 Z= 0.492 Chirality : 0.047 0.268 2488 Planarity : 0.006 0.127 2445 Dihedral : 21.565 70.073 3232 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.03 % Allowed : 15.18 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.21), residues: 1594 helix: 1.64 (0.21), residues: 645 sheet: 0.45 (0.42), residues: 134 loop : -0.92 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 575 TYR 0.015 0.002 TYR C 48 PHE 0.024 0.002 PHE B 228 TRP 0.020 0.001 TRP B 586 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 (16088) covalent geometry : angle 0.84181 / 0.49 (22387) hydrogen bonds : bond 0.05280 / 3.56 ( 699) hydrogen bonds : angle 4.07820 / 2.88 ( 1893) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: A 93 LYS cc_start: 0.8328 (pttp) cc_final: 0.7531 (tppt) REVERT: B 13 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7850 (m-30) REVERT: B 366 MET cc_start: 0.7113 (mmm) cc_final: 0.6721 (mmm) REVERT: C 186 LYS cc_start: 0.7997 (ptmm) cc_final: 0.7732 (ttpt) REVERT: C 269 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.6650 (ptm-80) REVERT: C 306 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8241 (mtp) REVERT: C 529 TRP cc_start: 0.7639 (OUTLIER) cc_final: 0.6597 (m100) REVERT: C 592 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6881 (pt0) REVERT: C 607 ARG cc_start: 0.7703 (ttm110) cc_final: 0.7405 (ttm110) REVERT: C 611 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6551 (mp0) REVERT: C 616 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7232 (tm-30) REVERT: D 289 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7071 (mtmt) outliers start: 27 outliers final: 15 residues processed: 152 average time/residue: 0.6635 time to fit residues: 110.2907 Evaluate side-chains 160 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 480 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 50 optimal weight: 0.0670 chunk 1 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 482 HIS C 12 ASN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.190775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.169103 restraints weight = 12779.915| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 0.54 r_work: 0.3674 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 16088 Z= 0.186 Angle : 0.842 59.148 22387 Z= 0.492 Chirality : 0.047 0.268 2488 Planarity : 0.006 0.127 2445 Dihedral : 21.565 70.073 3232 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.73 % Allowed : 15.40 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.21), residues: 1594 helix: 1.64 (0.21), residues: 645 sheet: 0.45 (0.42), residues: 134 loop : -0.92 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 575 TYR 0.015 0.002 TYR C 48 PHE 0.024 0.002 PHE B 228 TRP 0.020 0.001 TRP B 586 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 (16088) covalent geometry : angle 0.84181 / 0.49 (22387) hydrogen bonds : bond 0.05280 / 3.56 ( 699) hydrogen bonds : angle 4.07820 / 2.88 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7159.21 seconds wall clock time: 121 minutes 57.43 seconds (7317.43 seconds total)