Starting phenix.real_space_refine on Fri Jul 3 17:42:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pik_13439/07_2026/7pik_13439.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pik_13439/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7pik_13439/07_2026/7pik_13439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pik_13439/07_2026/7pik_13439.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pik_13439/07_2026/7pik_13439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pik_13439/07_2026/7pik_13439.map" } 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-dev-6108/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: 3.27, 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: 1.23 Conformation dependent library (CDL) restraints added in 578.3 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: 1.77 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: 3.21 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: 22101 2.44 - 4.87: 265 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: 10.970 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.220 Find NCS groups from input model: 0.190 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:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.550 ------------------------------------------------------------------------------- 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 : 0.673 12.186 22387 Z= 0.502 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 0.67333 / 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 : 0.533 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: 0.7536 time to fit residues: 162.3061 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 : 0.515 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.192195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.164044 restraints weight = 12828.839| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 0.91 r_work: 0.3680 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16088 Z= 0.152 Angle : 0.630 9.529 22387 Z= 0.360 Chirality : 0.047 0.260 2488 Planarity : 0.005 0.065 2445 Dihedral : 21.295 73.413 3236 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.58 % Allowed : 9.17 % Favored : 89.26 % 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: 0.34 (0.21), residues: 1594 helix: 1.54 (0.21), residues: 639 sheet: 0.44 (0.41), residues: 148 loop : -0.92 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 607 TYR 0.041 0.001 TYR C 48 PHE 0.021 0.001 PHE B 228 TRP 0.011 0.001 TRP B 586 HIS 0.006 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (16088) covalent geometry : angle 0.62984 / 0.36 (22387) hydrogen bonds : bond 0.05769 / 3.88 ( 699) hydrogen bonds : angle 4.34227 / 3.08 ( 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 172 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8331 (pttp) cc_final: 0.7603 (tmtt) REVERT: B 13 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: B 28 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.6902 (tpp) REVERT: B 366 MET cc_start: 0.7313 (mmm) cc_final: 0.7054 (mmm) REVERT: C 177 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7572 (tm-30) REVERT: C 529 TRP cc_start: 0.7581 (OUTLIER) cc_final: 0.6532 (m100) REVERT: C 592 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6979 (pt0) REVERT: C 616 GLN cc_start: 0.7519 (tm-30) cc_final: 0.7205 (tm-30) REVERT: D 289 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.7107 (mtmt) REVERT: D 323 MET cc_start: 0.8726 (mmp) cc_final: 0.8322 (mmp) REVERT: D 592 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7070 (mm-30) outliers start: 21 outliers final: 7 residues processed: 162 average time/residue: 0.7029 time to fit residues: 123.9283 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 : 0.462 ------------------------------------------------------------------------------- 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 293 ARG 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 559 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.0570 chunk 78 optimal weight: 0.0170 chunk 148 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 101 optimal weight: 0.0470 chunk 170 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 ASN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.191194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.162841 restraints weight = 12991.309| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 0.92 r_work: 0.3664 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16088 Z= 0.159 Angle : 0.617 7.319 22387 Z= 0.355 Chirality : 0.047 0.272 2488 Planarity : 0.005 0.065 2445 Dihedral : 21.571 71.842 3232 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.48 % Allowed : 10.37 % Favored : 87.15 % 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: 640 sheet: 0.31 (0.41), residues: 141 loop : -0.90 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 575 TYR 0.049 0.002 TYR C 48 PHE 0.022 0.002 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 0.00316 / 0.16 (16088) covalent geometry : angle 0.61736 / 0.36 (22387) hydrogen bonds : bond 0.05784 / 3.89 ( 699) hydrogen bonds : angle 4.20073 / 2.98 ( 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 181 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7654 (mp10) REVERT: A 93 LYS cc_start: 0.8320 (pttp) cc_final: 0.7616 (tmtt) REVERT: B 13 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7821 (m-30) REVERT: B 361 ASP cc_start: 0.7793 (t70) cc_final: 0.7593 (t0) REVERT: B 366 MET cc_start: 0.7192 (mmm) cc_final: 0.6893 (mmm) REVERT: B 449 ARG cc_start: 0.7499 (tmt170) cc_final: 0.7275 (tmt170) REVERT: C 177 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7555 (tm-30) REVERT: C 529 TRP cc_start: 0.7623 (OUTLIER) cc_final: 0.6561 (m100) REVERT: C 592 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6861 (pt0) REVERT: C 616 GLN cc_start: 0.7479 (tm-30) cc_final: 0.7161 (tm-30) REVERT: D 289 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6991 (mtmt) REVERT: D 323 MET cc_start: 0.8693 (mmp) cc_final: 0.8322 (mmp) REVERT: D 592 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7061 (mm-30) outliers start: 33 outliers final: 10 residues processed: 168 average time/residue: 0.6548 time to fit residues: 119.4869 Evaluate side-chains 160 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 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 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 480 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 44 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 16 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 HIS ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.191983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.161616 restraints weight = 12961.969| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.04 r_work: 0.3671 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1222 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= 0.142 Angle : 0.583 7.646 22387 Z= 0.337 Chirality : 0.045 0.246 2488 Planarity : 0.005 0.065 2445 Dihedral : 21.583 71.887 3232 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.55 % Allowed : 11.95 % Favored : 85.50 % 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: 0.47 (0.21), residues: 1594 helix: 1.68 (0.21), residues: 641 sheet: 0.55 (0.42), residues: 139 loop : -0.87 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 575 TYR 0.043 0.001 TYR C 48 PHE 0.026 0.001 PHE B 228 TRP 0.011 0.001 TRP B 586 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (16088) covalent geometry : angle 0.58336 / 0.34 (22387) hydrogen bonds : bond 0.05107 / 3.40 ( 699) hydrogen bonds : angle 4.09216 / 2.89 ( 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 180 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7626 (mp10) REVERT: A 81 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7560 (pt0) REVERT: A 93 LYS cc_start: 0.8317 (pttp) cc_final: 0.7591 (tmtt) REVERT: B 13 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: B 28 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.7046 (tpp) REVERT: B 306 MET cc_start: 0.8356 (ttt) cc_final: 0.7947 (ttt) REVERT: B 366 MET cc_start: 0.7096 (mmm) cc_final: 0.6725 (mmm) REVERT: B 449 ARG cc_start: 0.7512 (tmt170) cc_final: 0.7309 (tmt170) REVERT: C 177 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7526 (tm-30) REVERT: C 529 TRP cc_start: 0.7598 (OUTLIER) cc_final: 0.6546 (m100) REVERT: C 592 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6888 (pt0) REVERT: C 611 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6441 (mp0) REVERT: C 616 GLN cc_start: 0.7503 (tm-30) cc_final: 0.7175 (tm-30) REVERT: D 289 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6970 (mtmt) REVERT: D 592 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7080 (mm-30) outliers start: 34 outliers final: 12 residues processed: 163 average time/residue: 0.6982 time to fit residues: 123.6912 Evaluate side-chains 161 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 81 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain B residue 54 LEU 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 306 MET 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 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: 0.0470 chunk 53 optimal weight: 0.0000 chunk 114 optimal weight: 1.9990 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: 5.9990 overall best weight: 1.0088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 HIS ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.189846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.165322 restraints weight = 12892.527| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 0.69 r_work: 0.3654 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1269 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= 0.176 Angle : 0.640 8.225 22387 Z= 0.363 Chirality : 0.048 0.285 2488 Planarity : 0.005 0.066 2445 Dihedral : 21.631 70.965 3232 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.70 % Allowed : 12.62 % Favored : 84.67 % 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: 0.30 (0.21), residues: 1594 helix: 1.58 (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 0.054 0.002 TYR C 48 PHE 0.025 0.002 PHE B 228 TRP 0.013 0.001 TRP B 586 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (16088) covalent geometry : angle 0.63976 / 0.36 (22387) hydrogen bonds : bond 0.05910 / 3.98 ( 699) hydrogen bonds : angle 4.12026 / 2.91 ( 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 185 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: A 77 GLN cc_start: 0.8066 (mp10) cc_final: 0.7844 (mp10) REVERT: A 81 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7572 (pt0) REVERT: A 93 LYS cc_start: 0.8307 (pttp) cc_final: 0.7643 (tmtt) REVERT: B 13 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7876 (m-30) REVERT: B 306 MET cc_start: 0.8376 (ttt) cc_final: 0.7978 (ttt) REVERT: B 366 MET cc_start: 0.7230 (mmm) cc_final: 0.6840 (mmm) REVERT: C 529 TRP cc_start: 0.7660 (OUTLIER) cc_final: 0.6645 (m100) REVERT: C 592 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6963 (pt0) REVERT: C 611 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: C 616 GLN cc_start: 0.7569 (tm-30) cc_final: 0.7240 (tm-30) REVERT: D 289 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6969 (mtmt) REVERT: D 592 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7188 (mm-30) outliers start: 36 outliers final: 15 residues processed: 170 average time/residue: 0.7117 time to fit residues: 131.7019 Evaluate side-chains 166 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 81 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 504 LYS 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 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 Chi-restraints excluded: chain D residue 466 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 58 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.188277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.165379 restraints weight = 12796.632| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 0.60 r_work: 0.3624 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16088 Z= 0.229 Angle : 0.716 9.016 22387 Z= 0.402 Chirality : 0.053 0.319 2488 Planarity : 0.006 0.066 2445 Dihedral : 21.727 70.829 3232 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.70 % Allowed : 13.52 % Favored : 83.77 % 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: 0.02 (0.21), residues: 1594 helix: 1.30 (0.20), residues: 646 sheet: 0.11 (0.41), residues: 131 loop : -1.08 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 526 TYR 0.025 0.002 TYR C 48 PHE 0.024 0.002 PHE B 228 TRP 0.016 0.002 TRP B 586 HIS 0.006 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 (16088) covalent geometry : angle 0.71553 / 0.40 (22387) hydrogen bonds : bond 0.06931 / 4.68 ( 699) hydrogen bonds : angle 4.25595 / 3.02 ( 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 182 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: A 77 GLN cc_start: 0.8150 (mp10) cc_final: 0.7898 (mp10) REVERT: A 84 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7701 (mtp180) REVERT: A 93 LYS cc_start: 0.8338 (pttp) cc_final: 0.7649 (tmtt) REVERT: B 13 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: B 38 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.6973 (mp-120) REVERT: B 366 MET cc_start: 0.7352 (mmm) cc_final: 0.7012 (mmm) REVERT: C 65 ASP cc_start: 0.7383 (m-30) cc_final: 0.7134 (m-30) REVERT: C 106 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: C 529 TRP cc_start: 0.7834 (OUTLIER) cc_final: 0.6826 (m100) REVERT: C 611 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: D 289 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7045 (mtmt) REVERT: D 592 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7151 (mm-30) outliers start: 36 outliers final: 16 residues processed: 167 average time/residue: 0.7171 time to fit residues: 130.4454 Evaluate side-chains 167 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 A residue 143 SER Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain C residue 106 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 chunk 127 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.190981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.159884 restraints weight = 12760.084| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.04 r_work: 0.3660 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1405 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= 0.149 Angle : 0.610 10.565 22387 Z= 0.349 Chirality : 0.046 0.250 2488 Planarity : 0.005 0.067 2445 Dihedral : 21.656 70.738 3232 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.48 % Allowed : 15.03 % Favored : 82.49 % 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: 0.29 (0.21), residues: 1594 helix: 1.57 (0.21), residues: 645 sheet: 0.36 (0.42), residues: 134 loop : -1.00 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 526 TYR 0.021 0.001 TYR C 48 PHE 0.021 0.001 PHE B 228 TRP 0.019 0.001 TRP B 586 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (16088) covalent geometry : angle 0.60996 / 0.35 (22387) hydrogen bonds : bond 0.05316 / 3.56 ( 699) hydrogen bonds : angle 4.10479 / 2.90 ( 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 175 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: A 93 LYS cc_start: 0.8317 (pttp) cc_final: 0.7584 (tmtt) REVERT: B 13 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: B 366 MET cc_start: 0.7151 (mmm) cc_final: 0.6844 (mmm) REVERT: C 106 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: C 186 LYS cc_start: 0.8020 (ptmm) cc_final: 0.7762 (ttpt) REVERT: C 529 TRP cc_start: 0.7702 (OUTLIER) cc_final: 0.6639 (m100) REVERT: C 592 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6801 (pt0) REVERT: C 607 ARG cc_start: 0.7696 (ttm110) cc_final: 0.7391 (ttm110) REVERT: C 611 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6494 (mp0) REVERT: D 289 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6981 (mtmt) REVERT: D 592 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7155 (mm-30) outliers start: 33 outliers final: 13 residues processed: 162 average time/residue: 0.7263 time to fit residues: 127.9852 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 : 0.466 ------------------------------------------------------------------------------- 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 B residue 149 ARG Chi-restraints excluded: chain B residue 504 LYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 58 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 0.0570 chunk 99 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.189252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.166356 restraints weight = 12833.048| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 0.60 r_work: 0.3637 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16088 Z= 0.187 Angle : 0.661 10.582 22387 Z= 0.374 Chirality : 0.049 0.283 2488 Planarity : 0.005 0.067 2445 Dihedral : 21.681 70.250 3232 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.33 % Allowed : 15.33 % Favored : 82.34 % 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: 0.18 (0.21), residues: 1594 helix: 1.49 (0.21), residues: 645 sheet: 0.10 (0.41), residues: 131 loop : -1.03 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 575 TYR 0.016 0.002 TYR D 297 PHE 0.022 0.002 PHE B 228 TRP 0.020 0.002 TRP B 586 HIS 0.006 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (16088) covalent geometry : angle 0.66103 / 0.37 (22387) hydrogen bonds : bond 0.06089 / 4.10 ( 699) hydrogen bonds : angle 4.16219 / 2.96 ( 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 172 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7622 (mp10) REVERT: A 84 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7673 (mtp180) REVERT: A 93 LYS cc_start: 0.8325 (pttp) cc_final: 0.7644 (tmtt) REVERT: B 13 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7892 (m-30) REVERT: B 366 MET cc_start: 0.7249 (mmm) cc_final: 0.6811 (mmm) REVERT: C 186 LYS cc_start: 0.8043 (ptmm) cc_final: 0.7792 (ttpt) REVERT: C 269 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.6650 (ptm-80) REVERT: C 529 TRP cc_start: 0.7778 (OUTLIER) cc_final: 0.6701 (m100) REVERT: C 592 GLU cc_start: 0.7441 (tm-30) cc_final: 0.6920 (pt0) REVERT: C 607 ARG cc_start: 0.7755 (ttm110) cc_final: 0.7487 (ttm110) REVERT: C 611 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6701 (mp0) REVERT: D 289 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7003 (mtmt) REVERT: D 407 LYS cc_start: 0.7789 (pttm) cc_final: 0.7557 (pttm) REVERT: D 592 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7185 (mm-30) outliers start: 31 outliers final: 19 residues processed: 160 average time/residue: 0.7091 time to fit residues: 123.8172 Evaluate side-chains 165 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 B residue 149 ARG Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 269 ARG 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 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 473 VAL 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: 0.9990 chunk 101 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 114 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 0.0970 chunk 37 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.191690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.162363 restraints weight = 12901.022| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 0.93 r_work: 0.3675 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1454 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= 0.137 Angle : 0.598 11.431 22387 Z= 0.342 Chirality : 0.045 0.245 2488 Planarity : 0.005 0.066 2445 Dihedral : 21.628 70.360 3232 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.88 % Allowed : 15.78 % Favored : 82.34 % 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: 0.39 (0.21), residues: 1594 helix: 1.68 (0.21), residues: 645 sheet: 0.40 (0.42), residues: 134 loop : -0.95 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 575 TYR 0.015 0.001 TYR C 48 PHE 0.024 0.001 PHE B 228 TRP 0.025 0.001 TRP B 586 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (16088) covalent geometry : angle 0.59794 / 0.34 (22387) hydrogen bonds : bond 0.05055 / 3.37 ( 699) hydrogen bonds : angle 4.08670 / 2.90 ( 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 167 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7594 (mp10) REVERT: A 93 LYS cc_start: 0.8324 (pttp) cc_final: 0.7599 (tmtt) REVERT: B 13 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7835 (m-30) REVERT: B 366 MET cc_start: 0.7139 (mmm) cc_final: 0.6692 (mmm) REVERT: C 186 LYS cc_start: 0.8004 (ptmm) cc_final: 0.7742 (ttpt) REVERT: C 269 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.6592 (ptm-80) REVERT: C 529 TRP cc_start: 0.7677 (OUTLIER) cc_final: 0.6615 (m100) REVERT: C 592 GLU cc_start: 0.7374 (tm-30) cc_final: 0.6826 (pt0) REVERT: C 607 ARG cc_start: 0.7689 (ttm110) cc_final: 0.7388 (ttm110) REVERT: C 611 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6470 (mp0) REVERT: D 289 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6969 (mtmt) REVERT: D 407 LYS cc_start: 0.7749 (pttm) cc_final: 0.7503 (pttm) REVERT: D 592 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7096 (mm-30) outliers start: 25 outliers final: 12 residues processed: 157 average time/residue: 0.7473 time to fit residues: 127.6421 Evaluate side-chains 154 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 B residue 13 ASP Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain C residue 269 ARG 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 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 344 ILE Chi-restraints excluded: chain D residue 395 VAL 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: 0.5980 chunk 138 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.189764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.166316 restraints weight = 12803.845| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 0.63 r_work: 0.3646 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1468 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= 0.176 Angle : 0.651 11.580 22387 Z= 0.367 Chirality : 0.048 0.277 2488 Planarity : 0.005 0.067 2445 Dihedral : 21.646 69.980 3232 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.80 % Allowed : 15.93 % Favored : 82.27 % 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: 0.27 (0.21), residues: 1594 helix: 1.59 (0.21), residues: 645 sheet: 0.18 (0.42), residues: 129 loop : -1.00 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 575 TYR 0.018 0.002 TYR C 48 PHE 0.022 0.002 PHE B 228 TRP 0.031 0.002 TRP B 586 HIS 0.006 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (16088) covalent geometry : angle 0.65060 / 0.37 (22387) hydrogen bonds : bond 0.05778 / 3.88 ( 699) hydrogen bonds : angle 4.12614 / 2.94 ( 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 162 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7579 (mp10) REVERT: A 93 LYS cc_start: 0.8322 (pttp) cc_final: 0.7632 (tmtt) REVERT: B 13 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7865 (m-30) REVERT: B 366 MET cc_start: 0.7218 (mmm) cc_final: 0.6793 (mmm) REVERT: C 186 LYS cc_start: 0.8007 (ptmm) cc_final: 0.7757 (ttpt) REVERT: C 269 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.6642 (ptm-80) REVERT: C 529 TRP cc_start: 0.7724 (OUTLIER) cc_final: 0.6615 (m100) REVERT: C 592 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6874 (pt0) REVERT: C 607 ARG cc_start: 0.7737 (ttm110) cc_final: 0.7464 (ttm110) REVERT: C 611 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: D 289 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6998 (mtmt) REVERT: D 407 LYS cc_start: 0.7756 (pttm) cc_final: 0.7514 (pttm) REVERT: D 592 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7146 (mm-30) outliers start: 24 outliers final: 13 residues processed: 153 average time/residue: 0.7358 time to fit residues: 122.5456 Evaluate side-chains 154 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 B residue 13 ASP Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain C residue 100 VAL 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 395 VAL Chi-restraints excluded: chain C residue 453 LEU 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 344 ILE Chi-restraints excluded: chain D residue 395 VAL 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: 2.9990 chunk 1 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.188619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.163504 restraints weight = 12757.472| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 0.72 r_work: 0.3628 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16088 Z= 0.215 Angle : 0.711 11.753 22387 Z= 0.397 Chirality : 0.052 0.307 2488 Planarity : 0.006 0.068 2445 Dihedral : 21.700 69.803 3232 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.25 % Allowed : 15.55 % Favored : 82.19 % 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: 0.07 (0.21), residues: 1594 helix: 1.43 (0.21), residues: 645 sheet: -0.01 (0.41), residues: 131 loop : -1.11 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 575 TYR 0.021 0.002 TYR C 48 PHE 0.024 0.002 PHE B 228 TRP 0.035 0.002 TRP B 586 HIS 0.006 0.001 HIS B 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (16088) covalent geometry : angle 0.71102 / 0.40 (22387) hydrogen bonds : bond 0.06627 / 4.47 ( 699) hydrogen bonds : angle 4.24586 / 3.04 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7450.85 seconds wall clock time: 127 minutes 4.32 seconds (7624.32 seconds total)