Starting phenix.real_space_refine on Wed Mar 4 17:59:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pik_13439/03_2026/7pik_13439.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pik_13439/03_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_13439/03_2026/7pik_13439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pik_13439/03_2026/7pik_13439.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pik_13439/03_2026/7pik_13439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pik_13439/03_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-5986/lib/python3.9/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: 3.44, per 1000 atoms: 0.22 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: 1.59 Conformation dependent library (CDL) restraints added in 761.4 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: 2.08 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: 3.26 Time building geometry restraints manager: 2.12 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=" C SER D 346 " pdb=" O SER D 346 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.17e-02 7.31e+03 9.55e+00 bond pdb=" C VAL A 26 " pdb=" O VAL A 26 " ideal model delta sigma weight residual 1.238 1.202 0.036 1.17e-02 7.31e+03 9.46e+00 bond pdb=" N VAL C 26 " pdb=" CA VAL C 26 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.27e-02 6.20e+03 7.61e+00 bond pdb=" C VAL C 26 " pdb=" O VAL C 26 " ideal model delta sigma weight residual 1.238 1.206 0.032 1.17e-02 7.31e+03 7.39e+00 bond pdb=" C VAL B 26 " pdb=" O VAL B 26 " ideal model delta sigma weight residual 1.238 1.208 0.029 1.17e-02 7.31e+03 6.34e+00 ... (remaining 16083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 22186 2.44 - 4.87: 180 4.87 - 7.31: 17 7.31 - 9.75: 3 9.75 - 12.19: 1 Bond angle restraints: 22387 Sorted by residual: angle pdb=" CA TRP A 27 " pdb=" CB TRP A 27 " pdb=" CG TRP A 27 " ideal model delta sigma weight residual 113.60 120.92 -7.32 1.90e+00 2.77e-01 1.48e+01 angle pdb=" CA GLY C 353 " pdb=" C GLY C 353 " pdb=" O GLY C 353 " ideal model delta sigma weight residual 122.33 119.24 3.09 8.10e-01 1.52e+00 1.46e+01 angle pdb=" CA GLY C 353 " pdb=" C GLY C 353 " pdb=" N LEU C 354 " ideal model delta sigma weight residual 114.23 117.33 -3.10 8.80e-01 1.29e+00 1.24e+01 angle pdb=" N GLY C 353 " pdb=" CA GLY C 353 " pdb=" C GLY C 353 " ideal model delta sigma weight residual 111.85 115.58 -3.73 1.06e+00 8.90e-01 1.24e+01 angle pdb=" N TRP A 27 " pdb=" CA TRP A 27 " pdb=" C TRP A 27 " ideal model delta sigma weight residual 109.23 114.49 -5.26 1.55e+00 4.16e-01 1.15e+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: 2035 0.051 - 0.102: 339 0.102 - 0.154: 103 0.154 - 0.205: 8 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: 14.410 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: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.870 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16088 Z= 0.184 Angle : 0.613 12.186 22387 Z= 0.355 Chirality : 0.043 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 covalent geometry : bond 0.00348 (16088) covalent geometry : angle 0.61302 (22387) hydrogen bonds : bond 0.16949 ( 699) hydrogen bonds : angle 5.77647 ( 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 : 0.549 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: 0.7857 time to fit residues: 168.3168 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 : 0.467 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN C 128 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.191789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.163251 restraints weight = 12829.518| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 0.92 r_work: 0.3672 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0987 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= 0.159 Angle : 0.584 9.948 22387 Z= 0.331 Chirality : 0.042 0.174 2488 Planarity : 0.005 0.064 2445 Dihedral : 21.240 74.307 3236 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.50 % Allowed : 9.32 % Favored : 89.18 % 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: 1.53 (0.21), residues: 640 sheet: 0.53 (0.42), residues: 134 loop : -0.91 (0.21), residues: 820 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 0.024 0.001 PHE B 228 TRP 0.011 0.001 TRP B 586 HIS 0.004 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00343 (16088) covalent geometry : angle 0.58430 (22387) hydrogen bonds : bond 0.05208 ( 699) hydrogen bonds : angle 4.20812 ( 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 170 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8337 (pttp) cc_final: 0.7619 (tmtt) REVERT: B 13 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: B 306 MET cc_start: 0.8331 (ttt) cc_final: 0.7902 (ttt) REVERT: B 361 ASP cc_start: 0.7939 (t0) cc_final: 0.7705 (t0) REVERT: B 366 MET cc_start: 0.7122 (mmm) cc_final: 0.6860 (mmm) REVERT: B 449 ARG cc_start: 0.7547 (tmt170) cc_final: 0.7210 (tmt170) REVERT: C 529 TRP cc_start: 0.7619 (OUTLIER) cc_final: 0.6582 (m100) REVERT: C 592 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6930 (pt0) REVERT: C 616 GLN cc_start: 0.7478 (tm-30) cc_final: 0.7168 (tm-30) REVERT: D 289 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7154 (mtmt) REVERT: D 323 MET cc_start: 0.8719 (mmp) cc_final: 0.8335 (mmp) outliers start: 20 outliers final: 5 residues processed: 160 average time/residue: 0.7470 time to fit residues: 129.3272 Evaluate side-chains 150 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 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: 0.9980 chunk 78 optimal weight: 0.0020 chunk 148 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 170 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 GLN B 482 HIS B 513 ASN C 368 HIS ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.188963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.166165 restraints weight = 12973.837| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 0.62 r_work: 0.3637 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1232 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= 0.217 Angle : 0.645 7.995 22387 Z= 0.364 Chirality : 0.045 0.184 2488 Planarity : 0.005 0.067 2445 Dihedral : 21.450 72.152 3232 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.63 % Allowed : 10.74 % Favored : 86.63 % 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: 0.16 (0.21), residues: 1594 helix: 1.42 (0.21), residues: 640 sheet: 0.23 (0.42), residues: 129 loop : -0.99 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 575 TYR 0.043 0.002 TYR C 48 PHE 0.024 0.002 PHE B 228 TRP 0.013 0.002 TRP C 529 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00484 (16088) covalent geometry : angle 0.64499 (22387) hydrogen bonds : bond 0.06224 ( 699) hydrogen bonds : angle 4.23042 ( 1893) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7595 (mp10) REVERT: A 40 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7718 (ptp-170) REVERT: A 84 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7684 (mtp180) REVERT: A 93 LYS cc_start: 0.8321 (pttp) cc_final: 0.7657 (tmtt) REVERT: B 13 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: B 306 MET cc_start: 0.8400 (ttt) cc_final: 0.7989 (ttt) REVERT: B 366 MET cc_start: 0.7315 (mmm) cc_final: 0.6978 (mmm) REVERT: B 449 ARG cc_start: 0.7616 (tmt170) cc_final: 0.7352 (tmt170) REVERT: C 269 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6820 (ptm-80) REVERT: C 453 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8653 (tt) REVERT: C 529 TRP cc_start: 0.7802 (OUTLIER) cc_final: 0.6798 (m100) REVERT: C 592 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6897 (pt0) REVERT: C 616 GLN cc_start: 0.7540 (tm-30) cc_final: 0.7218 (tm-30) REVERT: D 289 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6993 (mtmt) REVERT: D 323 MET cc_start: 0.8724 (mmp) cc_final: 0.8457 (mmp) outliers start: 35 outliers final: 9 residues processed: 167 average time/residue: 0.7503 time to fit residues: 135.4044 Evaluate side-chains 157 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 206 LEU 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 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 D residue 289 LYS Chi-restraints excluded: chain D residue 395 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 44 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 66 optimal weight: 0.0470 chunk 120 optimal weight: 2.9990 chunk 16 optimal weight: 0.0020 overall best weight: 0.5690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.191702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.160944 restraints weight = 12984.865| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 1.05 r_work: 0.3672 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1328 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= 0.147 Angle : 0.554 7.153 22387 Z= 0.316 Chirality : 0.041 0.165 2488 Planarity : 0.005 0.067 2445 Dihedral : 21.208 71.239 3232 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.03 % Allowed : 12.70 % Favored : 85.27 % 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: 0.40 (0.21), residues: 1594 helix: 1.61 (0.21), residues: 646 sheet: 0.47 (0.43), residues: 129 loop : -0.89 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 575 TYR 0.040 0.001 TYR C 48 PHE 0.025 0.001 PHE B 228 TRP 0.012 0.001 TRP B 586 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00315 (16088) covalent geometry : angle 0.55382 (22387) hydrogen bonds : bond 0.04752 ( 699) hydrogen bonds : angle 4.02282 ( 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 173 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7663 (mp10) REVERT: A 40 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7696 (ptp-170) REVERT: A 77 GLN cc_start: 0.8008 (mp10) cc_final: 0.7804 (mp10) REVERT: A 93 LYS cc_start: 0.8311 (pttp) cc_final: 0.7589 (tmtt) REVERT: B 13 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: B 306 MET cc_start: 0.8341 (ttt) cc_final: 0.7945 (ttt) REVERT: B 366 MET cc_start: 0.7030 (mmm) cc_final: 0.6652 (mmm) REVERT: B 451 ASN cc_start: 0.7801 (m110) cc_final: 0.7601 (m-40) REVERT: C 106 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6569 (mp0) REVERT: C 217 GLU cc_start: 0.7650 (pp20) cc_final: 0.7449 (pp20) REVERT: C 218 ASP cc_start: 0.8298 (m-30) cc_final: 0.7735 (m-30) REVERT: C 269 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.6687 (ptm-80) REVERT: C 453 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8551 (tt) REVERT: C 529 TRP cc_start: 0.7601 (OUTLIER) cc_final: 0.6528 (m100) REVERT: C 592 GLU cc_start: 0.7362 (tm-30) cc_final: 0.6872 (pt0) REVERT: C 611 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6454 (mp0) REVERT: C 616 GLN cc_start: 0.7469 (tm-30) cc_final: 0.7145 (tm-30) REVERT: D 289 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6970 (mtmt) outliers start: 27 outliers final: 6 residues processed: 162 average time/residue: 0.6765 time to fit residues: 119.2406 Evaluate side-chains 158 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 C residue 106 GLU Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 293 ARG Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 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: 0.4980 chunk 53 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.190832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.161112 restraints weight = 12974.191| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 0.94 r_work: 0.3669 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1390 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= 0.167 Angle : 0.582 10.371 22387 Z= 0.329 Chirality : 0.042 0.182 2488 Planarity : 0.005 0.067 2445 Dihedral : 21.238 70.214 3232 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.25 % Allowed : 13.52 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.21), residues: 1594 helix: 1.66 (0.21), residues: 645 sheet: 0.44 (0.42), residues: 134 loop : -0.94 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 575 TYR 0.038 0.002 TYR C 48 PHE 0.021 0.001 PHE B 228 TRP 0.015 0.001 TRP B 586 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00365 (16088) covalent geometry : angle 0.58228 (22387) hydrogen bonds : bond 0.05164 ( 699) hydrogen bonds : angle 4.01376 ( 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 173 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7594 (mp10) REVERT: A 40 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7720 (ptp-170) REVERT: A 93 LYS cc_start: 0.8312 (pttp) cc_final: 0.7602 (tmtt) REVERT: B 13 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: B 38 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.6874 (mp-120) REVERT: B 306 MET cc_start: 0.8369 (ttt) cc_final: 0.7968 (ttt) REVERT: B 366 MET cc_start: 0.7134 (mmm) cc_final: 0.6734 (mmm) REVERT: B 451 ASN cc_start: 0.7812 (m110) cc_final: 0.7601 (m-40) REVERT: C 186 LYS cc_start: 0.8024 (ptmm) cc_final: 0.7765 (ttpt) REVERT: C 218 ASP cc_start: 0.8268 (m-30) cc_final: 0.7859 (m-30) REVERT: C 269 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.6696 (ptm-80) REVERT: C 453 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8569 (tt) REVERT: C 529 TRP cc_start: 0.7660 (OUTLIER) cc_final: 0.6601 (m100) REVERT: C 592 GLU cc_start: 0.7374 (tm-30) cc_final: 0.6907 (pt0) REVERT: C 607 ARG cc_start: 0.7695 (ttm110) cc_final: 0.7387 (ttm110) REVERT: C 611 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: C 616 GLN cc_start: 0.7521 (tm-30) cc_final: 0.7189 (tm-30) REVERT: D 289 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6986 (mtmt) outliers start: 30 outliers final: 11 residues processed: 160 average time/residue: 0.6955 time to fit residues: 120.9763 Evaluate side-chains 162 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 38 GLN Chi-restraints excluded: chain B residue 480 MET 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 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 395 VAL Chi-restraints excluded: chain D residue 480 MET 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: 2.9990 chunk 75 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 482 HIS C 12 ASN C 77 GLN C 209 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.188153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.162397 restraints weight = 12813.855| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 0.72 r_work: 0.3641 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1499 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= 0.243 Angle : 0.675 10.563 22387 Z= 0.377 Chirality : 0.046 0.182 2488 Planarity : 0.006 0.067 2445 Dihedral : 21.499 75.706 3232 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.93 % Allowed : 13.75 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.21), residues: 1594 helix: 1.43 (0.21), residues: 645 sheet: 0.03 (0.41), residues: 131 loop : -1.05 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 575 TYR 0.039 0.002 TYR C 48 PHE 0.023 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 covalent geometry : bond 0.00547 (16088) covalent geometry : angle 0.67517 (22387) hydrogen bonds : bond 0.06501 ( 699) hydrogen bonds : angle 4.22594 ( 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: 39 poor density : 143 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7542 (mp10) REVERT: A 40 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7745 (ptp-170) REVERT: A 84 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7657 (mtp180) REVERT: A 93 LYS cc_start: 0.8337 (pttp) cc_final: 0.7668 (tmtt) REVERT: B 13 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7861 (m-30) REVERT: B 38 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.6984 (mp-120) REVERT: B 361 ASP cc_start: 0.8087 (t0) cc_final: 0.7887 (t0) REVERT: B 366 MET cc_start: 0.7300 (mmm) cc_final: 0.6919 (mmm) REVERT: C 186 LYS cc_start: 0.8030 (ptmm) cc_final: 0.7814 (ttpt) REVERT: C 209 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7479 (tm130) REVERT: C 218 ASP cc_start: 0.8215 (m-30) cc_final: 0.7759 (m-30) REVERT: C 269 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.6743 (ptm-80) REVERT: C 529 TRP cc_start: 0.7913 (OUTLIER) cc_final: 0.6909 (m100) REVERT: C 607 ARG cc_start: 0.7753 (ttm110) cc_final: 0.7523 (ttm110) REVERT: C 611 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: C 616 GLN cc_start: 0.7554 (tm-30) cc_final: 0.7197 (tm-30) REVERT: D 289 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7035 (mtmt) outliers start: 39 outliers final: 15 residues processed: 165 average time/residue: 0.7284 time to fit residues: 130.1159 Evaluate side-chains 162 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 38 GLN Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 206 LEU 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 209 GLN 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 395 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 541 HIS Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 524 ILE 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: 0.7980 chunk 143 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 77 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.189033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.162753 restraints weight = 12689.331| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 0.71 r_work: 0.3657 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1491 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= 0.197 Angle : 0.633 10.874 22387 Z= 0.355 Chirality : 0.044 0.186 2488 Planarity : 0.005 0.067 2445 Dihedral : 21.405 71.487 3232 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.40 % Allowed : 14.80 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.21), residues: 1594 helix: 1.49 (0.21), residues: 645 sheet: 0.30 (0.42), residues: 134 loop : -1.02 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 526 TYR 0.038 0.002 TYR C 48 PHE 0.023 0.002 PHE B 228 TRP 0.022 0.001 TRP B 586 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00437 (16088) covalent geometry : angle 0.63251 (22387) hydrogen bonds : bond 0.05721 ( 699) hydrogen bonds : angle 4.16685 ( 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 173 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7547 (mp10) REVERT: A 40 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7630 (ptp-170) REVERT: A 93 LYS cc_start: 0.8323 (pttp) cc_final: 0.7653 (tmtt) REVERT: B 13 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7853 (m-30) REVERT: B 366 MET cc_start: 0.7244 (mmm) cc_final: 0.6882 (mmm) REVERT: C 186 LYS cc_start: 0.7961 (ptmm) cc_final: 0.7754 (ttpt) REVERT: C 218 ASP cc_start: 0.8166 (m-30) cc_final: 0.7710 (m-30) REVERT: C 269 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6689 (ptm-80) REVERT: C 529 TRP cc_start: 0.7799 (OUTLIER) cc_final: 0.6719 (m100) REVERT: C 592 GLU cc_start: 0.7434 (tm-30) cc_final: 0.6849 (pt0) REVERT: C 607 ARG cc_start: 0.7738 (ttm110) cc_final: 0.7487 (ttm110) REVERT: C 611 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6615 (mp0) REVERT: C 616 GLN cc_start: 0.7559 (tm-30) cc_final: 0.7203 (tm-30) REVERT: D 289 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7036 (mtmt) outliers start: 32 outliers final: 14 residues processed: 158 average time/residue: 0.7157 time to fit residues: 122.8631 Evaluate side-chains 157 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 113 LYS Chi-restraints excluded: chain B residue 182 LEU 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 306 MET Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 VAL 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 466 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 99 optimal weight: 0.2980 chunk 133 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 482 HIS C 12 ASN C 209 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.188890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.165332 restraints weight = 12819.281| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 0.60 r_work: 0.3663 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1531 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= 0.206 Angle : 0.642 11.735 22387 Z= 0.360 Chirality : 0.045 0.184 2488 Planarity : 0.005 0.067 2445 Dihedral : 21.411 70.385 3232 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.25 % Allowed : 15.33 % Favored : 82.42 % 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: 0.19 (0.21), residues: 1594 helix: 1.47 (0.21), residues: 645 sheet: 0.29 (0.42), residues: 134 loop : -1.04 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 575 TYR 0.045 0.002 TYR C 48 PHE 0.021 0.002 PHE B 228 TRP 0.026 0.002 TRP B 586 HIS 0.005 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00460 (16088) covalent geometry : angle 0.64249 (22387) hydrogen bonds : bond 0.05876 ( 699) hydrogen bonds : angle 4.16792 ( 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 168 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7540 (mp10) REVERT: A 40 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7641 (ptp-170) REVERT: A 84 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7640 (mtp180) REVERT: A 93 LYS cc_start: 0.8308 (pttp) cc_final: 0.7654 (tmtt) REVERT: B 13 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7849 (m-30) REVERT: B 149 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7517 (mpt180) REVERT: B 366 MET cc_start: 0.7236 (mmm) cc_final: 0.6876 (mmm) REVERT: C 209 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7357 (tm130) REVERT: C 269 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.6708 (ptm-80) REVERT: C 529 TRP cc_start: 0.7798 (OUTLIER) cc_final: 0.6711 (m100) REVERT: C 592 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6861 (pt0) REVERT: C 607 ARG cc_start: 0.7756 (ttm110) cc_final: 0.7528 (ttm110) REVERT: C 611 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: C 616 GLN cc_start: 0.7582 (tm-30) cc_final: 0.7231 (tm-30) REVERT: D 289 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.7035 (mtmt) outliers start: 30 outliers final: 11 residues processed: 157 average time/residue: 0.7289 time to fit residues: 124.0239 Evaluate side-chains 154 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 113 LYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 209 GLN 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 491 GLU Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 466 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 83 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN C 209 GLN ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.189812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.166119 restraints weight = 12813.891| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 0.59 r_work: 0.3673 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1519 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= 0.173 Angle : 0.609 12.151 22387 Z= 0.342 Chirality : 0.043 0.182 2488 Planarity : 0.005 0.067 2445 Dihedral : 21.316 70.113 3232 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.03 % Allowed : 15.93 % Favored : 82.04 % 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: 0.32 (0.21), residues: 1594 helix: 1.59 (0.21), residues: 645 sheet: 0.36 (0.42), residues: 134 loop : -0.98 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 526 TYR 0.051 0.002 TYR C 48 PHE 0.023 0.002 PHE B 228 TRP 0.032 0.001 TRP B 586 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00380 (16088) covalent geometry : angle 0.60869 (22387) hydrogen bonds : bond 0.05278 ( 699) hydrogen bonds : angle 4.08909 ( 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 166 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7572 (mp10) REVERT: A 40 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7659 (ptp-170) REVERT: A 93 LYS cc_start: 0.8310 (pttp) cc_final: 0.7642 (tmtt) REVERT: B 13 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: B 149 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7494 (mpt180) REVERT: B 366 MET cc_start: 0.7166 (mmm) cc_final: 0.6693 (mmm) REVERT: C 269 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.6673 (ptm-80) REVERT: C 529 TRP cc_start: 0.7729 (OUTLIER) cc_final: 0.6683 (m100) REVERT: C 592 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6826 (pt0) REVERT: C 607 ARG cc_start: 0.7724 (ttm110) cc_final: 0.7493 (ttm110) REVERT: C 611 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: C 616 GLN cc_start: 0.7608 (tm-30) cc_final: 0.7260 (tm-30) REVERT: D 289 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.7037 (mtmt) outliers start: 27 outliers final: 12 residues processed: 153 average time/residue: 0.6869 time to fit residues: 114.3013 Evaluate side-chains 153 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 113 LYS 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 394 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 466 THR 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: 2.9990 chunk 138 optimal weight: 0.0970 chunk 119 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 482 HIS C 77 GLN C 284 HIS ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.187419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.164596 restraints weight = 12803.114| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 0.57 r_work: 0.3643 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16088 Z= 0.275 Angle : 0.725 12.172 22387 Z= 0.403 Chirality : 0.048 0.209 2488 Planarity : 0.006 0.068 2445 Dihedral : 21.603 78.964 3232 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.73 % Allowed : 16.38 % Favored : 81.89 % 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: -0.00 (0.21), residues: 1594 helix: 1.34 (0.21), residues: 638 sheet: -0.04 (0.41), residues: 131 loop : -1.10 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 575 TYR 0.036 0.002 TYR C 48 PHE 0.019 0.002 PHE B 228 TRP 0.039 0.002 TRP B 586 HIS 0.006 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00624 (16088) covalent geometry : angle 0.72497 (22387) hydrogen bonds : bond 0.06976 ( 699) hydrogen bonds : angle 4.31003 ( 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 161 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: A 40 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7807 (ptp-170) REVERT: A 84 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7678 (mtp180) REVERT: A 93 LYS cc_start: 0.8327 (pttp) cc_final: 0.7672 (tmtt) REVERT: B 13 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7884 (m-30) REVERT: B 149 ARG cc_start: 0.7813 (mtm-85) cc_final: 0.7599 (mpt180) REVERT: B 366 MET cc_start: 0.7378 (mmm) cc_final: 0.7009 (mmm) REVERT: C 65 ASP cc_start: 0.7357 (m-30) cc_final: 0.7098 (m-30) REVERT: C 269 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.6700 (ptm-80) REVERT: C 529 TRP cc_start: 0.7872 (OUTLIER) cc_final: 0.6854 (m100) REVERT: C 592 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6818 (pt0) REVERT: C 611 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: C 616 GLN cc_start: 0.7565 (tm-30) cc_final: 0.7206 (tm-30) REVERT: D 289 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7052 (mtmt) outliers start: 23 outliers final: 13 residues processed: 150 average time/residue: 0.6823 time to fit residues: 111.2398 Evaluate side-chains 155 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 113 LYS 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 382 GLU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 529 TRP Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain D residue 289 LYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 524 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 50 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN C 187 HIS ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.190728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.158690 restraints weight = 12859.152| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.10 r_work: 0.3654 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1563 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= 0.162 Angle : 0.603 12.612 22387 Z= 0.339 Chirality : 0.042 0.170 2488 Planarity : 0.005 0.067 2445 Dihedral : 21.304 70.581 3232 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.73 % Allowed : 16.68 % Favored : 81.59 % 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: 1.56 (0.21), residues: 645 sheet: 0.35 (0.42), residues: 134 loop : -1.00 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 607 TYR 0.031 0.001 TYR C 48 PHE 0.022 0.001 PHE B 228 TRP 0.040 0.001 TRP B 586 HIS 0.004 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00350 (16088) covalent geometry : angle 0.60282 (22387) hydrogen bonds : bond 0.05023 ( 699) hydrogen bonds : angle 4.09422 ( 1893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7409.26 seconds wall clock time: 125 minutes 54.79 seconds (7554.79 seconds total)