Starting phenix.real_space_refine on Wed Mar 4 01:48:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b5n_12041/03_2026/7b5n_12041.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b5n_12041/03_2026/7b5n_12041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b5n_12041/03_2026/7b5n_12041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b5n_12041/03_2026/7b5n_12041.map" model { file = "/net/cci-nas-00/data/ceres_data/7b5n_12041/03_2026/7b5n_12041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b5n_12041/03_2026/7b5n_12041.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Zn 9 6.06 5 S 77 5.16 5 C 6321 2.51 5 N 1725 2.21 5 O 1833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 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: 9965 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3398 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3472 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 410} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "U" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 599 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "R" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 677 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1209 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 137} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' ZN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "U" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'SY8': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5255 SG CYS H 344 88.596 51.367 35.674 1.00 63.40 S ATOM 5277 SG CYS H 347 86.278 51.508 38.931 1.00 67.85 S ATOM 5388 SG CYS H 362 88.652 48.719 38.315 1.00 73.36 S ATOM 5427 SG CYS H 367 85.690 48.967 36.300 1.00 65.71 S ATOM 5467 SG CYS H 372 98.854 50.897 28.180 1.00 80.71 S ATOM 5494 SG CYS H 375 96.661 52.921 25.973 1.00 84.91 S ATOM 5588 SG CYS H 389 100.357 53.840 25.918 1.00121.79 S ATOM 4710 SG CYS H 276 74.024 61.875 53.700 1.00 35.62 S ATOM 4743 SG CYS H 281 71.906 59.754 55.671 1.00 42.39 S ATOM 4874 SG CYS H 297 70.375 62.156 53.287 1.00 49.44 S ATOM 4889 SG CYS H 299 72.147 63.354 56.656 1.00 55.96 S ATOM 4930 SG CYS H 304 74.535 68.765 42.090 1.00 29.12 S ATOM 4955 SG CYS H 307 78.447 68.267 42.721 1.00 31.97 S ATOM 5037 SG CYS H 317 77.181 69.509 39.463 1.00 28.90 S ATOM 3984 SG CYS H 186 86.173 17.376 47.279 1.00 86.68 S ATOM 4007 SG CYS H 189 87.143 16.632 50.772 1.00 91.82 S ATOM 4165 SG CYS H 208 83.833 17.858 50.099 1.00 77.45 S ATOM 4188 SG CYS H 211 86.634 20.319 49.968 1.00 66.51 S ATOM 4125 SG CYS H 203 78.738 23.933 36.909 1.00 86.78 S ATOM 4346 SG CYS H 231 81.354 24.858 39.376 1.00 37.03 S ATOM 4378 SG CYS H 236 81.750 25.783 35.500 1.00 50.91 S ATOM 8251 SG CYS R 42 68.670 100.376 33.343 1.00 27.14 S ATOM 8270 SG CYS R 45 68.786 99.018 37.078 1.00 22.21 S ATOM 8518 SG CYS R 83 70.525 102.157 36.148 1.00 23.15 S ATOM 8447 SG CYS R 75 72.299 101.999 20.644 1.00 23.78 S ATOM 8614 SG CYS R 94 74.157 100.704 23.838 1.00 26.05 S ATOM 8337 SG CYS R 53 68.751 104.522 40.231 1.00 26.92 S ATOM 8360 SG CYS R 56 67.762 107.652 42.111 1.00 34.82 S ATOM 8397 SG CYS R 68 66.092 106.653 38.683 1.00 28.19 S Time building chain proxies: 2.23, per 1000 atoms: 0.22 Number of scatterers: 9965 At special positions: 0 Unit cell: (135.16, 135.16, 95.92, 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) Zn 9 29.99 S 77 16.00 O 1833 8.00 N 1725 7.00 C 6321 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 additional links: simple=1, symmetry=0 Simple link: pdb=" C GLY U 75 " - pdb=" N SY8 U 101 " Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 405.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 601 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 347 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 344 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 367 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 362 " pdb=" ZN H 602 " pdb="ZN ZN H 602 " - pdb=" NE2 HIS H 382 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 372 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 389 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 375 " pdb=" ZN H 603 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 297 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 276 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 299 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 281 " pdb=" ZN H 604 " pdb="ZN ZN H 604 " - pdb=" NE2 HIS H 312 " pdb="ZN ZN H 604 " - pdb=" SG CYS H 304 " pdb="ZN ZN H 604 " - pdb=" SG CYS H 307 " pdb="ZN ZN H 604 " - pdb=" SG CYS H 317 " pdb=" ZN H 605 " pdb="ZN ZN H 605 " - pdb=" SG CYS H 208 " pdb="ZN ZN H 605 " - pdb=" SG CYS H 186 " pdb="ZN ZN H 605 " - pdb=" SG CYS H 189 " pdb="ZN ZN H 605 " - pdb=" SG CYS H 211 " pdb=" ZN H 606 " pdb="ZN ZN H 606 " - pdb=" ND1 HIS H 205 " pdb="ZN ZN H 606 " - pdb=" SG CYS H 236 " pdb="ZN ZN H 606 " - pdb=" SG CYS H 203 " pdb="ZN ZN H 606 " - pdb=" SG CYS H 231 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " Number of angles added : 33 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 50.4% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'C' and resid 336 through 354 removed outlier: 3.762A pdb=" N LEU C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 342 " --> pdb=" O LYS C 338 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C 350 " --> pdb=" O ASN C 346 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 351 " --> pdb=" O GLN C 347 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.766A pdb=" N LEU C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN C 361 " --> pdb=" O GLU C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 356 through 361' Processing helix chain 'C' and resid 362 through 384 removed outlier: 3.790A pdb=" N TYR C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 405 Processing helix chain 'C' and resid 406 through 413 removed outlier: 3.506A pdb=" N ALA C 412 " --> pdb=" O VAL C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 431 Processing helix chain 'C' and resid 438 through 456 removed outlier: 3.764A pdb=" N ILE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 476 Processing helix chain 'C' and resid 481 through 497 Processing helix chain 'C' and resid 501 through 526 removed outlier: 3.637A pdb=" N GLN C 505 " --> pdb=" O THR C 501 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE C 511 " --> pdb=" O MET C 507 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 574 removed outlier: 3.557A pdb=" N ARG C 573 " --> pdb=" O PHE C 569 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS C 574 " --> pdb=" O TYR C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 614 removed outlier: 3.558A pdb=" N TYR C 614 " --> pdb=" O ILE C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 630 removed outlier: 3.544A pdb=" N SER C 628 " --> pdb=" O GLN C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 646 removed outlier: 3.567A pdb=" N SER C 646 " --> pdb=" O ILE C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 722 Processing helix chain 'C' and resid 726 through 738 Processing helix chain 'C' and resid 745 through 759 Processing helix chain 'H' and resid 105 through 125 removed outlier: 3.910A pdb=" N MET H 113 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL H 114 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL H 123 " --> pdb=" O GLU H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 138 removed outlier: 3.551A pdb=" N PHE H 138 " --> pdb=" O LEU H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 150 Processing helix chain 'H' and resid 154 through 162 Processing helix chain 'H' and resid 194 through 198 Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 241 through 249 removed outlier: 3.939A pdb=" N VAL H 245 " --> pdb=" O ASP H 241 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE H 249 " --> pdb=" O VAL H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 270 Processing helix chain 'H' and resid 316 through 326 removed outlier: 4.146A pdb=" N LYS H 326 " --> pdb=" O LYS H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 341 Processing helix chain 'H' and resid 408 through 430 removed outlier: 3.739A pdb=" N GLN H 412 " --> pdb=" O ARG H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 448 removed outlier: 3.741A pdb=" N HIS H 448 " --> pdb=" O GLU H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 481 removed outlier: 3.951A pdb=" N TYR H 474 " --> pdb=" O ALA H 470 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR H 481 " --> pdb=" O VAL H 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 485 through 513 removed outlier: 3.525A pdb=" N ILE H 489 " --> pdb=" O ASN H 485 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE H 491 " --> pdb=" O GLN H 487 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA H 496 " --> pdb=" O GLU H 492 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP H 497 " --> pdb=" O ASN H 493 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU H 510 " --> pdb=" O SER H 506 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG H 511 " --> pdb=" O GLY H 507 " (cutoff:3.500A) Processing helix chain 'H' and resid 517 through 550 removed outlier: 4.263A pdb=" N GLN H 523 " --> pdb=" O GLN H 519 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 34 Processing helix chain 'N' and resid 22 through 35 removed outlier: 4.358A pdb=" N LYS N 33 " --> pdb=" O ARG N 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 Processing helix chain 'D' and resid 2 through 18 removed outlier: 3.621A pdb=" N LYS D 9 " --> pdb=" O ARG D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 114 removed outlier: 3.616A pdb=" N VAL D 104 " --> pdb=" O LYS D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 132 through 148 removed outlier: 4.083A pdb=" N PHE D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 540 removed outlier: 11.219A pdb=" N LYS R 26 " --> pdb=" O SER C 586 " (cutoff:3.500A) removed outlier: 10.761A pdb=" N SER C 586 " --> pdb=" O LYS R 26 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N ASN R 28 " --> pdb=" O GLN C 584 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N GLN C 584 " --> pdb=" O ASN R 28 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL R 30 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU R 32 " --> pdb=" O THR C 580 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 619 through 621 removed outlier: 4.223A pdb=" N TYR C 620 " --> pdb=" O ILE C 669 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 762 through 764 Processing sheet with id=AA4, first strand: chain 'H' and resid 294 through 296 Processing sheet with id=AA5, first strand: chain 'H' and resid 342 through 343 Processing sheet with id=AA6, first strand: chain 'U' and resid 10 through 16 removed outlier: 5.521A pdb=" N LYS U 11 " --> pdb=" O THR U 7 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR U 7 " --> pdb=" O LYS U 11 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N LEU U 67 " --> pdb=" O GLN U 2 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE U 4 " --> pdb=" O LEU U 67 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU U 69 " --> pdb=" O PHE U 4 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS U 6 " --> pdb=" O LEU U 69 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N LEU U 71 " --> pdb=" O LYS U 6 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 2 through 6 Processing sheet with id=AA8, first strand: chain 'N' and resid 48 through 49 Processing sheet with id=AA9, first strand: chain 'R' and resid 78 through 80 removed outlier: 3.525A pdb=" N LYS R 105 " --> pdb=" O TRP R 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 22 through 27 removed outlier: 5.047A pdb=" N ASN D 24 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 38 " --> pdb=" O ASN D 24 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE D 51 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS D 67 " --> pdb=" O ASN D 56 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3250 1.34 - 1.46: 2207 1.46 - 1.59: 4587 1.59 - 1.71: 0 1.71 - 1.83: 108 Bond restraints: 10152 Sorted by residual: bond pdb=" N PRO C 437 " pdb=" CA PRO C 437 " ideal model delta sigma weight residual 1.469 1.540 -0.070 1.22e-02 6.72e+03 3.32e+01 bond pdb=" C ASN C 436 " pdb=" N PRO C 437 " ideal model delta sigma weight residual 1.333 1.382 -0.049 1.17e-02 7.31e+03 1.79e+01 bond pdb=" C ASP C 532 " pdb=" N LEU C 533 " ideal model delta sigma weight residual 1.331 1.273 0.058 1.51e-02 4.39e+03 1.49e+01 bond pdb=" N GLU C 438 " pdb=" CA GLU C 438 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.30e-02 5.92e+03 6.46e+00 bond pdb=" CB TRP R 33 " pdb=" CG TRP R 33 " ideal model delta sigma weight residual 1.498 1.423 0.075 3.10e-02 1.04e+03 5.93e+00 ... (remaining 10147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 13351 2.10 - 4.19: 298 4.19 - 6.29: 31 6.29 - 8.38: 7 8.38 - 10.48: 4 Bond angle restraints: 13691 Sorted by residual: angle pdb=" C ASN C 436 " pdb=" N PRO C 437 " pdb=" CA PRO C 437 " ideal model delta sigma weight residual 119.90 128.47 -8.57 1.05e+00 9.07e-01 6.66e+01 angle pdb=" C GLU C 529 " pdb=" N PRO C 530 " pdb=" CA PRO C 530 " ideal model delta sigma weight residual 119.83 124.44 -4.61 1.08e+00 8.57e-01 1.83e+01 angle pdb=" CA GLY H 355 " pdb=" C GLY H 355 " pdb=" N GLY H 356 " ideal model delta sigma weight residual 114.65 117.77 -3.12 9.20e-01 1.18e+00 1.15e+01 angle pdb=" C GLN H 456 " pdb=" N PHE H 457 " pdb=" CA PHE H 457 " ideal model delta sigma weight residual 120.28 115.65 4.63 1.44e+00 4.82e-01 1.03e+01 angle pdb=" CA PRO C 437 " pdb=" N PRO C 437 " pdb=" CD PRO C 437 " ideal model delta sigma weight residual 112.00 107.68 4.32 1.40e+00 5.10e-01 9.53e+00 ... (remaining 13686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5458 17.93 - 35.85: 620 35.85 - 53.78: 100 53.78 - 71.71: 14 71.71 - 89.63: 15 Dihedral angle restraints: 6207 sinusoidal: 2573 harmonic: 3634 Sorted by residual: dihedral pdb=" CA PHE D 51 " pdb=" C PHE D 51 " pdb=" N ARG D 52 " pdb=" CA ARG D 52 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ASP R 97 " pdb=" C ASP R 97 " pdb=" N ASN R 98 " pdb=" CA ASN R 98 " ideal model delta harmonic sigma weight residual 180.00 -157.89 -22.11 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA PRO C 530 " pdb=" C PRO C 530 " pdb=" N LEU C 531 " pdb=" CA LEU C 531 " ideal model delta harmonic sigma weight residual 180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 6204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 975 0.041 - 0.082: 398 0.082 - 0.123: 103 0.123 - 0.165: 23 0.165 - 0.206: 4 Chirality restraints: 1503 Sorted by residual: chirality pdb=" CB ILE C 344 " pdb=" CA ILE C 344 " pdb=" CG1 ILE C 344 " pdb=" CG2 ILE C 344 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE H 513 " pdb=" CA ILE H 513 " pdb=" CG1 ILE H 513 " pdb=" CG2 ILE H 513 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA TYR H 529 " pdb=" N TYR H 529 " pdb=" C TYR H 529 " pdb=" CB TYR H 529 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.11e-01 ... (remaining 1500 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 664 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.01e+00 pdb=" N PRO C 665 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 665 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 665 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU H 509 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C LEU H 509 " -0.032 2.00e-02 2.50e+03 pdb=" O LEU H 509 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU H 510 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 380 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO H 381 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO H 381 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 381 " -0.025 5.00e-02 4.00e+02 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 102 2.58 - 3.16: 8537 3.16 - 3.74: 14813 3.74 - 4.32: 19486 4.32 - 4.90: 32292 Nonbonded interactions: 75230 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.998 2.230 nonbonded pdb=" O ARG H 408 " pdb=" NH1 ARG H 408 " model vdw 2.166 3.120 nonbonded pdb=" O ASN C 406 " pdb=" OG1 THR C 409 " model vdw 2.226 3.040 nonbonded pdb=" NE2 GLN H 523 " pdb=" OD2 ASP H 527 " model vdw 2.240 3.120 nonbonded pdb=" NH2 ARG D 15 " pdb=" O ILE D 25 " model vdw 2.247 3.120 ... (remaining 75225 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 10.820 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.008 0.270 10190 Z= 0.329 Angle : 0.836 11.323 13726 Z= 0.457 Chirality : 0.048 0.206 1503 Planarity : 0.004 0.050 1751 Dihedral : 15.391 89.633 3838 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.09 % Allowed : 0.37 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.23), residues: 1209 helix: 0.59 (0.21), residues: 569 sheet: -0.64 (0.59), residues: 86 loop : -2.65 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 473 TYR 0.019 0.002 TYR C 455 PHE 0.025 0.002 PHE D 143 TRP 0.019 0.002 TRP R 33 HIS 0.005 0.001 HIS R 80 Details of bonding type rmsd covalent geometry : bond 0.00686 (10152) covalent geometry : angle 0.79149 (13691) hydrogen bonds : bond 0.16928 ( 468) hydrogen bonds : angle 6.57625 ( 1383) metal coordination : bond 0.05162 ( 35) metal coordination : angle 5.48117 ( 33) Misc. bond : bond 0.05901 ( 2) link_TRANS : bond 0.01181 ( 1) link_TRANS : angle 3.56443 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.385 Fit side-chains REVERT: C 531 LEU cc_start: 0.8154 (pt) cc_final: 0.7948 (pt) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.0954 time to fit residues: 21.7432 Evaluate side-chains 136 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 432 HIS U 41 GLN N 41 GLN D 24 ASN D 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.105024 restraints weight = 17361.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.104123 restraints weight = 14562.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.104919 restraints weight = 16171.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.106044 restraints weight = 10135.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.106498 restraints weight = 8866.723| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10190 Z= 0.150 Angle : 0.619 8.375 13726 Z= 0.318 Chirality : 0.043 0.192 1503 Planarity : 0.004 0.039 1751 Dihedral : 4.731 28.265 1327 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.28 % Allowed : 9.52 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.70 (0.24), residues: 1209 helix: 1.18 (0.22), residues: 572 sheet: -0.49 (0.60), residues: 87 loop : -2.37 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 511 TYR 0.025 0.001 TYR H 529 PHE 0.031 0.002 PHE H 457 TRP 0.008 0.001 TRP C 581 HIS 0.007 0.001 HIS C 727 Details of bonding type rmsd covalent geometry : bond 0.00330 (10152) covalent geometry : angle 0.60047 (13691) hydrogen bonds : bond 0.06363 ( 468) hydrogen bonds : angle 4.93949 ( 1383) metal coordination : bond 0.00678 ( 35) metal coordination : angle 3.08933 ( 33) Misc. bond : bond 0.00048 ( 2) link_TRANS : bond 0.00103 ( 1) link_TRANS : angle 0.06516 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 719 MET cc_start: 0.7258 (tpp) cc_final: 0.6827 (tpp) REVERT: H 450 MET cc_start: 0.6656 (mmt) cc_final: 0.6396 (mmp) REVERT: U 6 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8466 (tttp) REVERT: N 28 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7002 (pt0) REVERT: D 13 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8158 (tm-30) REVERT: D 38 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7830 (tt) REVERT: D 80 ASP cc_start: 0.7261 (t0) cc_final: 0.6954 (t0) outliers start: 14 outliers final: 7 residues processed: 174 average time/residue: 0.0895 time to fit residues: 22.3101 Evaluate side-chains 149 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain H residue 407 SER Chi-restraints excluded: chain U residue 36 ILE Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 106 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 83 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 288 GLN H 432 HIS D 24 ASN D 139 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.137812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.105182 restraints weight = 17425.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107097 restraints weight = 16289.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107065 restraints weight = 15140.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107663 restraints weight = 9235.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109016 restraints weight = 8127.180| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10190 Z= 0.143 Angle : 0.584 7.750 13726 Z= 0.299 Chirality : 0.042 0.175 1503 Planarity : 0.004 0.038 1751 Dihedral : 4.508 23.040 1327 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.01 % Allowed : 12.45 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.46 (0.24), residues: 1209 helix: 1.39 (0.22), residues: 577 sheet: -0.40 (0.61), residues: 87 loop : -2.28 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 473 TYR 0.026 0.001 TYR H 529 PHE 0.025 0.001 PHE H 457 TRP 0.007 0.001 TRP H 275 HIS 0.007 0.001 HIS C 727 Details of bonding type rmsd covalent geometry : bond 0.00317 (10152) covalent geometry : angle 0.56613 (13691) hydrogen bonds : bond 0.05885 ( 468) hydrogen bonds : angle 4.68047 ( 1383) metal coordination : bond 0.00650 ( 35) metal coordination : angle 2.97160 ( 33) Misc. bond : bond 0.00012 ( 2) link_TRANS : bond 0.00124 ( 1) link_TRANS : angle 0.06114 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.405 Fit side-chains REVERT: C 719 MET cc_start: 0.7298 (tpp) cc_final: 0.6859 (tpp) REVERT: H 551 LEU cc_start: 0.8706 (tp) cc_final: 0.8399 (tp) REVERT: U 6 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8425 (tttp) REVERT: U 16 GLU cc_start: 0.7217 (pm20) cc_final: 0.6844 (pm20) REVERT: N 28 GLU cc_start: 0.7263 (mm-30) cc_final: 0.7038 (pt0) REVERT: D 38 LEU cc_start: 0.8143 (tp) cc_final: 0.7785 (tt) REVERT: D 46 TYR cc_start: 0.7621 (m-80) cc_final: 0.7310 (m-80) REVERT: D 56 ASN cc_start: 0.7838 (m-40) cc_final: 0.7317 (t0) REVERT: D 80 ASP cc_start: 0.7377 (t0) cc_final: 0.6905 (t0) outliers start: 22 outliers final: 13 residues processed: 168 average time/residue: 0.1004 time to fit residues: 23.7601 Evaluate side-chains 155 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 407 SER Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain U residue 36 ILE Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 51 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 77 optimal weight: 0.0770 chunk 71 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 432 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.107314 restraints weight = 17632.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106862 restraints weight = 14899.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.107674 restraints weight = 15304.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107972 restraints weight = 9531.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.110131 restraints weight = 8579.807| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10190 Z= 0.120 Angle : 0.564 9.594 13726 Z= 0.284 Chirality : 0.041 0.184 1503 Planarity : 0.003 0.035 1751 Dihedral : 4.206 17.538 1327 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.11 % Allowed : 14.65 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.24), residues: 1209 helix: 1.61 (0.22), residues: 582 sheet: -0.41 (0.61), residues: 87 loop : -2.13 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 29 TYR 0.024 0.001 TYR H 529 PHE 0.023 0.001 PHE H 457 TRP 0.007 0.001 TRP H 452 HIS 0.007 0.001 HIS C 727 Details of bonding type rmsd covalent geometry : bond 0.00257 (10152) covalent geometry : angle 0.54925 (13691) hydrogen bonds : bond 0.05051 ( 468) hydrogen bonds : angle 4.39577 ( 1383) metal coordination : bond 0.00475 ( 35) metal coordination : angle 2.70219 ( 33) Misc. bond : bond 0.00005 ( 2) link_TRANS : bond 0.00081 ( 1) link_TRANS : angle 0.08657 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.412 Fit side-chains REVERT: C 596 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7834 (ptpp) REVERT: C 719 MET cc_start: 0.7155 (tpp) cc_final: 0.6783 (tpp) REVERT: H 508 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.6941 (t80) REVERT: H 551 LEU cc_start: 0.8715 (tp) cc_final: 0.8426 (tp) REVERT: U 6 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8386 (tttp) REVERT: U 52 ASP cc_start: 0.7872 (p0) cc_final: 0.7656 (p0) REVERT: N 12 GLU cc_start: 0.5485 (tp30) cc_final: 0.4934 (tp30) REVERT: N 13 ILE cc_start: 0.6836 (mm) cc_final: 0.6593 (mm) REVERT: N 28 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7098 (pt0) REVERT: D 38 LEU cc_start: 0.8120 (tp) cc_final: 0.7916 (tt) REVERT: D 46 TYR cc_start: 0.7634 (m-80) cc_final: 0.7392 (m-80) REVERT: D 56 ASN cc_start: 0.7675 (m-40) cc_final: 0.7234 (t0) REVERT: D 80 ASP cc_start: 0.7558 (t0) cc_final: 0.6997 (t0) outliers start: 23 outliers final: 10 residues processed: 185 average time/residue: 0.0945 time to fit residues: 25.0169 Evaluate side-chains 157 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 508 TYR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 GLN H 121 ASN H 432 HIS ** D 21 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 = 0.3815 r_free = 0.3815 target = 0.137411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.104487 restraints weight = 17633.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.104592 restraints weight = 15638.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.104953 restraints weight = 16620.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.105810 restraints weight = 9821.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.107796 restraints weight = 8580.685| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10190 Z= 0.158 Angle : 0.589 10.020 13726 Z= 0.299 Chirality : 0.043 0.195 1503 Planarity : 0.003 0.040 1751 Dihedral : 4.274 16.792 1327 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.75 % Allowed : 16.39 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.24), residues: 1209 helix: 1.61 (0.22), residues: 580 sheet: -0.40 (0.61), residues: 87 loop : -2.12 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 473 TYR 0.026 0.001 TYR H 529 PHE 0.026 0.001 PHE H 457 TRP 0.008 0.001 TRP H 323 HIS 0.009 0.001 HIS C 727 Details of bonding type rmsd covalent geometry : bond 0.00363 (10152) covalent geometry : angle 0.56883 (13691) hydrogen bonds : bond 0.05794 ( 468) hydrogen bonds : angle 4.47931 ( 1383) metal coordination : bond 0.00742 ( 35) metal coordination : angle 3.18183 ( 33) Misc. bond : bond 0.00010 ( 2) link_TRANS : bond 0.00121 ( 1) link_TRANS : angle 0.07976 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: C 596 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7842 (ptpp) REVERT: C 719 MET cc_start: 0.7216 (tpp) cc_final: 0.6844 (tpp) REVERT: H 118 ARG cc_start: 0.8370 (mmm-85) cc_final: 0.7857 (mmp-170) REVERT: H 508 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.6758 (t80) REVERT: H 551 LEU cc_start: 0.8748 (tp) cc_final: 0.8411 (tp) REVERT: U 52 ASP cc_start: 0.7922 (p0) cc_final: 0.7285 (p0) REVERT: N 12 GLU cc_start: 0.5587 (tp30) cc_final: 0.5025 (tp30) REVERT: N 13 ILE cc_start: 0.6849 (mm) cc_final: 0.6542 (mm) REVERT: R 54 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8931 (tp) REVERT: D 46 TYR cc_start: 0.7666 (m-80) cc_final: 0.7401 (m-80) REVERT: D 56 ASN cc_start: 0.7796 (m-40) cc_final: 0.7343 (t0) REVERT: D 80 ASP cc_start: 0.7598 (t0) cc_final: 0.7024 (t0) outliers start: 30 outliers final: 19 residues processed: 166 average time/residue: 0.0914 time to fit residues: 21.6677 Evaluate side-chains 162 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 471 THR Chi-restraints excluded: chain H residue 508 TYR Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 106 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 2 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 46 optimal weight: 0.0970 chunk 111 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 432 HIS ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.137716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.104880 restraints weight = 17527.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.104379 restraints weight = 15770.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104846 restraints weight = 17400.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106199 restraints weight = 10189.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.106590 restraints weight = 8777.917| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10190 Z= 0.152 Angle : 0.590 9.846 13726 Z= 0.297 Chirality : 0.043 0.245 1503 Planarity : 0.003 0.047 1751 Dihedral : 4.250 16.679 1327 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.47 % Allowed : 16.85 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.14 (0.25), residues: 1209 helix: 1.62 (0.22), residues: 582 sheet: -0.33 (0.62), residues: 87 loop : -2.09 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 473 TYR 0.024 0.001 TYR H 529 PHE 0.027 0.001 PHE H 457 TRP 0.008 0.001 TRP H 323 HIS 0.009 0.001 HIS C 727 Details of bonding type rmsd covalent geometry : bond 0.00351 (10152) covalent geometry : angle 0.57035 (13691) hydrogen bonds : bond 0.05684 ( 468) hydrogen bonds : angle 4.43043 ( 1383) metal coordination : bond 0.00731 ( 35) metal coordination : angle 3.15625 ( 33) Misc. bond : bond 0.00010 ( 2) link_TRANS : bond 0.00103 ( 1) link_TRANS : angle 0.08833 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 719 MET cc_start: 0.7201 (tpp) cc_final: 0.6882 (tpp) REVERT: C 730 LEU cc_start: 0.7109 (mm) cc_final: 0.6806 (mp) REVERT: H 118 ARG cc_start: 0.8307 (mmm-85) cc_final: 0.7971 (mmp-170) REVERT: H 508 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.6740 (t80) REVERT: H 551 LEU cc_start: 0.8778 (tp) cc_final: 0.8432 (tp) REVERT: U 52 ASP cc_start: 0.7760 (p0) cc_final: 0.7519 (p0) REVERT: N 12 GLU cc_start: 0.5742 (tp30) cc_final: 0.5152 (tp30) REVERT: N 13 ILE cc_start: 0.6863 (mm) cc_final: 0.6532 (mm) REVERT: N 28 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6985 (pt0) REVERT: D 46 TYR cc_start: 0.7678 (m-80) cc_final: 0.7466 (m-80) REVERT: D 80 ASP cc_start: 0.7641 (t0) cc_final: 0.7066 (t0) outliers start: 27 outliers final: 19 residues processed: 161 average time/residue: 0.0899 time to fit residues: 20.6782 Evaluate side-chains 159 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 471 THR Chi-restraints excluded: chain H residue 508 TYR Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 106 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 0.0570 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 103 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 432 HIS ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.138731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.106096 restraints weight = 17501.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.106133 restraints weight = 15196.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106543 restraints weight = 16424.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107502 restraints weight = 9742.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.109652 restraints weight = 8439.113| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10190 Z= 0.128 Angle : 0.575 10.245 13726 Z= 0.288 Chirality : 0.042 0.227 1503 Planarity : 0.003 0.048 1751 Dihedral : 4.119 16.563 1327 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.75 % Allowed : 17.40 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.01 (0.25), residues: 1209 helix: 1.72 (0.22), residues: 582 sheet: -0.30 (0.62), residues: 87 loop : -1.97 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 29 TYR 0.023 0.001 TYR H 529 PHE 0.025 0.001 PHE H 457 TRP 0.006 0.001 TRP H 452 HIS 0.010 0.001 HIS C 727 Details of bonding type rmsd covalent geometry : bond 0.00284 (10152) covalent geometry : angle 0.55862 (13691) hydrogen bonds : bond 0.05170 ( 468) hydrogen bonds : angle 4.30180 ( 1383) metal coordination : bond 0.00548 ( 35) metal coordination : angle 2.87537 ( 33) Misc. bond : bond 0.00005 ( 2) link_TRANS : bond 0.00073 ( 1) link_TRANS : angle 0.10364 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 118 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.7975 (mmp-170) REVERT: H 146 MET cc_start: 0.7855 (mmm) cc_final: 0.7543 (mmm) REVERT: H 508 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.6748 (t80) REVERT: H 551 LEU cc_start: 0.8776 (tp) cc_final: 0.8443 (tp) REVERT: N 12 GLU cc_start: 0.5696 (tp30) cc_final: 0.5018 (tp30) REVERT: N 13 ILE cc_start: 0.6860 (mm) cc_final: 0.6443 (mm) REVERT: N 28 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7080 (pt0) REVERT: R 54 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8910 (tp) REVERT: D 46 TYR cc_start: 0.7649 (m-80) cc_final: 0.7434 (m-80) REVERT: D 56 ASN cc_start: 0.7782 (m-40) cc_final: 0.7257 (t0) REVERT: D 80 ASP cc_start: 0.7565 (t0) cc_final: 0.6965 (t0) outliers start: 30 outliers final: 25 residues processed: 175 average time/residue: 0.0870 time to fit residues: 21.9505 Evaluate side-chains 173 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 462 VAL Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 508 TYR Chi-restraints excluded: chain U residue 36 ILE Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 112 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 103 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 432 HIS ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.136333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103784 restraints weight = 17492.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.103247 restraints weight = 15789.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.103764 restraints weight = 16886.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.104881 restraints weight = 9964.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.105518 restraints weight = 8614.079| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10190 Z= 0.173 Angle : 0.627 12.000 13726 Z= 0.312 Chirality : 0.044 0.291 1503 Planarity : 0.004 0.053 1751 Dihedral : 4.281 16.232 1327 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.93 % Allowed : 18.41 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.10 (0.25), residues: 1209 helix: 1.52 (0.22), residues: 588 sheet: -0.30 (0.63), residues: 87 loop : -1.93 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 29 TYR 0.026 0.002 TYR H 529 PHE 0.027 0.001 PHE H 457 TRP 0.010 0.001 TRP H 323 HIS 0.011 0.001 HIS C 727 Details of bonding type rmsd covalent geometry : bond 0.00404 (10152) covalent geometry : angle 0.60496 (13691) hydrogen bonds : bond 0.05978 ( 468) hydrogen bonds : angle 4.46873 ( 1383) metal coordination : bond 0.00872 ( 35) metal coordination : angle 3.40462 ( 33) Misc. bond : bond 0.00011 ( 2) link_TRANS : bond 0.00112 ( 1) link_TRANS : angle 0.09340 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: C 719 MET cc_start: 0.7229 (tpp) cc_final: 0.6823 (tpp) REVERT: H 118 ARG cc_start: 0.8235 (mmm-85) cc_final: 0.7992 (mmp-170) REVERT: H 146 MET cc_start: 0.7978 (mmm) cc_final: 0.7632 (mmm) REVERT: H 508 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.6578 (t80) REVERT: H 551 LEU cc_start: 0.8855 (tp) cc_final: 0.8607 (tp) REVERT: U 52 ASP cc_start: 0.7639 (p0) cc_final: 0.7426 (p0) REVERT: N 28 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7076 (pt0) REVERT: R 54 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8971 (tp) REVERT: D 46 TYR cc_start: 0.7709 (m-80) cc_final: 0.7458 (m-80) REVERT: D 80 ASP cc_start: 0.7697 (t0) cc_final: 0.7133 (t0) outliers start: 32 outliers final: 28 residues processed: 166 average time/residue: 0.0876 time to fit residues: 20.9720 Evaluate side-chains 173 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 462 VAL Chi-restraints excluded: chain H residue 471 THR Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 508 TYR Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 112 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 12 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 432 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.137408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104602 restraints weight = 17457.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103666 restraints weight = 14127.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.104556 restraints weight = 15542.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.105131 restraints weight = 9829.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105631 restraints weight = 8650.364| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10190 Z= 0.148 Angle : 0.610 14.108 13726 Z= 0.304 Chirality : 0.043 0.262 1503 Planarity : 0.004 0.053 1751 Dihedral : 4.258 16.611 1327 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.56 % Allowed : 19.23 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.25), residues: 1209 helix: 1.53 (0.22), residues: 590 sheet: -0.29 (0.63), residues: 87 loop : -1.93 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 29 TYR 0.024 0.001 TYR H 529 PHE 0.026 0.001 PHE H 457 TRP 0.007 0.001 TRP H 323 HIS 0.011 0.001 HIS C 727 Details of bonding type rmsd covalent geometry : bond 0.00338 (10152) covalent geometry : angle 0.59014 (13691) hydrogen bonds : bond 0.05602 ( 468) hydrogen bonds : angle 4.39169 ( 1383) metal coordination : bond 0.00702 ( 35) metal coordination : angle 3.20915 ( 33) Misc. bond : bond 0.00173 ( 2) link_TRANS : bond 0.00176 ( 1) link_TRANS : angle 0.03862 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: C 719 MET cc_start: 0.7278 (tpp) cc_final: 0.6814 (tpp) REVERT: H 118 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.8055 (mmp-170) REVERT: H 146 MET cc_start: 0.7981 (mmm) cc_final: 0.7628 (mmm) REVERT: H 508 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.6793 (t80) REVERT: H 551 LEU cc_start: 0.8861 (tp) cc_final: 0.8646 (tp) REVERT: U 52 ASP cc_start: 0.7630 (p0) cc_final: 0.7408 (p0) REVERT: N 28 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7064 (pt0) REVERT: D 46 TYR cc_start: 0.7692 (m-80) cc_final: 0.7448 (m-80) REVERT: D 80 ASP cc_start: 0.7645 (t0) cc_final: 0.7046 (t0) REVERT: D 106 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8303 (mp10) outliers start: 28 outliers final: 26 residues processed: 165 average time/residue: 0.0932 time to fit residues: 22.0439 Evaluate side-chains 170 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 438 VAL Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 462 VAL Chi-restraints excluded: chain H residue 471 THR Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 508 TYR Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain U residue 36 ILE Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 7 optimal weight: 0.0370 chunk 98 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 432 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.139406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.105979 restraints weight = 17432.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105040 restraints weight = 13871.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106146 restraints weight = 14556.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106668 restraints weight = 9639.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.107344 restraints weight = 8591.659| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10190 Z= 0.122 Angle : 0.591 13.939 13726 Z= 0.294 Chirality : 0.042 0.248 1503 Planarity : 0.003 0.050 1751 Dihedral : 4.098 16.825 1327 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.47 % Allowed : 19.14 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.09 (0.25), residues: 1209 helix: 1.69 (0.22), residues: 589 sheet: -0.26 (0.63), residues: 87 loop : -1.85 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 29 TYR 0.023 0.001 TYR H 529 PHE 0.023 0.001 PHE H 457 TRP 0.008 0.001 TRP C 581 HIS 0.013 0.001 HIS C 727 Details of bonding type rmsd covalent geometry : bond 0.00265 (10152) covalent geometry : angle 0.57558 (13691) hydrogen bonds : bond 0.04904 ( 468) hydrogen bonds : angle 4.25822 ( 1383) metal coordination : bond 0.00445 ( 35) metal coordination : angle 2.81811 ( 33) Misc. bond : bond 0.00115 ( 2) link_TRANS : bond 0.00042 ( 1) link_TRANS : angle 0.02363 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: C 719 MET cc_start: 0.7258 (tpp) cc_final: 0.6841 (tpp) REVERT: H 118 ARG cc_start: 0.8230 (mmm-85) cc_final: 0.7993 (mmp-170) REVERT: H 508 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.6794 (t80) REVERT: U 52 ASP cc_start: 0.7625 (p0) cc_final: 0.7390 (p0) REVERT: N 28 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7066 (pt0) REVERT: N 61 ILE cc_start: 0.6861 (mt) cc_final: 0.6451 (mm) REVERT: D 46 TYR cc_start: 0.7654 (m-80) cc_final: 0.7434 (m-80) REVERT: D 80 ASP cc_start: 0.7606 (t0) cc_final: 0.7010 (t0) REVERT: D 106 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8288 (mp10) outliers start: 27 outliers final: 22 residues processed: 167 average time/residue: 0.0829 time to fit residues: 20.1675 Evaluate side-chains 162 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 462 VAL Chi-restraints excluded: chain H residue 471 THR Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 492 GLU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 508 TYR Chi-restraints excluded: chain U residue 36 ILE Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 0.0670 chunk 31 optimal weight: 0.5980 chunk 113 optimal weight: 0.0270 chunk 111 optimal weight: 0.9980 chunk 57 optimal weight: 0.4980 chunk 68 optimal weight: 7.9990 chunk 73 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN H 432 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.140466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.107842 restraints weight = 17625.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.107623 restraints weight = 13748.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.108565 restraints weight = 14257.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.108908 restraints weight = 9114.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109379 restraints weight = 8212.588| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10190 Z= 0.117 Angle : 0.586 13.593 13726 Z= 0.291 Chirality : 0.042 0.289 1503 Planarity : 0.004 0.066 1751 Dihedral : 4.032 16.921 1327 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.38 % Allowed : 19.41 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.17 (0.25), residues: 1209 helix: 1.74 (0.22), residues: 589 sheet: -0.25 (0.62), residues: 87 loop : -1.79 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 29 TYR 0.022 0.001 TYR H 529 PHE 0.020 0.001 PHE H 457 TRP 0.008 0.001 TRP R 87 HIS 0.012 0.001 HIS C 727 Details of bonding type rmsd covalent geometry : bond 0.00254 (10152) covalent geometry : angle 0.57242 (13691) hydrogen bonds : bond 0.04674 ( 468) hydrogen bonds : angle 4.20944 ( 1383) metal coordination : bond 0.00384 ( 35) metal coordination : angle 2.66288 ( 33) Misc. bond : bond 0.00083 ( 2) link_TRANS : bond 0.00041 ( 1) link_TRANS : angle 0.01816 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1723.64 seconds wall clock time: 30 minutes 30.34 seconds (1830.34 seconds total)