Starting phenix.real_space_refine on Mon Jul 28 03:18:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b5n_12041/07_2025/7b5n_12041.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b5n_12041/07_2025/7b5n_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_12041/07_2025/7b5n_12041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b5n_12041/07_2025/7b5n_12041.map" model { file = "/net/cci-nas-00/data/ceres_data/7b5n_12041/07_2025/7b5n_12041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b5n_12041/07_2025/7b5n_12041.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 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: 6.37, per 1000 atoms: 0.64 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: 2.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.91 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: 2.73 Time building geometry restraints manager: 3.10 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: 22.870 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 27.090 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.450 ------------------------------------------------------------------------------- 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 : 13.46 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.002 TRP R 33 HIS 0.005 0.001 HIS R 80 PHE 0.025 0.002 PHE D 143 TYR 0.019 0.002 TYR C 455 ARG 0.009 0.001 ARG C 473 Details of bonding type rmsd link_TRANS : bond 0.01181 ( 1) link_TRANS : angle 3.56443 ( 2) hydrogen bonds : bond 0.16928 ( 468) hydrogen bonds : angle 6.57625 ( 1383) metal coordination : bond 0.05162 ( 35) metal coordination : angle 5.48117 ( 33) covalent geometry : bond 0.00686 (10152) covalent geometry : angle 0.79149 (13691) Misc. bond : bond 0.05901 ( 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 : 1.091 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: 0.2298 time to fit residues: 52.3877 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 : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.0370 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 N 41 GLN D 24 ASN D 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.137854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.104793 restraints weight = 17242.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.103304 restraints weight = 14459.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.104330 restraints weight = 15623.064| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1310 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= 0.148 Angle : 0.618 8.428 13726 Z= 0.318 Chirality : 0.043 0.191 1503 Planarity : 0.004 0.039 1751 Dihedral : 4.718 27.655 1327 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.28 % Allowed : 9.34 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1209 helix: 1.20 (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 TRP 0.007 0.001 TRP C 581 HIS 0.007 0.001 HIS C 727 PHE 0.031 0.002 PHE H 457 TYR 0.026 0.001 TYR H 529 ARG 0.004 0.000 ARG H 511 Details of bonding type rmsd link_TRANS : bond 0.00106 ( 1) link_TRANS : angle 0.01589 ( 2) hydrogen bonds : bond 0.06285 ( 468) hydrogen bonds : angle 4.92723 ( 1383) metal coordination : bond 0.00668 ( 35) metal coordination : angle 3.03973 ( 33) covalent geometry : bond 0.00324 (10152) covalent geometry : angle 0.60025 (13691) Misc. bond : bond 0.00011 ( 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 184 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: C 719 MET cc_start: 0.7273 (tpp) cc_final: 0.6843 (tpp) REVERT: H 450 MET cc_start: 0.6707 (mmt) cc_final: 0.6429 (mmp) REVERT: U 6 LYS cc_start: 0.8870 (ttmm) cc_final: 0.8475 (tttp) REVERT: N 28 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7004 (pt0) REVERT: D 13 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8157 (tm-30) REVERT: D 38 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7654 (tt) REVERT: D 48 LYS cc_start: 0.7811 (mptt) cc_final: 0.7476 (mppt) REVERT: D 80 ASP cc_start: 0.7256 (t0) cc_final: 0.6917 (t0) outliers start: 14 outliers final: 7 residues processed: 176 average time/residue: 0.2144 time to fit residues: 53.3010 Evaluate side-chains 147 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 101 optimal weight: 0.1980 chunk 75 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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 = 0.3822 r_free = 0.3822 target = 0.137975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104871 restraints weight = 17559.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.103551 restraints weight = 15381.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.105093 restraints weight = 11839.631| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10190 Z= 0.144 Angle : 0.581 7.733 13726 Z= 0.298 Chirality : 0.042 0.178 1503 Planarity : 0.004 0.037 1751 Dihedral : 4.516 22.809 1327 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.01 % Allowed : 12.55 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.24), residues: 1209 helix: 1.40 (0.22), residues: 577 sheet: -0.38 (0.61), residues: 87 loop : -2.28 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 275 HIS 0.007 0.001 HIS C 727 PHE 0.025 0.001 PHE H 457 TYR 0.026 0.001 TYR H 529 ARG 0.002 0.000 ARG C 473 Details of bonding type rmsd link_TRANS : bond 0.00138 ( 1) link_TRANS : angle 0.05198 ( 2) hydrogen bonds : bond 0.05909 ( 468) hydrogen bonds : angle 4.66951 ( 1383) metal coordination : bond 0.00661 ( 35) metal coordination : angle 2.98317 ( 33) covalent geometry : bond 0.00322 (10152) covalent geometry : angle 0.56294 (13691) Misc. bond : bond 0.00010 ( 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 174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.164 Fit side-chains REVERT: C 719 MET cc_start: 0.7302 (tpp) cc_final: 0.6885 (tpp) REVERT: H 551 LEU cc_start: 0.8738 (tp) cc_final: 0.8420 (tp) REVERT: U 6 LYS cc_start: 0.8834 (ttmm) cc_final: 0.8401 (tttp) REVERT: U 16 GLU cc_start: 0.7231 (pm20) cc_final: 0.6834 (pm20) REVERT: N 28 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7099 (pt0) REVERT: D 38 LEU cc_start: 0.8260 (tp) cc_final: 0.7920 (tt) REVERT: D 46 TYR cc_start: 0.7598 (m-80) cc_final: 0.7255 (m-80) REVERT: D 56 ASN cc_start: 0.7868 (m-40) cc_final: 0.7311 (t0) REVERT: D 80 ASP cc_start: 0.7457 (t0) cc_final: 0.6954 (t0) outliers start: 22 outliers final: 13 residues processed: 166 average time/residue: 0.2268 time to fit residues: 52.8199 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 : 1.188 ------------------------------------------------------------------------------- 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 80 optimal weight: 0.0050 chunk 7 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.138862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.106214 restraints weight = 17398.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.106426 restraints weight = 15021.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106879 restraints weight = 15639.363| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10190 Z= 0.129 Angle : 0.569 9.288 13726 Z= 0.287 Chirality : 0.042 0.188 1503 Planarity : 0.003 0.036 1751 Dihedral : 4.269 17.715 1327 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.20 % Allowed : 14.93 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1209 helix: 1.57 (0.22), residues: 578 sheet: -0.40 (0.61), residues: 87 loop : -2.14 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 452 HIS 0.007 0.001 HIS C 727 PHE 0.024 0.001 PHE H 457 TYR 0.024 0.001 TYR H 529 ARG 0.003 0.000 ARG N 29 Details of bonding type rmsd link_TRANS : bond 0.00096 ( 1) link_TRANS : angle 0.08435 ( 2) hydrogen bonds : bond 0.05332 ( 468) hydrogen bonds : angle 4.46143 ( 1383) metal coordination : bond 0.00542 ( 35) metal coordination : angle 2.84624 ( 33) covalent geometry : bond 0.00282 (10152) covalent geometry : angle 0.55195 (13691) Misc. bond : bond 0.00009 ( 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 185 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 1.254 Fit side-chains REVERT: C 596 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7853 (ptpp) REVERT: C 719 MET cc_start: 0.7214 (tpp) cc_final: 0.6829 (tpp) REVERT: H 508 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.6936 (t80) REVERT: H 551 LEU cc_start: 0.8722 (tp) cc_final: 0.8422 (tp) REVERT: U 6 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8408 (tttp) REVERT: U 52 ASP cc_start: 0.7849 (p0) cc_final: 0.7644 (p0) REVERT: N 12 GLU cc_start: 0.5468 (tp30) cc_final: 0.4828 (tp30) REVERT: N 13 ILE cc_start: 0.6842 (mm) cc_final: 0.6613 (mm) REVERT: N 28 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7100 (pt0) REVERT: D 38 LEU cc_start: 0.8093 (tp) cc_final: 0.7871 (tt) REVERT: D 46 TYR cc_start: 0.7679 (m-80) cc_final: 0.7432 (m-80) REVERT: D 56 ASN cc_start: 0.7735 (m-40) cc_final: 0.7262 (t0) REVERT: D 80 ASP cc_start: 0.7537 (t0) cc_final: 0.7017 (t0) outliers start: 24 outliers final: 14 residues processed: 179 average time/residue: 0.2689 time to fit residues: 68.6886 Evaluate side-chains 159 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain D residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 118 optimal weight: 0.0670 chunk 32 optimal weight: 7.9990 chunk 94 optimal weight: 0.0770 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 0.0270 chunk 42 optimal weight: 0.9980 overall best weight: 0.2934 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.140790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108012 restraints weight = 17445.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.107940 restraints weight = 14922.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.108539 restraints weight = 15860.841| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10190 Z= 0.112 Angle : 0.545 9.701 13726 Z= 0.276 Chirality : 0.041 0.195 1503 Planarity : 0.003 0.035 1751 Dihedral : 4.073 17.288 1327 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.29 % Allowed : 15.93 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.25), residues: 1209 helix: 1.75 (0.22), residues: 582 sheet: -0.33 (0.62), residues: 87 loop : -2.04 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 452 HIS 0.009 0.001 HIS C 727 PHE 0.022 0.001 PHE H 457 TYR 0.022 0.001 TYR H 529 ARG 0.002 0.000 ARG H 118 Details of bonding type rmsd link_TRANS : bond 0.00067 ( 1) link_TRANS : angle 0.10073 ( 2) hydrogen bonds : bond 0.04705 ( 468) hydrogen bonds : angle 4.26449 ( 1383) metal coordination : bond 0.00393 ( 35) metal coordination : angle 2.58345 ( 33) covalent geometry : bond 0.00237 (10152) covalent geometry : angle 0.53064 (13691) Misc. bond : bond 0.00008 ( 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 190 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.085 Fit side-chains REVERT: C 596 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7702 (ptpp) REVERT: C 719 MET cc_start: 0.7065 (tpp) cc_final: 0.6760 (tpp) REVERT: H 118 ARG cc_start: 0.8313 (mmm-85) cc_final: 0.7832 (mmp-170) REVERT: H 508 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.6881 (t80) REVERT: H 551 LEU cc_start: 0.8675 (tp) cc_final: 0.8363 (tp) REVERT: U 52 ASP cc_start: 0.7933 (p0) cc_final: 0.7720 (p0) REVERT: N 12 GLU cc_start: 0.5526 (tp30) cc_final: 0.5042 (tp30) REVERT: N 13 ILE cc_start: 0.6797 (mm) cc_final: 0.6510 (mm) REVERT: N 28 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7152 (pt0) REVERT: N 61 ILE cc_start: 0.6484 (mt) cc_final: 0.6174 (mm) REVERT: D 56 ASN cc_start: 0.7749 (m-40) cc_final: 0.7345 (t0) REVERT: D 80 ASP cc_start: 0.7687 (t0) cc_final: 0.7127 (t0) REVERT: D 116 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7852 (mt0) outliers start: 25 outliers final: 15 residues processed: 183 average time/residue: 0.2033 time to fit residues: 53.9017 Evaluate side-chains 168 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 361 VAL Chi-restraints excluded: chain H residue 407 SER Chi-restraints excluded: chain H residue 411 LEU 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 R residue 33 TRP 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 40 VAL Chi-restraints excluded: chain D residue 51 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 101 optimal weight: 0.3980 chunk 114 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 0.1980 chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.0000 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 432 HIS U 41 GLN ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.140540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.108207 restraints weight = 17631.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107071 restraints weight = 14327.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.108185 restraints weight = 15493.719| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10190 Z= 0.114 Angle : 0.557 10.271 13726 Z= 0.277 Chirality : 0.041 0.189 1503 Planarity : 0.003 0.041 1751 Dihedral : 3.974 17.176 1327 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.84 % Allowed : 16.58 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1209 helix: 1.83 (0.22), residues: 582 sheet: -0.28 (0.62), residues: 87 loop : -1.97 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 452 HIS 0.009 0.001 HIS C 727 PHE 0.022 0.001 PHE H 457 TYR 0.022 0.001 TYR H 529 ARG 0.002 0.000 ARG N 29 Details of bonding type rmsd link_TRANS : bond 0.00070 ( 1) link_TRANS : angle 0.08706 ( 2) hydrogen bonds : bond 0.04727 ( 468) hydrogen bonds : angle 4.24676 ( 1383) metal coordination : bond 0.00405 ( 35) metal coordination : angle 2.60350 ( 33) covalent geometry : bond 0.00244 (10152) covalent geometry : angle 0.54297 (13691) Misc. bond : bond 0.00008 ( 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 190 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 3.041 Fit side-chains revert: symmetry clash REVERT: C 596 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7620 (ptpp) REVERT: C 719 MET cc_start: 0.7141 (tpp) cc_final: 0.6840 (tpp) REVERT: H 118 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.7920 (mmp-170) REVERT: H 425 MET cc_start: 0.8502 (tpt) cc_final: 0.8177 (tpt) REVERT: H 508 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.6798 (t80) REVERT: H 551 LEU cc_start: 0.8674 (tp) cc_final: 0.8358 (tp) REVERT: U 52 ASP cc_start: 0.7891 (p0) cc_final: 0.7221 (p0) REVERT: N 12 GLU cc_start: 0.5561 (tp30) cc_final: 0.5032 (tp30) REVERT: N 13 ILE cc_start: 0.6794 (mm) cc_final: 0.6482 (mm) REVERT: N 28 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7243 (pt0) REVERT: N 61 ILE cc_start: 0.6483 (mt) cc_final: 0.6178 (mm) REVERT: D 56 ASN cc_start: 0.7671 (m-40) cc_final: 0.7248 (t0) REVERT: D 80 ASP cc_start: 0.7653 (t0) cc_final: 0.7093 (t0) REVERT: D 116 GLN cc_start: 0.8319 (mm-40) cc_final: 0.7883 (mt0) outliers start: 31 outliers final: 20 residues processed: 180 average time/residue: 0.2738 time to fit residues: 73.1894 Evaluate side-chains 175 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 511 ILE Chi-restraints excluded: chain C residue 582 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 202 GLU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 492 GLU 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 R residue 33 TRP 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 40 VAL Chi-restraints excluded: chain D residue 51 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 115 optimal weight: 0.0770 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 19 optimal weight: 0.0030 chunk 6 optimal weight: 0.6980 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 404 ASN ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 432 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.140030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.107496 restraints weight = 17888.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108854 restraints weight = 16000.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.108879 restraints weight = 16532.546| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10190 Z= 0.122 Angle : 0.572 13.655 13726 Z= 0.284 Chirality : 0.042 0.234 1503 Planarity : 0.003 0.043 1751 Dihedral : 3.982 16.783 1327 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.75 % Allowed : 17.12 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.25), residues: 1209 helix: 1.81 (0.22), residues: 583 sheet: -0.31 (0.62), residues: 87 loop : -1.88 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 275 HIS 0.011 0.001 HIS C 727 PHE 0.023 0.001 PHE H 457 TYR 0.023 0.001 TYR H 529 ARG 0.003 0.000 ARG N 29 Details of bonding type rmsd link_TRANS : bond 0.00075 ( 1) link_TRANS : angle 0.08421 ( 2) hydrogen bonds : bond 0.04841 ( 468) hydrogen bonds : angle 4.24654 ( 1383) metal coordination : bond 0.00455 ( 35) metal coordination : angle 2.69823 ( 33) covalent geometry : bond 0.00270 (10152) covalent geometry : angle 0.55761 (13691) Misc. bond : bond 0.00007 ( 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 186 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 2.361 Fit side-chains revert: symmetry clash REVERT: C 596 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7305 (ptpp) REVERT: H 118 ARG cc_start: 0.8180 (mmm-85) cc_final: 0.7939 (mmp-170) REVERT: H 425 MET cc_start: 0.8505 (tpt) cc_final: 0.8169 (tpt) REVERT: H 508 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.6752 (t80) REVERT: H 551 LEU cc_start: 0.8749 (tp) cc_final: 0.8441 (tp) REVERT: U 52 ASP cc_start: 0.7684 (p0) cc_final: 0.7391 (p0) REVERT: N 12 GLU cc_start: 0.5683 (tp30) cc_final: 0.5147 (tp30) REVERT: N 13 ILE cc_start: 0.6822 (mm) cc_final: 0.6518 (mm) REVERT: R 54 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8895 (tp) REVERT: D 56 ASN cc_start: 0.7625 (m-40) cc_final: 0.7167 (t0) REVERT: D 80 ASP cc_start: 0.7623 (t0) cc_final: 0.7050 (t0) REVERT: D 106 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8324 (mp10) REVERT: D 116 GLN cc_start: 0.8355 (mm-40) cc_final: 0.7908 (mt0) outliers start: 30 outliers final: 21 residues processed: 176 average time/residue: 0.3269 time to fit residues: 85.1734 Evaluate side-chains 171 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 402 PHE 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 C residue 684 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 452 TRP Chi-restraints excluded: chain H residue 458 LEU 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 508 TYR 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 74 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 115 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 120 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 69 optimal weight: 0.0870 chunk 60 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.138716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105923 restraints weight = 17672.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106228 restraints weight = 15281.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.106345 restraints weight = 17208.854| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 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 = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10190 Z= 0.145 Angle : 0.603 13.764 13726 Z= 0.299 Chirality : 0.043 0.258 1503 Planarity : 0.004 0.063 1751 Dihedral : 4.089 16.490 1327 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.56 % Allowed : 18.41 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1209 helix: 1.70 (0.22), residues: 582 sheet: -0.29 (0.62), residues: 87 loop : -1.81 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 275 HIS 0.011 0.001 HIS C 727 PHE 0.020 0.001 PHE H 457 TYR 0.024 0.001 TYR H 529 ARG 0.003 0.000 ARG N 29 Details of bonding type rmsd link_TRANS : bond 0.00092 ( 1) link_TRANS : angle 0.07754 ( 2) hydrogen bonds : bond 0.05396 ( 468) hydrogen bonds : angle 4.32961 ( 1383) metal coordination : bond 0.00631 ( 35) metal coordination : angle 3.00033 ( 33) covalent geometry : bond 0.00332 (10152) covalent geometry : angle 0.58594 (13691) Misc. bond : bond 0.00007 ( 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 179 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 596 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7380 (ptpp) REVERT: C 719 MET cc_start: 0.7335 (tpp) cc_final: 0.6903 (tpp) REVERT: H 425 MET cc_start: 0.8512 (tpt) cc_final: 0.8177 (tpt) REVERT: H 508 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.6695 (t80) REVERT: H 551 LEU cc_start: 0.8796 (tp) cc_final: 0.8469 (tp) REVERT: U 52 ASP cc_start: 0.7710 (p0) cc_final: 0.7413 (p0) REVERT: N 12 GLU cc_start: 0.5748 (tp30) cc_final: 0.5045 (tp30) REVERT: N 13 ILE cc_start: 0.6783 (mm) cc_final: 0.6379 (mm) REVERT: R 54 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8921 (tp) REVERT: D 56 ASN cc_start: 0.7653 (m-40) cc_final: 0.7167 (t0) REVERT: D 80 ASP cc_start: 0.7647 (t0) cc_final: 0.7059 (t0) REVERT: D 116 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7843 (mt0) outliers start: 28 outliers final: 22 residues processed: 170 average time/residue: 0.2328 time to fit residues: 56.9908 Evaluate side-chains 166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 511 ILE 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 452 TRP 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 477 VAL Chi-restraints excluded: chain H residue 492 GLU 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 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 74 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.137775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104994 restraints weight = 17584.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104800 restraints weight = 14771.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.105255 restraints weight = 16445.054| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 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 = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10190 Z= 0.160 Angle : 0.642 13.153 13726 Z= 0.317 Chirality : 0.044 0.257 1503 Planarity : 0.004 0.065 1751 Dihedral : 4.203 16.234 1327 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.75 % Allowed : 18.68 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1209 helix: 1.61 (0.22), residues: 584 sheet: -0.30 (0.62), residues: 87 loop : -1.83 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 275 HIS 0.012 0.001 HIS C 727 PHE 0.023 0.001 PHE H 457 TYR 0.025 0.001 TYR H 529 ARG 0.005 0.000 ARG N 29 Details of bonding type rmsd link_TRANS : bond 0.00185 ( 1) link_TRANS : angle 0.01738 ( 2) hydrogen bonds : bond 0.05686 ( 468) hydrogen bonds : angle 4.40808 ( 1383) metal coordination : bond 0.00735 ( 35) metal coordination : angle 3.19866 ( 33) covalent geometry : bond 0.00369 (10152) covalent geometry : angle 0.62338 (13691) Misc. bond : bond 0.00100 ( 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 176 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 596 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7552 (ptpp) REVERT: C 719 MET cc_start: 0.7282 (tpp) cc_final: 0.6835 (tpp) REVERT: H 508 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.6598 (t80) REVERT: H 551 LEU cc_start: 0.8821 (tp) cc_final: 0.8487 (tp) REVERT: N 28 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7061 (pt0) REVERT: R 54 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8947 (tp) REVERT: D 80 ASP cc_start: 0.7659 (t0) cc_final: 0.7055 (t0) REVERT: D 116 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7843 (mt0) outliers start: 30 outliers final: 25 residues processed: 167 average time/residue: 0.3191 time to fit residues: 79.5124 Evaluate side-chains 173 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 2.190 ------------------------------------------------------------------------------- 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 452 TRP 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 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 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 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 101 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 96 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 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 = 0.3825 r_free = 0.3825 target = 0.138165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105636 restraints weight = 17705.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.104470 restraints weight = 15576.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.104990 restraints weight = 17439.917| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 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 = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10190 Z= 0.152 Angle : 0.649 18.508 13726 Z= 0.317 Chirality : 0.044 0.399 1503 Planarity : 0.004 0.066 1751 Dihedral : 4.203 17.358 1327 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.47 % Allowed : 19.05 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.25), residues: 1209 helix: 1.55 (0.22), residues: 590 sheet: -0.28 (0.62), residues: 87 loop : -1.82 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 275 HIS 0.012 0.001 HIS C 727 PHE 0.021 0.001 PHE H 457 TYR 0.024 0.001 TYR H 529 ARG 0.003 0.000 ARG N 29 Details of bonding type rmsd link_TRANS : bond 0.00084 ( 1) link_TRANS : angle 0.04867 ( 2) hydrogen bonds : bond 0.05602 ( 468) hydrogen bonds : angle 4.37297 ( 1383) metal coordination : bond 0.00677 ( 35) metal coordination : angle 3.17848 ( 33) covalent geometry : bond 0.00349 (10152) covalent geometry : angle 0.63108 (13691) Misc. bond : bond 0.00134 ( 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 174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: C 596 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7520 (ptpp) REVERT: C 719 MET cc_start: 0.7249 (tpp) cc_final: 0.6827 (tpp) REVERT: H 442 MET cc_start: 0.7865 (tpp) cc_final: 0.7613 (tpt) REVERT: H 508 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.6640 (t80) REVERT: N 28 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6940 (pt0) REVERT: R 54 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8951 (tp) REVERT: D 56 ASN cc_start: 0.7785 (m-40) cc_final: 0.7268 (t0) REVERT: D 80 ASP cc_start: 0.7661 (t0) cc_final: 0.7044 (t0) outliers start: 27 outliers final: 24 residues processed: 165 average time/residue: 0.2163 time to fit residues: 50.7207 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 : 1.100 ------------------------------------------------------------------------------- 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 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 452 TRP 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 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 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 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 chunk 71 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 31 optimal weight: 0.0070 chunk 62 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.139074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.107003 restraints weight = 17762.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.106856 restraints weight = 16981.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.107505 restraints weight = 17521.825| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 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 = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10190 Z= 0.129 Angle : 0.633 17.757 13726 Z= 0.308 Chirality : 0.043 0.310 1503 Planarity : 0.003 0.063 1751 Dihedral : 4.091 16.818 1327 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.56 % Allowed : 18.96 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1209 helix: 1.75 (0.22), residues: 582 sheet: -0.31 (0.62), residues: 87 loop : -1.76 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 552 HIS 0.012 0.001 HIS C 727 PHE 0.022 0.001 PHE H 457 TYR 0.022 0.001 TYR H 529 ARG 0.003 0.000 ARG N 29 Details of bonding type rmsd link_TRANS : bond 0.00050 ( 1) link_TRANS : angle 0.03078 ( 2) hydrogen bonds : bond 0.05043 ( 468) hydrogen bonds : angle 4.27452 ( 1383) metal coordination : bond 0.00473 ( 35) metal coordination : angle 2.83611 ( 33) covalent geometry : bond 0.00287 (10152) covalent geometry : angle 0.61787 (13691) Misc. bond : bond 0.00088 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3941.37 seconds wall clock time: 72 minutes 22.97 seconds (4342.97 seconds total)