Starting phenix.real_space_refine on Thu Feb 5 00:05:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e3n_47491/02_2026/9e3n_47491.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e3n_47491/02_2026/9e3n_47491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e3n_47491/02_2026/9e3n_47491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e3n_47491/02_2026/9e3n_47491.map" model { file = "/net/cci-nas-00/data/ceres_data/9e3n_47491/02_2026/9e3n_47491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e3n_47491/02_2026/9e3n_47491.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 15 5.49 5 S 114 5.16 5 C 8640 2.51 5 N 2262 2.21 5 O 2579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13616 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4349 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'TRP:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4349 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'TRP:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4349 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 513} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'TRP:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'GDP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 125 Unusual residues: {' ZN': 2, 'ATP': 1, 'NAG': 3, 'PLM': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PLM:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'GDP': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 125 Unusual residues: {' ZN': 2, 'ATP': 1, 'NAG': 3, 'PLM': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PLM:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 167 Unusual residues: {' ZN': 2, 'ATP': 1, 'GDP': 1, 'NAG': 4, 'PLM': 5} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PLM:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3428 SG CYS A 479 19.565 50.427 16.121 1.00 89.35 S ATOM 3567 SG CYS A 499 22.286 51.936 18.256 1.00 89.15 S ATOM 3618 SG CYS A 506 23.162 50.604 14.863 1.00 84.13 S ATOM 4152 SG CYS A 572 22.333 48.142 17.556 1.00 85.05 S ATOM 3413 SG CYS A 477 15.899 49.927 17.048 1.00 89.61 S ATOM 3428 SG CYS A 479 19.565 50.427 16.121 1.00 89.35 S ATOM 3444 SG CYS A 482 18.596 47.647 18.472 1.00 89.78 S ATOM 3561 SG CYS A 498 18.376 51.246 19.645 1.00 88.69 S ATOM 7777 SG CYS C 479 65.691 70.101 17.257 1.00 89.58 S ATOM 7916 SG CYS C 499 65.549 66.957 19.337 1.00 87.87 S ATOM 7967 SG CYS C 506 64.099 66.920 15.880 1.00 84.09 S ATOM 8501 SG CYS C 572 62.272 68.827 18.531 1.00 85.27 S ATOM 7762 SG CYS C 477 67.053 73.510 18.297 1.00 89.16 S ATOM 7777 SG CYS C 479 65.691 70.101 17.257 1.00 89.58 S ATOM 7793 SG CYS C 482 63.673 72.294 19.562 1.00 91.61 S ATOM 7910 SG CYS C 498 66.848 70.663 20.843 1.00 87.05 S ATOM 12126 SG CYS B 479 59.653 20.278 17.313 1.00 86.33 S ATOM 12265 SG CYS B 499 56.915 21.941 19.306 1.00 87.34 S ATOM 12316 SG CYS B 506 57.751 23.268 15.902 1.00 83.57 S ATOM 12850 SG CYS B 572 60.202 23.856 18.667 1.00 83.36 S ATOM 12111 SG CYS B 477 61.880 17.378 18.402 1.00 88.80 S ATOM 12126 SG CYS B 479 59.653 20.278 17.313 1.00 86.33 S ATOM 12142 SG CYS B 482 62.461 20.894 19.749 1.00 89.02 S ATOM 12259 SG CYS B 498 59.411 18.939 20.870 1.00 87.97 S Time building chain proxies: 2.76, per 1000 atoms: 0.20 Number of scatterers: 13616 At special positions: 0 Unit cell: (91.368, 92.664, 159.408, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 114 16.00 P 15 15.00 O 2579 8.00 N 2262 7.00 C 8640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 168 " distance=2.02 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 269 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 168 " distance=2.02 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 168 " distance=2.02 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 269 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=15, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 241 " " NAG A 605 " - " ASN A 202 " " NAG A 606 " - " ASN A 213 " " NAG A 607 " - " ASN A 187 " " NAG B 602 " - " ASN B 241 " " NAG B 606 " - " ASN B 202 " " NAG B 607 " - " ASN B 213 " " NAG B 608 " - " ASN B 187 " " NAG C 601 " - " ASN C 241 " " NAG C 605 " - " ASN C 202 " " NAG C 606 " - " ASN C 213 " " NAG C 607 " - " ASN C 187 " Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 529.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 506 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 499 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 572 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 479 " pdb=" ZN A 604 " pdb="ZN ZN A 604 " - pdb=" SG CYS A 482 " pdb="ZN ZN A 604 " - pdb=" SG CYS A 479 " pdb="ZN ZN A 604 " - pdb=" SG CYS A 498 " pdb="ZN ZN A 604 " - pdb=" SG CYS A 477 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 506 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 499 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 572 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 479 " pdb=" ZN B 605 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 479 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 482 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 498 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 477 " pdb=" ZN C 603 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 506 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 499 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 572 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 479 " pdb=" ZN C 604 " pdb="ZN ZN C 604 " - pdb=" SG CYS C 482 " pdb="ZN ZN C 604 " - pdb=" SG CYS C 479 " pdb="ZN ZN C 604 " - pdb=" SG CYS C 498 " pdb="ZN ZN C 604 " - pdb=" SG CYS C 477 " Number of angles added : 36 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 15 sheets defined 34.3% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 23 through 49 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.652A pdb=" N GLU A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 241 through 249 removed outlier: 3.676A pdb=" N ILE A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 344 removed outlier: 3.545A pdb=" N LEU A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 removed outlier: 3.647A pdb=" N VAL A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 366 removed outlier: 4.164A pdb=" N ARG A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.510A pdb=" N TRP A 370 " --> pdb=" O HIS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 378 through 387 removed outlier: 4.171A pdb=" N TYR A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 496 removed outlier: 3.800A pdb=" N GLU A 495 " --> pdb=" O HIS A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 517 Processing helix chain 'A' and resid 519 through 531 Processing helix chain 'A' and resid 538 through 558 removed outlier: 3.707A pdb=" N ASN A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 566 removed outlier: 4.092A pdb=" N PHE A 566 " --> pdb=" O ASP A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 23 through 49 Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 182 through 187 removed outlier: 3.652A pdb=" N GLU C 186 " --> pdb=" O ASN C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 237 Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.677A pdb=" N ILE C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 344 removed outlier: 3.545A pdb=" N LEU C 333 " --> pdb=" O ASP C 329 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C 343 " --> pdb=" O SER C 339 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 358 removed outlier: 3.647A pdb=" N VAL C 349 " --> pdb=" O GLY C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 366 removed outlier: 4.164A pdb=" N ARG C 364 " --> pdb=" O SER C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 372 removed outlier: 3.510A pdb=" N TRP C 370 " --> pdb=" O HIS C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 377 Processing helix chain 'C' and resid 378 through 387 removed outlier: 4.171A pdb=" N TYR C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 496 removed outlier: 3.801A pdb=" N GLU C 495 " --> pdb=" O HIS C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 517 Processing helix chain 'C' and resid 519 through 531 Processing helix chain 'C' and resid 538 through 558 removed outlier: 3.710A pdb=" N ASN C 542 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 566 removed outlier: 4.090A pdb=" N PHE C 566 " --> pdb=" O ASP C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 23 through 49 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.652A pdb=" N GLU B 186 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 241 through 249 removed outlier: 3.674A pdb=" N ILE B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.544A pdb=" N LEU B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.647A pdb=" N VAL B 349 " --> pdb=" O GLY B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 366 removed outlier: 4.164A pdb=" N ARG B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.509A pdb=" N TRP B 370 " --> pdb=" O HIS B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 377 Processing helix chain 'B' and resid 378 through 387 removed outlier: 4.170A pdb=" N TYR B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 496 removed outlier: 3.800A pdb=" N GLU B 495 " --> pdb=" O HIS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 517 Processing helix chain 'B' and resid 519 through 531 Processing helix chain 'B' and resid 538 through 558 removed outlier: 3.707A pdb=" N ASN B 542 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 566 removed outlier: 4.091A pdb=" N PHE B 566 " --> pdb=" O ASP B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 581 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 Processing sheet with id=AA2, first strand: chain 'C' and resid 388 through 391 Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 56 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 52 through 56 current: chain 'A' and resid 159 through 168 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 159 through 168 current: chain 'A' and resid 267 through 268 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 267 through 268 current: chain 'A' and resid 304 through 328 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 66 Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 391 removed outlier: 6.556A pdb=" N GLU A 389 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 399 through 401 Processing sheet with id=AA8, first strand: chain 'C' and resid 52 through 56 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 52 through 56 current: chain 'C' and resid 159 through 168 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 159 through 168 current: chain 'C' and resid 267 through 268 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 267 through 268 current: chain 'C' and resid 304 through 328 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 66 Processing sheet with id=AB1, first strand: chain 'C' and resid 69 through 71 Processing sheet with id=AB2, first strand: chain 'C' and resid 399 through 401 Processing sheet with id=AB3, first strand: chain 'B' and resid 52 through 56 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 52 through 56 current: chain 'B' and resid 159 through 168 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 159 through 168 current: chain 'B' and resid 267 through 268 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 267 through 268 current: chain 'B' and resid 304 through 328 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 60 through 66 Processing sheet with id=AB5, first strand: chain 'B' and resid 69 through 71 Processing sheet with id=AB6, first strand: chain 'B' and resid 399 through 401 399 hydrogen bonds defined for protein. 1098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2969 1.33 - 1.45: 3230 1.45 - 1.57: 7526 1.57 - 1.70: 24 1.70 - 1.82: 132 Bond restraints: 13881 Sorted by residual: bond pdb=" C4 ATP C 613 " pdb=" C5 ATP C 613 " ideal model delta sigma weight residual 1.388 1.489 -0.101 1.00e-02 1.00e+04 1.02e+02 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.489 -0.101 1.00e-02 1.00e+04 1.02e+02 bond pdb=" C4 ATP A 613 " pdb=" C5 ATP A 613 " ideal model delta sigma weight residual 1.388 1.489 -0.101 1.00e-02 1.00e+04 1.02e+02 bond pdb=" C5 ATP A 613 " pdb=" C6 ATP A 613 " ideal model delta sigma weight residual 1.409 1.490 -0.081 1.00e-02 1.00e+04 6.62e+01 bond pdb=" C5 ATP C 613 " pdb=" C6 ATP C 613 " ideal model delta sigma weight residual 1.409 1.490 -0.081 1.00e-02 1.00e+04 6.58e+01 ... (remaining 13876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 18654 3.94 - 7.88: 126 7.88 - 11.82: 0 11.82 - 15.77: 0 15.77 - 19.71: 6 Bond angle restraints: 18786 Sorted by residual: angle pdb=" PB ATP C 613 " pdb=" O3B ATP C 613 " pdb=" PG ATP C 613 " ideal model delta sigma weight residual 139.87 120.16 19.71 1.00e+00 1.00e+00 3.88e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 120.21 19.66 1.00e+00 1.00e+00 3.86e+02 angle pdb=" PB ATP A 613 " pdb=" O3B ATP A 613 " pdb=" PG ATP A 613 " ideal model delta sigma weight residual 139.87 120.21 19.66 1.00e+00 1.00e+00 3.86e+02 angle pdb=" PA ATP C 613 " pdb=" O3A ATP C 613 " pdb=" PB ATP C 613 " ideal model delta sigma weight residual 136.83 120.95 15.88 1.00e+00 1.00e+00 2.52e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 120.96 15.87 1.00e+00 1.00e+00 2.52e+02 ... (remaining 18781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 7730 18.11 - 36.23: 624 36.23 - 54.34: 82 54.34 - 72.45: 33 72.45 - 90.56: 18 Dihedral angle restraints: 8487 sinusoidal: 3714 harmonic: 4773 Sorted by residual: dihedral pdb=" O5' GDP B 603 " pdb=" O3A GDP B 603 " pdb=" PA GDP B 603 " pdb=" PB GDP B 603 " ideal model delta sinusoidal sigma weight residual -179.98 -89.42 -90.56 1 2.00e+01 2.50e-03 2.42e+01 dihedral pdb=" O5' GDP A 602 " pdb=" O3A GDP A 602 " pdb=" PA GDP A 602 " pdb=" PB GDP A 602 " ideal model delta sinusoidal sigma weight residual -179.98 -89.42 -90.56 1 2.00e+01 2.50e-03 2.42e+01 dihedral pdb=" O5' GDP C 602 " pdb=" O3A GDP C 602 " pdb=" PA GDP C 602 " pdb=" PB GDP C 602 " ideal model delta sinusoidal sigma weight residual -179.98 -89.56 -90.42 1 2.00e+01 2.50e-03 2.42e+01 ... (remaining 8484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1414 0.052 - 0.105: 423 0.105 - 0.157: 147 0.157 - 0.209: 38 0.209 - 0.262: 15 Chirality restraints: 2037 Sorted by residual: chirality pdb=" C1 NAG C 605 " pdb=" ND2 ASN C 202 " pdb=" C2 NAG C 605 " pdb=" O5 NAG C 605 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C1 NAG A 605 " pdb=" ND2 ASN A 202 " pdb=" C2 NAG A 605 " pdb=" O5 NAG A 605 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C1 NAG B 606 " pdb=" ND2 ASN B 202 " pdb=" C2 NAG B 606 " pdb=" O5 NAG B 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 2034 not shown) Planarity restraints: 2355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 605 " 0.051 2.00e-02 2.50e+03 4.18e-02 2.18e+01 pdb=" C7 NAG A 605 " -0.015 2.00e-02 2.50e+03 pdb=" C8 NAG A 605 " 0.039 2.00e-02 2.50e+03 pdb=" N2 NAG A 605 " -0.066 2.00e-02 2.50e+03 pdb=" O7 NAG A 605 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 606 " -0.050 2.00e-02 2.50e+03 4.14e-02 2.15e+01 pdb=" C7 NAG B 606 " 0.014 2.00e-02 2.50e+03 pdb=" C8 NAG B 606 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG B 606 " 0.065 2.00e-02 2.50e+03 pdb=" O7 NAG B 606 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 605 " 0.050 2.00e-02 2.50e+03 4.12e-02 2.12e+01 pdb=" C7 NAG C 605 " -0.015 2.00e-02 2.50e+03 pdb=" C8 NAG C 605 " 0.038 2.00e-02 2.50e+03 pdb=" N2 NAG C 605 " -0.065 2.00e-02 2.50e+03 pdb=" O7 NAG C 605 " -0.009 2.00e-02 2.50e+03 ... (remaining 2352 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 376 2.70 - 3.25: 13256 3.25 - 3.80: 21608 3.80 - 4.35: 29238 4.35 - 4.90: 48664 Nonbonded interactions: 113142 Sorted by model distance: nonbonded pdb=" O THR B 90 " pdb=" OG1 THR B 94 " model vdw 2.155 3.040 nonbonded pdb=" O THR C 90 " pdb=" OG1 THR C 94 " model vdw 2.156 3.040 nonbonded pdb=" O THR A 90 " pdb=" OG1 THR A 94 " model vdw 2.156 3.040 nonbonded pdb=" OD1 ASP A 92 " pdb=" OH TYR C 298 " model vdw 2.173 3.040 nonbonded pdb=" OH TYR A 298 " pdb=" OD1 ASP B 92 " model vdw 2.193 3.040 ... (remaining 113137 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 595 or resid 604 or resid 606 through 607 or (re \ sid 609 through 610 and (name C1 or name C2 or name C3 or name C4 or name C5 or \ name C6 or name C7 or name O2 )) or (resid 611 through 612 and (name C1 or name \ C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name O2 \ )))) selection = (chain 'B' and (resid 4 through 595 or resid 604 or resid 606 through 607 or (re \ sid 609 through 610 and (name C1 or name C2 or name C3 or name C4 or name C5 or \ name C6 or name C7 or name O2 )) or (resid 611 through 612 and (name C1 or name \ C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name O2 \ )))) selection = (chain 'C' and (resid 4 through 595 or resid 604 or resid 606 through 607 or (re \ sid 609 through 610 and (name C1 or name C2 or name C3 or name C4 or name C5 or \ name C6 or name C7 or name O2 )) or (resid 611 through 612 and (name C1 or name \ C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name O2 \ )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.390 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 0.101 13944 Z= 0.515 Angle : 1.006 19.708 18882 Z= 0.706 Chirality : 0.062 0.262 2037 Planarity : 0.005 0.048 2343 Dihedral : 13.575 90.564 5379 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.21), residues: 1608 helix: -0.76 (0.23), residues: 483 sheet: -0.26 (0.27), residues: 354 loop : -0.16 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 410 TYR 0.023 0.002 TYR C 155 PHE 0.042 0.002 PHE B 591 TRP 0.007 0.001 TRP C 258 HIS 0.008 0.001 HIS B 547 Details of bonding type rmsd covalent geometry : bond 0.00758 (13881) covalent geometry : angle 0.98946 (18786) SS BOND : bond 0.00513 ( 12) SS BOND : angle 1.22286 ( 24) hydrogen bonds : bond 0.17567 ( 399) hydrogen bonds : angle 8.02870 ( 1098) metal coordination : bond 0.00308 ( 24) metal coordination : angle 1.51582 ( 36) Misc. bond : bond 0.03151 ( 15) link_NAG-ASN : bond 0.00784 ( 12) link_NAG-ASN : angle 4.04807 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 395 LYS cc_start: 0.7534 (ptpt) cc_final: 0.7315 (ptpp) REVERT: C 22 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7551 (tm-30) REVERT: C 53 ARG cc_start: 0.6797 (ttp80) cc_final: 0.6541 (ttp80) REVERT: C 393 GLU cc_start: 0.7610 (tt0) cc_final: 0.7406 (tt0) REVERT: C 395 LYS cc_start: 0.7659 (ptpt) cc_final: 0.7122 (ptpp) REVERT: C 563 MET cc_start: 0.8648 (ttm) cc_final: 0.8439 (ttp) REVERT: B 22 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7499 (tm-30) REVERT: B 395 LYS cc_start: 0.7670 (ptpt) cc_final: 0.7443 (ptpp) REVERT: B 563 MET cc_start: 0.8669 (ttm) cc_final: 0.8408 (ttp) outliers start: 0 outliers final: 1 residues processed: 187 average time/residue: 0.4873 time to fit residues: 100.7519 Evaluate side-chains 139 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 408 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 HIS A 524 GLN C 366 HIS C 524 GLN B 524 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.190150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.153340 restraints weight = 14317.427| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.51 r_work: 0.3284 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13944 Z= 0.159 Angle : 0.563 6.847 18882 Z= 0.286 Chirality : 0.044 0.140 2037 Planarity : 0.004 0.040 2343 Dihedral : 9.518 83.175 2267 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.65 % Allowed : 7.92 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1608 helix: 0.18 (0.23), residues: 492 sheet: -0.34 (0.27), residues: 363 loop : 0.04 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 410 TYR 0.017 0.002 TYR A 553 PHE 0.014 0.002 PHE A 313 TRP 0.009 0.001 TRP A 556 HIS 0.007 0.001 HIS C 366 Details of bonding type rmsd covalent geometry : bond 0.00375 (13881) covalent geometry : angle 0.55063 (18786) SS BOND : bond 0.00446 ( 12) SS BOND : angle 1.20293 ( 24) hydrogen bonds : bond 0.04595 ( 399) hydrogen bonds : angle 5.65841 ( 1098) metal coordination : bond 0.00354 ( 24) metal coordination : angle 1.99149 ( 36) Misc. bond : bond 0.00111 ( 15) link_NAG-ASN : bond 0.00162 ( 12) link_NAG-ASN : angle 1.82787 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7739 (tm-30) REVERT: A 305 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: A 381 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: A 395 LYS cc_start: 0.7629 (ptpt) cc_final: 0.7265 (ptpp) REVERT: C 22 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7730 (tm-30) REVERT: C 53 ARG cc_start: 0.6988 (ttp80) cc_final: 0.6765 (ttp80) REVERT: C 305 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: C 395 LYS cc_start: 0.7754 (ptpt) cc_final: 0.7125 (ptpp) REVERT: C 561 GLN cc_start: 0.6980 (tp40) cc_final: 0.6730 (tm-30) REVERT: C 563 MET cc_start: 0.8720 (ttm) cc_final: 0.8518 (ttp) REVERT: B 22 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7758 (tm-30) REVERT: B 305 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: B 395 LYS cc_start: 0.7724 (ptpt) cc_final: 0.7437 (ptpp) REVERT: B 544 ARG cc_start: 0.7147 (mmm160) cc_final: 0.6597 (mmm160) outliers start: 24 outliers final: 14 residues processed: 176 average time/residue: 0.4585 time to fit residues: 89.8510 Evaluate side-chains 158 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain C residue 265 TRP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 408 HIS Chi-restraints excluded: chain B residue 571 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 137 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.188870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148926 restraints weight = 14372.674| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.71 r_work: 0.3237 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13944 Z= 0.168 Angle : 0.545 5.647 18882 Z= 0.278 Chirality : 0.044 0.141 2037 Planarity : 0.004 0.037 2343 Dihedral : 9.113 79.289 2267 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.86 % Allowed : 10.67 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.21), residues: 1608 helix: 0.31 (0.24), residues: 495 sheet: -0.44 (0.26), residues: 384 loop : 0.05 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 20 TYR 0.013 0.001 TYR B 155 PHE 0.020 0.002 PHE C 591 TRP 0.008 0.001 TRP A 258 HIS 0.002 0.000 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00406 (13881) covalent geometry : angle 0.53103 (18786) SS BOND : bond 0.00455 ( 12) SS BOND : angle 1.19384 ( 24) hydrogen bonds : bond 0.04239 ( 399) hydrogen bonds : angle 5.27511 ( 1098) metal coordination : bond 0.00409 ( 24) metal coordination : angle 1.99349 ( 36) Misc. bond : bond 0.00036 ( 15) link_NAG-ASN : bond 0.00154 ( 12) link_NAG-ASN : angle 1.89016 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8347 (tm-30) cc_final: 0.7726 (tm-30) REVERT: A 381 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: A 395 LYS cc_start: 0.7785 (ptpt) cc_final: 0.7415 (ptpp) REVERT: A 544 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6926 (mmm160) REVERT: C 22 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7723 (tm-30) REVERT: C 53 ARG cc_start: 0.7017 (ttp80) cc_final: 0.6778 (ttp80) REVERT: C 160 LYS cc_start: 0.7460 (mmmt) cc_final: 0.7085 (mtmt) REVERT: C 305 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: C 381 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7723 (mt-10) REVERT: C 515 LYS cc_start: 0.8556 (ptmt) cc_final: 0.7940 (pttp) REVERT: C 561 GLN cc_start: 0.6993 (tp40) cc_final: 0.6732 (tt0) REVERT: B 22 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7792 (tm-30) REVERT: B 160 LYS cc_start: 0.7504 (mmmt) cc_final: 0.7136 (mtmt) REVERT: B 305 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: B 395 LYS cc_start: 0.7845 (ptpt) cc_final: 0.7533 (ptpp) REVERT: B 515 LYS cc_start: 0.8507 (ptmt) cc_final: 0.7851 (pttp) REVERT: B 544 ARG cc_start: 0.7156 (mmm160) cc_final: 0.6711 (mmm160) REVERT: B 561 GLN cc_start: 0.7144 (tp40) cc_final: 0.6858 (tm-30) outliers start: 27 outliers final: 16 residues processed: 168 average time/residue: 0.4313 time to fit residues: 80.4939 Evaluate side-chains 157 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 265 TRP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 408 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 128 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 92 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 51 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.189958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153121 restraints weight = 14361.875| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.63 r_work: 0.3253 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13944 Z= 0.126 Angle : 0.525 6.444 18882 Z= 0.262 Chirality : 0.043 0.132 2037 Planarity : 0.004 0.034 2343 Dihedral : 8.865 78.781 2267 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.27 % Allowed : 12.88 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1608 helix: 0.50 (0.24), residues: 495 sheet: -0.49 (0.25), residues: 387 loop : 0.08 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 410 TYR 0.013 0.001 TYR A 93 PHE 0.027 0.002 PHE A 591 TRP 0.006 0.001 TRP B 556 HIS 0.007 0.000 HIS C 366 Details of bonding type rmsd covalent geometry : bond 0.00298 (13881) covalent geometry : angle 0.50767 (18786) SS BOND : bond 0.00374 ( 12) SS BOND : angle 1.08014 ( 24) hydrogen bonds : bond 0.03650 ( 399) hydrogen bonds : angle 4.98363 ( 1098) metal coordination : bond 0.00562 ( 24) metal coordination : angle 2.47298 ( 36) Misc. bond : bond 0.00026 ( 15) link_NAG-ASN : bond 0.00078 ( 12) link_NAG-ASN : angle 1.72318 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7751 (tm-30) REVERT: A 305 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: A 381 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: A 395 LYS cc_start: 0.7791 (ptpt) cc_final: 0.7402 (ptpp) REVERT: A 544 ARG cc_start: 0.7286 (mmm160) cc_final: 0.6948 (mmm160) REVERT: C 22 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7688 (tm-30) REVERT: C 53 ARG cc_start: 0.6995 (ttp80) cc_final: 0.6760 (ttp80) REVERT: C 160 LYS cc_start: 0.7470 (mmmt) cc_final: 0.7074 (mtmt) REVERT: C 305 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: C 515 LYS cc_start: 0.8555 (ptmt) cc_final: 0.7933 (pttp) REVERT: C 561 GLN cc_start: 0.6974 (tp40) cc_final: 0.6762 (tm-30) REVERT: B 22 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7674 (tm-30) REVERT: B 160 LYS cc_start: 0.7541 (mmmt) cc_final: 0.7132 (mtmt) REVERT: B 305 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: B 395 LYS cc_start: 0.7905 (ptpt) cc_final: 0.7514 (ptpp) REVERT: B 515 LYS cc_start: 0.8516 (ptmt) cc_final: 0.7853 (pttp) REVERT: B 531 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7490 (mt-10) REVERT: B 561 GLN cc_start: 0.7077 (tp40) cc_final: 0.6789 (tm-30) outliers start: 33 outliers final: 17 residues processed: 166 average time/residue: 0.4793 time to fit residues: 87.6058 Evaluate side-chains 159 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 265 TRP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 391 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 125 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 HIS C 366 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.187707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.148019 restraints weight = 14376.030| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.79 r_work: 0.3208 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13944 Z= 0.182 Angle : 0.561 7.192 18882 Z= 0.279 Chirality : 0.044 0.137 2037 Planarity : 0.004 0.036 2343 Dihedral : 8.833 83.151 2267 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.41 % Allowed : 13.77 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.21), residues: 1608 helix: 0.51 (0.24), residues: 492 sheet: -0.39 (0.25), residues: 378 loop : 0.04 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 546 TYR 0.012 0.001 TYR C 155 PHE 0.025 0.002 PHE B 591 TRP 0.008 0.001 TRP B 556 HIS 0.008 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00445 (13881) covalent geometry : angle 0.54273 (18786) SS BOND : bond 0.00506 ( 12) SS BOND : angle 1.21240 ( 24) hydrogen bonds : bond 0.03775 ( 399) hydrogen bonds : angle 4.98625 ( 1098) metal coordination : bond 0.00563 ( 24) metal coordination : angle 2.64020 ( 36) Misc. bond : bond 0.00034 ( 15) link_NAG-ASN : bond 0.00153 ( 12) link_NAG-ASN : angle 1.87473 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 305 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7676 (tt0) REVERT: A 381 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: A 395 LYS cc_start: 0.7817 (ptpt) cc_final: 0.7421 (ptpp) REVERT: A 544 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6973 (mmm160) REVERT: C 22 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7649 (tm-30) REVERT: C 53 ARG cc_start: 0.6966 (ttp80) cc_final: 0.6708 (ttp80) REVERT: C 160 LYS cc_start: 0.7524 (mmmt) cc_final: 0.7043 (mtmt) REVERT: C 305 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: C 515 LYS cc_start: 0.8591 (ptmt) cc_final: 0.7957 (pttp) REVERT: C 544 ARG cc_start: 0.7282 (mmm160) cc_final: 0.6639 (mmm160) REVERT: C 561 GLN cc_start: 0.6987 (tp40) cc_final: 0.6743 (tm-30) REVERT: B 22 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 160 LYS cc_start: 0.7603 (mmmt) cc_final: 0.7102 (mtmt) REVERT: B 305 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: B 395 LYS cc_start: 0.7973 (ptpt) cc_final: 0.7629 (ptpp) REVERT: B 515 LYS cc_start: 0.8513 (ptmt) cc_final: 0.7839 (pttp) REVERT: B 544 ARG cc_start: 0.7287 (mmm160) cc_final: 0.6765 (mmm160) REVERT: B 561 GLN cc_start: 0.7120 (tp40) cc_final: 0.6775 (tm-30) REVERT: B 592 LYS cc_start: 0.7821 (tptt) cc_final: 0.7564 (tppt) outliers start: 35 outliers final: 20 residues processed: 167 average time/residue: 0.4765 time to fit residues: 88.0934 Evaluate side-chains 160 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 265 TRP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 408 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 83 optimal weight: 0.0870 chunk 47 optimal weight: 2.9990 chunk 131 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.189092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152244 restraints weight = 14336.421| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.66 r_work: 0.3236 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13944 Z= 0.131 Angle : 0.533 6.408 18882 Z= 0.264 Chirality : 0.043 0.133 2037 Planarity : 0.004 0.035 2343 Dihedral : 8.711 85.334 2267 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.48 % Allowed : 14.53 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.22), residues: 1608 helix: 0.63 (0.24), residues: 480 sheet: -0.47 (0.25), residues: 384 loop : 0.33 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 546 TYR 0.013 0.001 TYR A 93 PHE 0.025 0.001 PHE A 591 TRP 0.007 0.001 TRP B 556 HIS 0.005 0.000 HIS C 366 Details of bonding type rmsd covalent geometry : bond 0.00313 (13881) covalent geometry : angle 0.51626 (18786) SS BOND : bond 0.00415 ( 12) SS BOND : angle 1.25620 ( 24) hydrogen bonds : bond 0.03416 ( 399) hydrogen bonds : angle 4.84086 ( 1098) metal coordination : bond 0.00460 ( 24) metal coordination : angle 2.41387 ( 36) Misc. bond : bond 0.00023 ( 15) link_NAG-ASN : bond 0.00056 ( 12) link_NAG-ASN : angle 1.72611 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7781 (tm-30) REVERT: A 305 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: A 381 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: A 544 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.7039 (mmm160) REVERT: C 22 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7642 (tm-30) REVERT: C 53 ARG cc_start: 0.6996 (ttp80) cc_final: 0.6726 (ttp80) REVERT: C 160 LYS cc_start: 0.7598 (mmmt) cc_final: 0.7117 (mtmt) REVERT: C 261 ASN cc_start: 0.8321 (p0) cc_final: 0.8094 (p0) REVERT: C 305 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7675 (tt0) REVERT: C 515 LYS cc_start: 0.8589 (ptmt) cc_final: 0.7967 (pttp) REVERT: C 544 ARG cc_start: 0.7291 (mmm160) cc_final: 0.6756 (mmm160) REVERT: C 561 GLN cc_start: 0.6995 (tp40) cc_final: 0.6771 (tm-30) REVERT: B 22 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7746 (tm-30) REVERT: B 160 LYS cc_start: 0.7599 (mmmt) cc_final: 0.7036 (mtmt) REVERT: B 305 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: B 395 LYS cc_start: 0.7998 (ptpt) cc_final: 0.7639 (ptpp) REVERT: B 515 LYS cc_start: 0.8541 (ptmt) cc_final: 0.7825 (pttp) REVERT: B 544 ARG cc_start: 0.7310 (mmm160) cc_final: 0.6823 (mmm160) REVERT: B 561 GLN cc_start: 0.7142 (tp40) cc_final: 0.6824 (tm-30) REVERT: B 592 LYS cc_start: 0.7937 (tptt) cc_final: 0.7680 (tppt) outliers start: 36 outliers final: 21 residues processed: 167 average time/residue: 0.4779 time to fit residues: 88.2537 Evaluate side-chains 163 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 265 TRP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 408 HIS Chi-restraints excluded: chain B residue 530 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 48 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 160 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 HIS C 366 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.187507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.151348 restraints weight = 14222.320| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.06 r_work: 0.3267 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13944 Z= 0.206 Angle : 0.582 6.936 18882 Z= 0.290 Chirality : 0.045 0.141 2037 Planarity : 0.004 0.038 2343 Dihedral : 8.832 88.270 2267 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.69 % Allowed : 14.46 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.21), residues: 1608 helix: 0.60 (0.24), residues: 477 sheet: -0.53 (0.25), residues: 384 loop : 0.20 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 20 TYR 0.012 0.001 TYR C 155 PHE 0.046 0.002 PHE B 591 TRP 0.008 0.001 TRP C 556 HIS 0.008 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00511 (13881) covalent geometry : angle 0.56382 (18786) SS BOND : bond 0.00576 ( 12) SS BOND : angle 1.38580 ( 24) hydrogen bonds : bond 0.03700 ( 399) hydrogen bonds : angle 4.96657 ( 1098) metal coordination : bond 0.00583 ( 24) metal coordination : angle 2.56127 ( 36) Misc. bond : bond 0.00038 ( 15) link_NAG-ASN : bond 0.00189 ( 12) link_NAG-ASN : angle 1.93634 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8287 (tm-30) cc_final: 0.7739 (tm-30) REVERT: A 305 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: A 381 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: A 395 LYS cc_start: 0.7884 (ptpt) cc_final: 0.7431 (ptpp) REVERT: A 544 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.7021 (mmm160) REVERT: A 561 GLN cc_start: 0.7150 (tp40) cc_final: 0.6916 (tm-30) REVERT: C 22 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7579 (tm-30) REVERT: C 53 ARG cc_start: 0.6949 (ttp80) cc_final: 0.6731 (ttp80) REVERT: C 160 LYS cc_start: 0.7688 (mmmt) cc_final: 0.7198 (mtmt) REVERT: C 261 ASN cc_start: 0.8265 (p0) cc_final: 0.8048 (p0) REVERT: C 305 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: C 395 LYS cc_start: 0.7931 (ptpt) cc_final: 0.7571 (ptpp) REVERT: C 515 LYS cc_start: 0.8607 (ptmt) cc_final: 0.7933 (pttp) REVERT: C 544 ARG cc_start: 0.7249 (mmm160) cc_final: 0.6707 (mmm160) REVERT: C 561 GLN cc_start: 0.6987 (tp40) cc_final: 0.6775 (tt0) REVERT: B 22 GLN cc_start: 0.8331 (tm-30) cc_final: 0.7664 (tm-30) REVERT: B 160 LYS cc_start: 0.7674 (mmmt) cc_final: 0.7116 (mtmt) REVERT: B 305 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: B 395 LYS cc_start: 0.8081 (ptpt) cc_final: 0.7637 (ptpp) REVERT: B 515 LYS cc_start: 0.8563 (ptmt) cc_final: 0.7844 (pttp) REVERT: B 544 ARG cc_start: 0.7293 (mmm160) cc_final: 0.6896 (mmm160) REVERT: B 561 GLN cc_start: 0.7129 (tp40) cc_final: 0.6829 (tm-30) REVERT: B 592 LYS cc_start: 0.7969 (tptt) cc_final: 0.7765 (tppt) outliers start: 39 outliers final: 23 residues processed: 168 average time/residue: 0.4582 time to fit residues: 85.6988 Evaluate side-chains 164 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 265 TRP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 408 HIS Chi-restraints excluded: chain B residue 530 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 42 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.188663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.149372 restraints weight = 14172.063| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.56 r_work: 0.3247 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13944 Z= 0.141 Angle : 0.544 7.325 18882 Z= 0.270 Chirality : 0.044 0.189 2037 Planarity : 0.004 0.037 2343 Dihedral : 8.691 88.815 2265 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.48 % Allowed : 14.12 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1608 helix: 0.66 (0.24), residues: 480 sheet: -0.46 (0.25), residues: 384 loop : 0.23 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 410 TYR 0.013 0.001 TYR A 553 PHE 0.039 0.002 PHE B 591 TRP 0.008 0.001 TRP A 556 HIS 0.006 0.000 HIS C 366 Details of bonding type rmsd covalent geometry : bond 0.00342 (13881) covalent geometry : angle 0.52726 (18786) SS BOND : bond 0.00424 ( 12) SS BOND : angle 1.20908 ( 24) hydrogen bonds : bond 0.03354 ( 399) hydrogen bonds : angle 4.81819 ( 1098) metal coordination : bond 0.00486 ( 24) metal coordination : angle 2.45142 ( 36) Misc. bond : bond 0.00023 ( 15) link_NAG-ASN : bond 0.00053 ( 12) link_NAG-ASN : angle 1.75884 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 153 VAL cc_start: 0.8384 (t) cc_final: 0.8176 (p) REVERT: A 305 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: A 381 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: A 395 LYS cc_start: 0.7922 (ptpt) cc_final: 0.7562 (ptpp) REVERT: A 544 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.7064 (mmm160) REVERT: A 561 GLN cc_start: 0.7232 (tp40) cc_final: 0.6939 (tt0) REVERT: C 22 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7635 (tm-30) REVERT: C 53 ARG cc_start: 0.6954 (ttp80) cc_final: 0.6743 (ttp80) REVERT: C 160 LYS cc_start: 0.7681 (mmmt) cc_final: 0.7159 (mtmt) REVERT: C 261 ASN cc_start: 0.8300 (p0) cc_final: 0.8087 (p0) REVERT: C 305 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: C 395 LYS cc_start: 0.7973 (ptpt) cc_final: 0.7379 (pttp) REVERT: C 515 LYS cc_start: 0.8592 (ptmt) cc_final: 0.7933 (pttp) REVERT: C 544 ARG cc_start: 0.7291 (mmm160) cc_final: 0.6761 (mmm160) REVERT: C 561 GLN cc_start: 0.7011 (tp40) cc_final: 0.6806 (tm-30) REVERT: B 22 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7733 (tm-30) REVERT: B 160 LYS cc_start: 0.7667 (mmmt) cc_final: 0.7087 (mtmt) REVERT: B 305 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: B 395 LYS cc_start: 0.8120 (ptpt) cc_final: 0.7693 (ptpp) REVERT: B 515 LYS cc_start: 0.8576 (ptmt) cc_final: 0.7859 (pttp) REVERT: B 544 ARG cc_start: 0.7325 (mmm160) cc_final: 0.6934 (mmm160) REVERT: B 561 GLN cc_start: 0.7160 (tp40) cc_final: 0.6872 (tm-30) REVERT: B 592 LYS cc_start: 0.7926 (tptt) cc_final: 0.7707 (tppt) outliers start: 36 outliers final: 20 residues processed: 164 average time/residue: 0.4931 time to fit residues: 89.6020 Evaluate side-chains 160 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 265 TRP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 530 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 HIS C 366 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.188032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.147762 restraints weight = 14330.086| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.70 r_work: 0.3213 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13944 Z= 0.160 Angle : 0.557 7.521 18882 Z= 0.277 Chirality : 0.044 0.167 2037 Planarity : 0.004 0.037 2343 Dihedral : 8.672 89.994 2265 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.27 % Allowed : 14.60 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.21), residues: 1608 helix: 0.68 (0.25), residues: 480 sheet: -0.47 (0.25), residues: 384 loop : 0.19 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 410 TYR 0.012 0.001 TYR C 553 PHE 0.032 0.002 PHE C 513 TRP 0.007 0.001 TRP C 556 HIS 0.008 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00395 (13881) covalent geometry : angle 0.53887 (18786) SS BOND : bond 0.00454 ( 12) SS BOND : angle 1.25330 ( 24) hydrogen bonds : bond 0.03420 ( 399) hydrogen bonds : angle 4.82522 ( 1098) metal coordination : bond 0.00509 ( 24) metal coordination : angle 2.55932 ( 36) Misc. bond : bond 0.00029 ( 15) link_NAG-ASN : bond 0.00111 ( 12) link_NAG-ASN : angle 1.83184 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7825 (tm-30) REVERT: A 153 VAL cc_start: 0.8346 (t) cc_final: 0.8131 (p) REVERT: A 305 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: A 381 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: A 395 LYS cc_start: 0.7887 (ptpt) cc_final: 0.7506 (ptpp) REVERT: A 544 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7045 (mmm160) REVERT: A 561 GLN cc_start: 0.7209 (tp40) cc_final: 0.6875 (tt0) REVERT: A 592 LYS cc_start: 0.7793 (tptt) cc_final: 0.7415 (tppt) REVERT: C 22 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7676 (tm-30) REVERT: C 53 ARG cc_start: 0.6953 (ttp80) cc_final: 0.6675 (ttp80) REVERT: C 160 LYS cc_start: 0.7704 (mmmt) cc_final: 0.7125 (mtmt) REVERT: C 261 ASN cc_start: 0.8277 (p0) cc_final: 0.8076 (p0) REVERT: C 305 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: C 395 LYS cc_start: 0.7943 (ptpt) cc_final: 0.7350 (pttp) REVERT: C 515 LYS cc_start: 0.8591 (ptmt) cc_final: 0.7905 (pttp) REVERT: C 544 ARG cc_start: 0.7307 (mmm160) cc_final: 0.6697 (mmm160) REVERT: C 561 GLN cc_start: 0.7018 (tp40) cc_final: 0.6783 (tt0) REVERT: B 22 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7748 (tm-30) REVERT: B 160 LYS cc_start: 0.7679 (mmmt) cc_final: 0.7061 (mtmt) REVERT: B 305 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: B 395 LYS cc_start: 0.8110 (ptpt) cc_final: 0.7662 (ptpp) REVERT: B 515 LYS cc_start: 0.8565 (ptmt) cc_final: 0.7814 (pttp) REVERT: B 544 ARG cc_start: 0.7369 (mmm160) cc_final: 0.6879 (mmm160) REVERT: B 561 GLN cc_start: 0.7209 (tp40) cc_final: 0.6853 (tm-30) REVERT: B 592 LYS cc_start: 0.7917 (tptt) cc_final: 0.7623 (tppt) outliers start: 33 outliers final: 24 residues processed: 160 average time/residue: 0.4964 time to fit residues: 87.7990 Evaluate side-chains 162 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain A residue 544 ARG Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 265 TRP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 530 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 81 optimal weight: 0.0060 chunk 20 optimal weight: 0.0870 chunk 139 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 96 optimal weight: 0.0270 overall best weight: 0.2032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 366 HIS C 366 HIS B 148 GLN B 366 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.191201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.151669 restraints weight = 14256.650| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.65 r_work: 0.3277 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13944 Z= 0.101 Angle : 0.518 7.697 18882 Z= 0.259 Chirality : 0.043 0.161 2037 Planarity : 0.003 0.035 2343 Dihedral : 8.387 89.329 2265 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.86 % Allowed : 15.36 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.21), residues: 1608 helix: 0.81 (0.25), residues: 483 sheet: -0.17 (0.25), residues: 366 loop : 0.13 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 410 TYR 0.020 0.001 TYR C 553 PHE 0.028 0.001 PHE A 513 TRP 0.015 0.001 TRP C 556 HIS 0.009 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00233 (13881) covalent geometry : angle 0.50208 (18786) SS BOND : bond 0.00303 ( 12) SS BOND : angle 1.03891 ( 24) hydrogen bonds : bond 0.03065 ( 399) hydrogen bonds : angle 4.60392 ( 1098) metal coordination : bond 0.00388 ( 24) metal coordination : angle 2.47907 ( 36) Misc. bond : bond 0.00016 ( 15) link_NAG-ASN : bond 0.00119 ( 12) link_NAG-ASN : angle 1.57148 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3216 Ramachandran restraints generated. 1608 Oldfield, 0 Emsley, 1608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7743 (tm-30) REVERT: A 140 MET cc_start: 0.6117 (mtm) cc_final: 0.5828 (mtm) REVERT: A 153 VAL cc_start: 0.8257 (t) cc_final: 0.8051 (p) REVERT: A 395 LYS cc_start: 0.7894 (ptpt) cc_final: 0.7411 (ptpp) REVERT: A 544 ARG cc_start: 0.7262 (mmm160) cc_final: 0.6971 (mmm160) REVERT: A 561 GLN cc_start: 0.7169 (tp40) cc_final: 0.6828 (tt0) REVERT: C 22 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7622 (tm-30) REVERT: C 53 ARG cc_start: 0.6932 (ttp80) cc_final: 0.6646 (ttp80) REVERT: C 160 LYS cc_start: 0.7635 (mmmt) cc_final: 0.7064 (mtmt) REVERT: C 395 LYS cc_start: 0.7985 (ptpt) cc_final: 0.7395 (pttp) REVERT: C 515 LYS cc_start: 0.8598 (ptmt) cc_final: 0.7899 (pttp) REVERT: C 544 ARG cc_start: 0.7227 (mmm160) cc_final: 0.6593 (mmm160) REVERT: C 561 GLN cc_start: 0.6953 (tp40) cc_final: 0.6686 (tt0) REVERT: C 563 MET cc_start: 0.8677 (ttm) cc_final: 0.8344 (ttp) REVERT: B 22 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7663 (tm-30) REVERT: B 160 LYS cc_start: 0.7654 (mmmt) cc_final: 0.7039 (mtmt) REVERT: B 395 LYS cc_start: 0.8139 (ptpt) cc_final: 0.7681 (ptpp) REVERT: B 515 LYS cc_start: 0.8541 (ptmt) cc_final: 0.7775 (pttp) REVERT: B 530 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6157 (mt0) REVERT: B 544 ARG cc_start: 0.7278 (mmm160) cc_final: 0.6774 (mmm160) REVERT: B 561 GLN cc_start: 0.7148 (tp40) cc_final: 0.6790 (tm-30) outliers start: 27 outliers final: 17 residues processed: 165 average time/residue: 0.4987 time to fit residues: 90.4480 Evaluate side-chains 151 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 408 HIS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 265 TRP Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 530 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 112 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 0.0870 chunk 116 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 114 optimal weight: 0.0010 overall best weight: 0.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 HIS A 427 GLN C 366 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.190565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.154385 restraints weight = 14345.870| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.50 r_work: 0.3276 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13944 Z= 0.112 Angle : 0.523 7.705 18882 Z= 0.261 Chirality : 0.043 0.151 2037 Planarity : 0.004 0.035 2343 Dihedral : 8.253 89.950 2265 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.52 % Allowed : 16.05 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.21), residues: 1608 helix: 0.80 (0.25), residues: 489 sheet: -0.19 (0.26), residues: 342 loop : 0.09 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 410 TYR 0.013 0.001 TYR A 93 PHE 0.031 0.001 PHE C 513 TRP 0.007 0.001 TRP C 556 HIS 0.009 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00266 (13881) covalent geometry : angle 0.50640 (18786) SS BOND : bond 0.00334 ( 12) SS BOND : angle 1.07707 ( 24) hydrogen bonds : bond 0.03097 ( 399) hydrogen bonds : angle 4.58825 ( 1098) metal coordination : bond 0.00408 ( 24) metal coordination : angle 2.49432 ( 36) Misc. bond : bond 0.00017 ( 15) link_NAG-ASN : bond 0.00073 ( 12) link_NAG-ASN : angle 1.61516 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3675.14 seconds wall clock time: 63 minutes 42.02 seconds (3822.02 seconds total)