Starting phenix.real_space_refine on Thu Feb 5 00:09:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e3q_47494/02_2026/9e3q_47494.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e3q_47494/02_2026/9e3q_47494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e3q_47494/02_2026/9e3q_47494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e3q_47494/02_2026/9e3q_47494.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e3q_47494/02_2026/9e3q_47494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e3q_47494/02_2026/9e3q_47494.map" } resolution = 2.53 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= 0.019 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 6 5.49 5 S 102 5.16 5 Na 1 4.78 5 C 8568 2.51 5 N 2283 2.21 5 O 2656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 13622 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4366 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 510} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 4366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4366 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 510} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 4366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4366 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 510} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 83 Unusual residues: {' NA': 1, ' ZN': 2, 'NAG': 2, 'PLM': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PLM:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 82 Unusual residues: {' ZN': 2, 'NAG': 2, 'PLM': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PLM:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 82 Unusual residues: {' ZN': 2, 'NAG': 2, 'PLM': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PLM:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3409 SG CYS A 479 20.303 50.263 15.427 1.00 49.44 S ATOM 3565 SG CYS A 499 23.312 51.328 17.437 1.00 40.42 S ATOM 3624 SG CYS A 506 23.712 49.633 13.976 1.00 48.36 S ATOM 4162 SG CYS A 572 22.634 47.632 17.000 1.00 37.32 S ATOM 3394 SG CYS A 477 16.714 49.773 16.234 1.00 47.57 S ATOM 3409 SG CYS A 479 20.303 50.263 15.427 1.00 49.44 S ATOM 3427 SG CYS A 482 19.189 47.366 17.765 1.00 44.55 S ATOM 3559 SG CYS A 498 19.260 50.973 18.934 1.00 38.29 S ATOM 7775 SG CYS B 479 59.234 18.772 15.685 1.00 49.44 S ATOM 7931 SG CYS B 499 56.804 20.862 17.673 1.00 40.42 S ATOM 7990 SG CYS B 506 58.076 22.025 14.203 1.00 48.36 S ATOM 8528 SG CYS B 572 60.344 22.121 17.230 1.00 37.32 S ATOM 7760 SG CYS B 477 61.453 15.917 16.521 1.00 47.57 S ATOM 7775 SG CYS B 479 59.234 18.772 15.685 1.00 49.44 S ATOM 7793 SG CYS B 482 62.297 19.278 18.023 1.00 44.55 S ATOM 7925 SG CYS B 498 59.137 17.545 19.203 1.00 38.29 S ATOM 12141 SG CYS C 479 67.022 68.221 15.501 1.00 49.44 S ATOM 12297 SG CYS C 499 66.425 65.089 17.517 1.00 40.42 S ATOM 12356 SG CYS C 506 64.785 65.577 14.041 1.00 48.36 S ATOM 12894 SG CYS C 572 63.566 67.521 17.048 1.00 37.32 S ATOM 12126 SG CYS C 477 68.384 71.577 16.307 1.00 47.57 S ATOM 12141 SG CYS C 479 67.022 68.221 15.501 1.00 49.44 S ATOM 12159 SG CYS C 482 65.050 70.641 17.814 1.00 44.55 S ATOM 12291 SG CYS C 498 68.129 68.782 19.015 1.00 38.29 S Time building chain proxies: 2.86, per 1000 atoms: 0.21 Number of scatterers: 13622 At special positions: 0 Unit cell: (92.016, 94.608, 161.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 102 16.00 P 6 15.00 Na 1 11.00 O 2656 8.00 N 2283 7.00 C 8568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 226 " distance=2.04 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 226 " distance=2.04 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 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 704 " - " ASN A 187 " " NAG A 705 " - " ASN A 241 " " NAG B 704 " - " ASN B 187 " " NAG B 705 " - " ASN B 241 " " NAG C 704 " - " ASN C 187 " " NAG C 705 " - " ASN C 241 " Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 521.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 499 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 506 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 572 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 479 " pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 479 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 498 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 482 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 477 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 499 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 506 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 572 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 479 " pdb=" ZN B 703 " pdb="ZN ZN B 703 " - pdb=" SG CYS B 479 " pdb="ZN ZN B 703 " - pdb=" SG CYS B 498 " pdb="ZN ZN B 703 " - pdb=" SG CYS B 482 " pdb="ZN ZN B 703 " - pdb=" SG CYS B 477 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 499 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 506 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 572 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 479 " pdb=" ZN C 703 " pdb="ZN ZN C 703 " - pdb=" SG CYS C 479 " pdb="ZN ZN C 703 " - pdb=" SG CYS C 498 " pdb="ZN ZN C 703 " - pdb=" SG CYS C 482 " pdb="ZN ZN C 703 " - pdb=" SG CYS C 477 " Number of angles added : 36 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 21 sheets defined 36.4% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 23 through 48 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 263 through 267 removed outlier: 4.016A pdb=" N HIS A 267 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.762A pdb=" N CYS A 374 " --> pdb=" O CYS A 371 " (cutoff:3.500A) Proline residue: A 376 - end of helix Processing helix chain 'A' and resid 378 through 387 removed outlier: 4.014A pdb=" N TYR A 382 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 491 through 496 removed outlier: 4.322A pdb=" N GLU A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 510 through 517 removed outlier: 3.900A pdb=" N HIS A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 531 Processing helix chain 'A' and resid 537 through 559 Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'B' and resid 7 through 11 Processing helix chain 'B' and resid 23 through 48 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 231 through 238 Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 263 through 267 removed outlier: 4.016A pdb=" N HIS B 267 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 340 through 344 Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 371 through 377 removed outlier: 3.762A pdb=" N CYS B 374 " --> pdb=" O CYS B 371 " (cutoff:3.500A) Proline residue: B 376 - end of helix Processing helix chain 'B' and resid 378 through 387 removed outlier: 4.014A pdb=" N TYR B 382 " --> pdb=" O THR B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 491 through 496 removed outlier: 4.322A pdb=" N GLU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 509 Processing helix chain 'B' and resid 510 through 517 removed outlier: 3.900A pdb=" N HIS B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 531 Processing helix chain 'B' and resid 537 through 559 Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 570 through 581 Processing helix chain 'C' and resid 7 through 11 Processing helix chain 'C' and resid 23 through 48 Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 231 through 238 Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 263 through 267 removed outlier: 4.016A pdb=" N HIS C 267 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 340 through 344 Processing helix chain 'C' and resid 345 through 358 Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 371 through 377 removed outlier: 3.761A pdb=" N CYS C 374 " --> pdb=" O CYS C 371 " (cutoff:3.500A) Proline residue: C 376 - end of helix Processing helix chain 'C' and resid 378 through 387 removed outlier: 4.014A pdb=" N TYR C 382 " --> pdb=" O THR C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 490 No H-bonds generated for 'chain 'C' and resid 488 through 490' Processing helix chain 'C' and resid 491 through 496 removed outlier: 4.322A pdb=" N GLU C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 509 Processing helix chain 'C' and resid 510 through 517 removed outlier: 3.901A pdb=" N HIS C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 531 Processing helix chain 'C' and resid 537 through 559 Processing helix chain 'C' and resid 560 through 565 Processing helix chain 'C' 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 'B' and resid 13 through 16 removed outlier: 6.608A pdb=" N VAL A 18 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE C 391 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ARG A 20 " --> pdb=" O ILE C 391 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 137 through 140 removed outlier: 5.261A pdb=" N GLN A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ILE A 147 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N TRP A 167 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR A 149 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N SER A 165 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ARG A 151 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE A 313 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR A 108 " --> pdb=" O LYS A 311 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS A 311 " --> pdb=" O TYR A 108 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS A 110 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU A 309 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU A 112 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ARG A 307 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLN A 114 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU A 305 " --> pdb=" O GLN A 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 66 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 66 Processing sheet with id=AA7, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA8, first strand: chain 'A' and resid 388 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 400 through 402 Processing sheet with id=AB1, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AB2, first strand: chain 'B' and resid 137 through 140 removed outlier: 5.261A pdb=" N GLN B 148 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N ILE B 147 " --> pdb=" O TRP B 167 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N TRP B 167 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR B 149 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N SER B 165 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG B 151 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE B 313 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR B 108 " --> pdb=" O LYS B 311 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS B 311 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS B 110 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 309 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU B 112 " --> pdb=" O ARG B 307 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ARG B 307 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLN B 114 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU B 305 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 58 through 66 Processing sheet with id=AB4, first strand: chain 'B' and resid 58 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 400 through 402 Processing sheet with id=AB7, first strand: chain 'C' and resid 52 through 56 Processing sheet with id=AB8, first strand: chain 'C' and resid 137 through 140 removed outlier: 5.261A pdb=" N GLN C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ILE C 147 " --> pdb=" O TRP C 167 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N TRP C 167 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR C 149 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N SER C 165 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG C 151 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE C 313 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR C 108 " --> pdb=" O LYS C 311 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS C 311 " --> pdb=" O TYR C 108 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS C 110 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU C 309 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU C 112 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ARG C 307 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLN C 114 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU C 305 " --> pdb=" O GLN C 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 66 Processing sheet with id=AC1, first strand: chain 'C' and resid 58 through 66 Processing sheet with id=AC2, first strand: chain 'C' and resid 69 through 71 Processing sheet with id=AC3, first strand: chain 'C' and resid 400 through 402 594 hydrogen bonds defined for protein. 1593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4225 1.34 - 1.46: 3354 1.46 - 1.58: 6041 1.58 - 1.70: 9 1.70 - 1.82: 126 Bond restraints: 13755 Sorted by residual: bond pdb=" N ASN C 107 " pdb=" CA ASN C 107 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.50e+00 bond pdb=" N ASN A 107 " pdb=" CA ASN A 107 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.37e+00 bond pdb=" N ASP A 413 " pdb=" CA ASP A 413 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.35e+00 bond pdb=" N ASN B 107 " pdb=" CA ASN B 107 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.25e+00 bond pdb=" N ASP B 413 " pdb=" CA ASP B 413 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.25e+00 ... (remaining 13750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 17686 1.38 - 2.76: 658 2.76 - 4.13: 169 4.13 - 5.51: 45 5.51 - 6.89: 24 Bond angle restraints: 18582 Sorted by residual: angle pdb=" CA CYS A 373 " pdb=" C CYS A 373 " pdb=" O CYS A 373 " ideal model delta sigma weight residual 119.31 124.36 -5.05 1.24e+00 6.50e-01 1.66e+01 angle pdb=" CA CYS B 373 " pdb=" C CYS B 373 " pdb=" O CYS B 373 " ideal model delta sigma weight residual 119.31 124.33 -5.02 1.24e+00 6.50e-01 1.64e+01 angle pdb=" CA CYS C 373 " pdb=" C CYS C 373 " pdb=" O CYS C 373 " ideal model delta sigma weight residual 119.31 124.32 -5.01 1.24e+00 6.50e-01 1.63e+01 angle pdb=" CA CYS B 374 " pdb=" C CYS B 374 " pdb=" O CYS B 374 " ideal model delta sigma weight residual 119.43 124.06 -4.63 1.21e+00 6.83e-01 1.46e+01 angle pdb=" CA CYS A 374 " pdb=" C CYS A 374 " pdb=" O CYS A 374 " ideal model delta sigma weight residual 119.43 124.03 -4.60 1.21e+00 6.83e-01 1.45e+01 ... (remaining 18577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.57: 7649 22.57 - 45.14: 561 45.14 - 67.71: 103 67.71 - 90.29: 18 90.29 - 112.86: 3 Dihedral angle restraints: 8334 sinusoidal: 3585 harmonic: 4749 Sorted by residual: dihedral pdb=" C5' GDP B 701 " pdb=" O5' GDP B 701 " pdb=" PA GDP B 701 " pdb=" O3A GDP B 701 " ideal model delta sinusoidal sigma weight residual 179.98 67.12 112.86 1 2.00e+01 2.50e-03 3.33e+01 dihedral pdb=" C5' GDP A 701 " pdb=" O5' GDP A 701 " pdb=" PA GDP A 701 " pdb=" O3A GDP A 701 " ideal model delta sinusoidal sigma weight residual 179.98 67.15 112.83 1 2.00e+01 2.50e-03 3.33e+01 dihedral pdb=" C5' GDP C 701 " pdb=" O5' GDP C 701 " pdb=" PA GDP C 701 " pdb=" O3A GDP C 701 " ideal model delta sinusoidal sigma weight residual 179.98 67.15 112.83 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 8331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1299 0.037 - 0.075: 479 0.075 - 0.112: 156 0.112 - 0.150: 40 0.150 - 0.187: 6 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CA ARG C 53 " pdb=" N ARG C 53 " pdb=" C ARG C 53 " pdb=" CB ARG C 53 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CA ARG B 53 " pdb=" N ARG B 53 " pdb=" C ARG B 53 " pdb=" CB ARG B 53 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA ARG A 53 " pdb=" N ARG A 53 " pdb=" C ARG A 53 " pdb=" CB ARG A 53 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 1977 not shown) Planarity restraints: 2346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 241 " 0.079 2.00e-02 2.50e+03 9.29e-02 1.08e+02 pdb=" CG ASN B 241 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 241 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 241 " -0.153 2.00e-02 2.50e+03 pdb=" C1 NAG B 705 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 241 " 0.079 2.00e-02 2.50e+03 9.27e-02 1.07e+02 pdb=" CG ASN A 241 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 241 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 241 " -0.153 2.00e-02 2.50e+03 pdb=" C1 NAG A 705 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 241 " 0.079 2.00e-02 2.50e+03 9.25e-02 1.07e+02 pdb=" CG ASN C 241 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN C 241 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 241 " -0.152 2.00e-02 2.50e+03 pdb=" C1 NAG C 705 " 0.111 2.00e-02 2.50e+03 ... (remaining 2343 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2153 2.76 - 3.30: 12112 3.30 - 3.83: 24015 3.83 - 4.37: 30349 4.37 - 4.90: 49253 Nonbonded interactions: 117882 Sorted by model distance: nonbonded pdb=" O CYS B 269 " pdb=" O HOH B 801 " model vdw 2.227 3.040 nonbonded pdb=" O CYS A 269 " pdb=" O HOH A 801 " model vdw 2.236 3.040 nonbonded pdb=" O CYS C 269 " pdb=" O HOH C 801 " model vdw 2.246 3.040 nonbonded pdb=" O ASP C 259 " pdb=" O HOH C 802 " model vdw 2.265 3.040 nonbonded pdb=" OG SER A 274 " pdb=" O HOH A 802 " model vdw 2.267 3.040 ... (remaining 117877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 710) selection = chain 'B' selection = chain 'C' } 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: 19.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.070 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 : 0.005 0.044 13815 Z= 0.273 Angle : 0.718 8.237 18666 Z= 0.393 Chirality : 0.045 0.187 1980 Planarity : 0.006 0.101 2340 Dihedral : 15.769 112.858 5241 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.41 % Allowed : 14.29 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.81 (0.21), residues: 1602 helix: 0.20 (0.24), residues: 444 sheet: 0.23 (0.26), residues: 360 loop : 1.15 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 307 TYR 0.010 0.001 TYR C 336 PHE 0.014 0.002 PHE C 275 TRP 0.013 0.002 TRP C 575 HIS 0.003 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00474 (13755) covalent geometry : angle 0.69633 (18582) SS BOND : bond 0.00250 ( 15) SS BOND : angle 0.93924 ( 30) hydrogen bonds : bond 0.19238 ( 564) hydrogen bonds : angle 7.87988 ( 1593) metal coordination : bond 0.00358 ( 24) metal coordination : angle 2.55277 ( 36) Misc. bond : bond 0.03510 ( 15) link_NAG-ASN : bond 0.02649 ( 6) link_NAG-ASN : angle 4.45059 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 ARG cc_start: 0.7892 (mtp180) cc_final: 0.7688 (mtt180) REVERT: A 592 LYS cc_start: 0.7955 (pttt) cc_final: 0.7306 (ptmm) REVERT: B 592 LYS cc_start: 0.7896 (pttt) cc_final: 0.7261 (ptmm) REVERT: C 592 LYS cc_start: 0.7956 (pttt) cc_final: 0.7284 (ptmm) outliers start: 6 outliers final: 5 residues processed: 156 average time/residue: 0.8285 time to fit residues: 138.8088 Evaluate side-chains 126 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain C residue 363 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 85 HIS A 100 ASN A 408 HIS ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS B 100 ASN C 22 GLN C 85 HIS C 100 ASN C 408 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.154670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107401 restraints weight = 11798.924| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.52 r_work: 0.2989 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13815 Z= 0.146 Angle : 0.560 6.086 18666 Z= 0.278 Chirality : 0.043 0.135 1980 Planarity : 0.005 0.046 2340 Dihedral : 7.812 117.869 2066 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.86 % Allowed : 15.18 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.21), residues: 1602 helix: 1.09 (0.25), residues: 432 sheet: 0.16 (0.26), residues: 363 loop : 1.24 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 544 TYR 0.011 0.001 TYR C 336 PHE 0.015 0.002 PHE C 275 TRP 0.012 0.002 TRP C 575 HIS 0.003 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00330 (13755) covalent geometry : angle 0.53496 (18582) SS BOND : bond 0.00321 ( 15) SS BOND : angle 0.99295 ( 30) hydrogen bonds : bond 0.04121 ( 564) hydrogen bonds : angle 5.44363 ( 1593) metal coordination : bond 0.00353 ( 24) metal coordination : angle 3.05680 ( 36) Misc. bond : bond 0.00040 ( 15) link_NAG-ASN : bond 0.00173 ( 6) link_NAG-ASN : angle 2.99615 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7340 (mtp180) REVERT: A 592 LYS cc_start: 0.7905 (pttt) cc_final: 0.7072 (ptmm) REVERT: B 143 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6897 (mm-40) REVERT: B 217 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8360 (t) REVERT: B 284 ASP cc_start: 0.7867 (t0) cc_final: 0.7656 (t70) REVERT: B 385 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7379 (mtp180) REVERT: B 592 LYS cc_start: 0.7846 (pttt) cc_final: 0.7018 (ptmm) REVERT: C 174 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6967 (mtpt) REVERT: C 385 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7397 (ttm110) outliers start: 27 outliers final: 12 residues processed: 148 average time/residue: 0.7901 time to fit residues: 125.5684 Evaluate side-chains 149 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 525 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 60 optimal weight: 0.9980 chunk 40 optimal weight: 0.0030 chunk 119 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.0060 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 408 HIS B 100 ASN C 100 ASN C 408 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.156363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.107050 restraints weight = 11973.695| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.57 r_work: 0.3025 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13815 Z= 0.107 Angle : 0.506 6.298 18666 Z= 0.249 Chirality : 0.042 0.132 1980 Planarity : 0.004 0.047 2340 Dihedral : 7.193 109.313 2064 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.07 % Allowed : 15.73 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.22), residues: 1602 helix: 1.39 (0.26), residues: 432 sheet: 0.15 (0.26), residues: 363 loop : 1.26 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 20 TYR 0.010 0.001 TYR C 336 PHE 0.011 0.001 PHE C 275 TRP 0.011 0.001 TRP A 575 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00233 (13755) covalent geometry : angle 0.48499 (18582) SS BOND : bond 0.00321 ( 15) SS BOND : angle 0.96827 ( 30) hydrogen bonds : bond 0.03415 ( 564) hydrogen bonds : angle 5.03321 ( 1593) metal coordination : bond 0.00288 ( 24) metal coordination : angle 2.82969 ( 36) Misc. bond : bond 0.00015 ( 15) link_NAG-ASN : bond 0.00100 ( 6) link_NAG-ASN : angle 2.36206 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7732 (t0) cc_final: 0.7504 (t0) REVERT: A 385 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7231 (mtp180) REVERT: A 511 LYS cc_start: 0.6449 (OUTLIER) cc_final: 0.6119 (ptmm) REVERT: A 544 ARG cc_start: 0.7511 (mtt90) cc_final: 0.7213 (mmm-85) REVERT: B 284 ASP cc_start: 0.7642 (t0) cc_final: 0.7374 (t0) REVERT: B 385 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7270 (mtp180) REVERT: B 429 VAL cc_start: 0.7212 (t) cc_final: 0.6914 (m) REVERT: B 511 LYS cc_start: 0.6552 (OUTLIER) cc_final: 0.6227 (ptmm) REVERT: B 579 LYS cc_start: 0.8280 (ptmt) cc_final: 0.7512 (ptpp) REVERT: B 592 LYS cc_start: 0.7750 (pttt) cc_final: 0.6933 (ptmm) REVERT: C 174 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6819 (mtpt) REVERT: C 284 ASP cc_start: 0.7801 (t70) cc_final: 0.7575 (t0) REVERT: C 305 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6778 (tm-30) REVERT: C 385 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7371 (ttm110) REVERT: C 392 MET cc_start: 0.8501 (mmm) cc_final: 0.8296 (tpp) outliers start: 30 outliers final: 9 residues processed: 152 average time/residue: 0.7358 time to fit residues: 119.9558 Evaluate side-chains 150 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 525 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 111 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 161 optimal weight: 0.0970 chunk 157 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 96 optimal weight: 0.0970 chunk 120 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 408 HIS B 100 ASN C 100 ASN C 408 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.156263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.106941 restraints weight = 11967.476| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.57 r_work: 0.3021 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13815 Z= 0.109 Angle : 0.507 6.613 18666 Z= 0.247 Chirality : 0.042 0.133 1980 Planarity : 0.004 0.047 2340 Dihedral : 7.113 109.933 2064 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.86 % Allowed : 16.63 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.22), residues: 1602 helix: 1.52 (0.26), residues: 432 sheet: 0.19 (0.27), residues: 363 loop : 1.29 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 501 TYR 0.011 0.001 TYR C 336 PHE 0.011 0.001 PHE B 102 TRP 0.011 0.001 TRP C 575 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00241 (13755) covalent geometry : angle 0.48717 (18582) SS BOND : bond 0.00326 ( 15) SS BOND : angle 0.98368 ( 30) hydrogen bonds : bond 0.03254 ( 564) hydrogen bonds : angle 4.89770 ( 1593) metal coordination : bond 0.00284 ( 24) metal coordination : angle 2.74111 ( 36) Misc. bond : bond 0.00012 ( 15) link_NAG-ASN : bond 0.00084 ( 6) link_NAG-ASN : angle 2.21640 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7731 (t0) cc_final: 0.7482 (t0) REVERT: A 385 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7339 (ttm110) REVERT: A 511 LYS cc_start: 0.6413 (OUTLIER) cc_final: 0.6068 (ptmm) REVERT: A 544 ARG cc_start: 0.7504 (mtt90) cc_final: 0.7209 (mmm-85) REVERT: B 143 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6897 (mm-40) REVERT: B 217 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8288 (t) REVERT: B 284 ASP cc_start: 0.7621 (t0) cc_final: 0.7319 (t0) REVERT: B 385 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7287 (mtp180) REVERT: B 429 VAL cc_start: 0.7196 (t) cc_final: 0.6901 (m) REVERT: B 579 LYS cc_start: 0.8236 (ptmt) cc_final: 0.7517 (ptpp) REVERT: B 592 LYS cc_start: 0.7770 (pttt) cc_final: 0.6948 (ptmm) REVERT: C 174 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6879 (mtpt) REVERT: C 217 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8281 (t) REVERT: C 284 ASP cc_start: 0.7758 (t70) cc_final: 0.7515 (t0) REVERT: C 305 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6752 (tm-30) REVERT: C 385 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7376 (ttm110) REVERT: C 392 MET cc_start: 0.8500 (mmm) cc_final: 0.8298 (tpp) REVERT: C 429 VAL cc_start: 0.7288 (t) cc_final: 0.6966 (m) outliers start: 27 outliers final: 11 residues processed: 150 average time/residue: 0.7752 time to fit residues: 124.8476 Evaluate side-chains 149 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 525 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 150 optimal weight: 0.0030 chunk 34 optimal weight: 4.9990 chunk 129 optimal weight: 0.0670 chunk 41 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 119 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 overall best weight: 0.4328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 HIS B 100 ASN B 356 ASN C 100 ASN C 408 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.156510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.107202 restraints weight = 11970.062| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.57 r_work: 0.3026 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13815 Z= 0.107 Angle : 0.500 6.987 18666 Z= 0.243 Chirality : 0.042 0.133 1980 Planarity : 0.004 0.048 2340 Dihedral : 7.035 109.384 2064 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.79 % Allowed : 16.77 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.22), residues: 1602 helix: 1.66 (0.25), residues: 429 sheet: 0.12 (0.26), residues: 381 loop : 1.30 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.011 0.001 TYR C 336 PHE 0.012 0.001 PHE B 102 TRP 0.010 0.001 TRP C 575 HIS 0.002 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00236 (13755) covalent geometry : angle 0.48118 (18582) SS BOND : bond 0.00313 ( 15) SS BOND : angle 0.98118 ( 30) hydrogen bonds : bond 0.03131 ( 564) hydrogen bonds : angle 4.83732 ( 1593) metal coordination : bond 0.00266 ( 24) metal coordination : angle 2.68349 ( 36) Misc. bond : bond 0.00013 ( 15) link_NAG-ASN : bond 0.00081 ( 6) link_NAG-ASN : angle 2.11871 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7700 (t0) cc_final: 0.7414 (t0) REVERT: A 305 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6785 (tm-30) REVERT: A 385 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7337 (ttm170) REVERT: A 501 ARG cc_start: 0.7313 (tpt170) cc_final: 0.7081 (tpt170) REVERT: A 511 LYS cc_start: 0.6442 (OUTLIER) cc_final: 0.6083 (ptmm) REVERT: A 544 ARG cc_start: 0.7504 (mtt90) cc_final: 0.7207 (mmm-85) REVERT: B 143 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6923 (mm-40) REVERT: B 175 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6522 (pp20) REVERT: B 217 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8294 (t) REVERT: B 284 ASP cc_start: 0.7608 (t0) cc_final: 0.7379 (t0) REVERT: B 305 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6689 (tp30) REVERT: B 385 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7309 (mtp180) REVERT: B 511 LYS cc_start: 0.6569 (OUTLIER) cc_final: 0.6295 (ptmm) REVERT: B 579 LYS cc_start: 0.8220 (ptmt) cc_final: 0.7526 (ptpp) REVERT: B 592 LYS cc_start: 0.7751 (pttt) cc_final: 0.6913 (ptmm) REVERT: C 174 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6823 (mtpt) REVERT: C 217 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8259 (t) REVERT: C 284 ASP cc_start: 0.7687 (t70) cc_final: 0.7438 (t0) REVERT: C 305 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6772 (tm-30) REVERT: C 385 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7365 (ttm110) REVERT: C 429 VAL cc_start: 0.7259 (t) cc_final: 0.6952 (m) outliers start: 26 outliers final: 10 residues processed: 160 average time/residue: 0.7761 time to fit residues: 133.2530 Evaluate side-chains 159 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 525 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 50 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 144 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN C 100 ASN C 356 ASN C 408 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.152859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.103038 restraints weight = 11959.762| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.56 r_work: 0.2963 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13815 Z= 0.215 Angle : 0.606 7.701 18666 Z= 0.296 Chirality : 0.046 0.151 1980 Planarity : 0.005 0.048 2340 Dihedral : 8.414 138.414 2064 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.14 % Allowed : 17.39 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.21), residues: 1602 helix: 1.44 (0.25), residues: 432 sheet: 0.10 (0.25), residues: 381 loop : 1.19 (0.24), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 20 TYR 0.018 0.002 TYR C 336 PHE 0.018 0.003 PHE C 275 TRP 0.012 0.002 TRP B 575 HIS 0.006 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00502 (13755) covalent geometry : angle 0.58364 (18582) SS BOND : bond 0.00354 ( 15) SS BOND : angle 1.17604 ( 30) hydrogen bonds : bond 0.04011 ( 564) hydrogen bonds : angle 5.20227 ( 1593) metal coordination : bond 0.00465 ( 24) metal coordination : angle 3.11056 ( 36) Misc. bond : bond 0.00039 ( 15) link_NAG-ASN : bond 0.00235 ( 6) link_NAG-ASN : angle 2.78663 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.378 Fit side-chains REVERT: A 284 ASP cc_start: 0.7777 (t0) cc_final: 0.7503 (t0) REVERT: A 385 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7291 (ttm110) REVERT: A 543 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7391 (p) REVERT: A 592 LYS cc_start: 0.7889 (pttt) cc_final: 0.7063 (ptmm) REVERT: B 143 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6909 (mm-40) REVERT: B 217 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8343 (t) REVERT: B 284 ASP cc_start: 0.7741 (t0) cc_final: 0.7404 (t0) REVERT: B 411 MET cc_start: 0.8804 (ttm) cc_final: 0.8498 (ttp) REVERT: B 511 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.6275 (ptmt) REVERT: B 515 LYS cc_start: 0.7890 (ttmt) cc_final: 0.7603 (ttmm) REVERT: B 548 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7587 (tpt170) REVERT: B 579 LYS cc_start: 0.8264 (ptmt) cc_final: 0.7546 (ptpp) REVERT: B 592 LYS cc_start: 0.7864 (pttt) cc_final: 0.7050 (ptmm) REVERT: C 284 ASP cc_start: 0.7814 (t70) cc_final: 0.7567 (t0) REVERT: C 305 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6780 (tm-30) REVERT: C 385 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7305 (ttm110) REVERT: C 592 LYS cc_start: 0.7823 (pttt) cc_final: 0.6974 (ptmm) outliers start: 31 outliers final: 17 residues processed: 151 average time/residue: 0.6901 time to fit residues: 112.0776 Evaluate side-chains 152 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 525 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 50 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 0.3980 chunk 149 optimal weight: 0.0470 chunk 148 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN C 100 ASN C 408 HIS C 561 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.155170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.105924 restraints weight = 11904.799| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.55 r_work: 0.3008 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13815 Z= 0.122 Angle : 0.524 7.557 18666 Z= 0.255 Chirality : 0.042 0.133 1980 Planarity : 0.004 0.051 2340 Dihedral : 7.483 117.467 2064 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.66 % Allowed : 17.67 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.22), residues: 1602 helix: 1.57 (0.25), residues: 432 sheet: 0.13 (0.26), residues: 381 loop : 1.25 (0.24), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 20 TYR 0.012 0.001 TYR C 336 PHE 0.012 0.002 PHE C 275 TRP 0.011 0.001 TRP C 575 HIS 0.005 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00274 (13755) covalent geometry : angle 0.50368 (18582) SS BOND : bond 0.00319 ( 15) SS BOND : angle 1.05845 ( 30) hydrogen bonds : bond 0.03265 ( 564) hydrogen bonds : angle 4.95430 ( 1593) metal coordination : bond 0.00288 ( 24) metal coordination : angle 2.84390 ( 36) Misc. bond : bond 0.00015 ( 15) link_NAG-ASN : bond 0.00079 ( 6) link_NAG-ASN : angle 2.25858 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7696 (t0) cc_final: 0.7429 (t0) REVERT: A 305 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6756 (tm-30) REVERT: A 385 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7352 (ttm110) REVERT: A 511 LYS cc_start: 0.6469 (OUTLIER) cc_final: 0.6126 (ptmm) REVERT: B 143 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6892 (mm-40) REVERT: B 175 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6495 (pp20) REVERT: B 217 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8295 (t) REVERT: B 284 ASP cc_start: 0.7676 (t0) cc_final: 0.7431 (t0) REVERT: B 305 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6655 (tp30) REVERT: B 511 LYS cc_start: 0.6604 (OUTLIER) cc_final: 0.6325 (ptmm) REVERT: B 515 LYS cc_start: 0.7847 (ttmt) cc_final: 0.7572 (ttmm) REVERT: B 579 LYS cc_start: 0.8253 (ptmt) cc_final: 0.7529 (ptpp) REVERT: B 592 LYS cc_start: 0.7773 (pttt) cc_final: 0.6969 (ptmm) REVERT: C 174 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6848 (mtpt) REVERT: C 217 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8353 (t) REVERT: C 284 ASP cc_start: 0.7696 (t70) cc_final: 0.7482 (t0) REVERT: C 305 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6798 (tm-30) REVERT: C 385 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7378 (ttm110) REVERT: C 543 SER cc_start: 0.7716 (OUTLIER) cc_final: 0.7282 (p) REVERT: C 548 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7619 (tpt170) outliers start: 24 outliers final: 10 residues processed: 149 average time/residue: 0.6549 time to fit residues: 104.9701 Evaluate side-chains 151 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 548 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 68 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 100 ASN B 356 ASN C 100 ASN C 408 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.153109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.103473 restraints weight = 11861.437| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.56 r_work: 0.2968 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13815 Z= 0.197 Angle : 0.586 7.956 18666 Z= 0.287 Chirality : 0.045 0.137 1980 Planarity : 0.005 0.050 2340 Dihedral : 8.265 133.636 2064 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.79 % Allowed : 17.74 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.21), residues: 1602 helix: 1.47 (0.25), residues: 432 sheet: 0.14 (0.26), residues: 378 loop : 1.19 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 20 TYR 0.017 0.002 TYR C 336 PHE 0.017 0.002 PHE C 275 TRP 0.012 0.002 TRP B 575 HIS 0.005 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00463 (13755) covalent geometry : angle 0.56335 (18582) SS BOND : bond 0.00357 ( 15) SS BOND : angle 1.19357 ( 30) hydrogen bonds : bond 0.03830 ( 564) hydrogen bonds : angle 5.15252 ( 1593) metal coordination : bond 0.00429 ( 24) metal coordination : angle 3.11051 ( 36) Misc. bond : bond 0.00033 ( 15) link_NAG-ASN : bond 0.00215 ( 6) link_NAG-ASN : angle 2.66329 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.519 Fit side-chains REVERT: A 284 ASP cc_start: 0.7758 (t0) cc_final: 0.7467 (t0) REVERT: A 305 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6775 (tm-30) REVERT: A 385 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7263 (ttm110) REVERT: A 511 LYS cc_start: 0.6552 (OUTLIER) cc_final: 0.6275 (ptmt) REVERT: A 543 SER cc_start: 0.7863 (OUTLIER) cc_final: 0.7399 (p) REVERT: A 544 ARG cc_start: 0.7611 (mtt90) cc_final: 0.7395 (mmm-85) REVERT: A 548 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7523 (tpt170) REVERT: A 592 LYS cc_start: 0.7861 (pttt) cc_final: 0.7032 (ptmm) REVERT: B 143 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6926 (mm-40) REVERT: B 217 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8354 (t) REVERT: B 284 ASP cc_start: 0.7729 (t0) cc_final: 0.7374 (t0) REVERT: B 305 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6646 (tp30) REVERT: B 385 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7418 (ttm170) REVERT: B 511 LYS cc_start: 0.6629 (OUTLIER) cc_final: 0.6377 (ptmt) REVERT: B 515 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7667 (ttmm) REVERT: B 579 LYS cc_start: 0.8267 (ptmt) cc_final: 0.7548 (ptpp) REVERT: B 592 LYS cc_start: 0.7843 (pttt) cc_final: 0.7040 (ptmm) REVERT: C 284 ASP cc_start: 0.7752 (t70) cc_final: 0.7516 (t0) REVERT: C 305 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6772 (tm-30) REVERT: C 543 SER cc_start: 0.7761 (OUTLIER) cc_final: 0.7279 (p) REVERT: C 548 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7673 (tpt170) REVERT: C 592 LYS cc_start: 0.7830 (pttt) cc_final: 0.6987 (ptmm) outliers start: 26 outliers final: 13 residues processed: 147 average time/residue: 0.7598 time to fit residues: 119.5749 Evaluate side-chains 154 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 548 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.4980 chunk 25 optimal weight: 0.0060 chunk 129 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN C 100 ASN C 408 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.155094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.105781 restraints weight = 12015.002| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.56 r_work: 0.3004 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13815 Z= 0.123 Angle : 0.527 7.780 18666 Z= 0.257 Chirality : 0.043 0.133 1980 Planarity : 0.004 0.051 2340 Dihedral : 7.529 117.312 2064 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.79 % Allowed : 18.15 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.21), residues: 1602 helix: 1.58 (0.25), residues: 432 sheet: 0.10 (0.26), residues: 381 loop : 1.20 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 501 TYR 0.012 0.001 TYR C 336 PHE 0.013 0.002 PHE C 275 TRP 0.011 0.001 TRP C 575 HIS 0.004 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00276 (13755) covalent geometry : angle 0.50695 (18582) SS BOND : bond 0.00316 ( 15) SS BOND : angle 1.08768 ( 30) hydrogen bonds : bond 0.03271 ( 564) hydrogen bonds : angle 4.95008 ( 1593) metal coordination : bond 0.00286 ( 24) metal coordination : angle 2.82992 ( 36) Misc. bond : bond 0.00015 ( 15) link_NAG-ASN : bond 0.00068 ( 6) link_NAG-ASN : angle 2.24346 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.430 Fit side-chains REVERT: A 284 ASP cc_start: 0.7690 (t0) cc_final: 0.7420 (t0) REVERT: A 305 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6760 (tm-30) REVERT: A 385 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7356 (ttm110) REVERT: A 511 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.6230 (ptmt) REVERT: A 543 SER cc_start: 0.7800 (OUTLIER) cc_final: 0.7409 (p) REVERT: A 544 ARG cc_start: 0.7549 (mtt90) cc_final: 0.7330 (mmm-85) REVERT: A 548 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7463 (tpt170) REVERT: B 143 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6873 (mm-40) REVERT: B 175 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6532 (pp20) REVERT: B 217 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8290 (t) REVERT: B 284 ASP cc_start: 0.7678 (t0) cc_final: 0.7419 (t0) REVERT: B 305 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6640 (tp30) REVERT: B 385 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7449 (ttm110) REVERT: B 511 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.6306 (ptmt) REVERT: B 515 LYS cc_start: 0.7909 (ttmt) cc_final: 0.7637 (ttmm) REVERT: B 543 SER cc_start: 0.7703 (OUTLIER) cc_final: 0.7306 (p) REVERT: B 579 LYS cc_start: 0.8255 (ptmt) cc_final: 0.7538 (ptpp) REVERT: B 592 LYS cc_start: 0.7792 (pttt) cc_final: 0.6993 (ptmm) REVERT: C 174 LYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6952 (mtpt) REVERT: C 217 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8358 (t) REVERT: C 284 ASP cc_start: 0.7696 (t70) cc_final: 0.7484 (t0) REVERT: C 305 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6763 (tm-30) REVERT: C 385 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7407 (ttm110) REVERT: C 543 SER cc_start: 0.7721 (OUTLIER) cc_final: 0.7283 (p) REVERT: C 548 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7628 (tpt170) outliers start: 26 outliers final: 10 residues processed: 152 average time/residue: 0.7653 time to fit residues: 124.7522 Evaluate side-chains 159 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 548 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 27 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 100 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN C 100 ASN C 408 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.154954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.105609 restraints weight = 11850.663| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.55 r_work: 0.3003 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13815 Z= 0.132 Angle : 0.539 7.858 18666 Z= 0.262 Chirality : 0.043 0.135 1980 Planarity : 0.004 0.051 2340 Dihedral : 7.556 118.300 2064 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.73 % Allowed : 18.36 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.22), residues: 1602 helix: 1.81 (0.26), residues: 414 sheet: 0.09 (0.26), residues: 381 loop : 1.16 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 20 TYR 0.013 0.001 TYR C 336 PHE 0.014 0.002 PHE C 275 TRP 0.012 0.002 TRP C 575 HIS 0.004 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00300 (13755) covalent geometry : angle 0.51827 (18582) SS BOND : bond 0.00328 ( 15) SS BOND : angle 1.10684 ( 30) hydrogen bonds : bond 0.03332 ( 564) hydrogen bonds : angle 4.96576 ( 1593) metal coordination : bond 0.00298 ( 24) metal coordination : angle 2.86846 ( 36) Misc. bond : bond 0.00016 ( 15) link_NAG-ASN : bond 0.00114 ( 6) link_NAG-ASN : angle 2.27952 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.555 Fit side-chains REVERT: A 284 ASP cc_start: 0.7677 (t0) cc_final: 0.7412 (t0) REVERT: A 305 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6772 (tm-30) REVERT: A 385 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7258 (mtp180) REVERT: A 511 LYS cc_start: 0.6551 (OUTLIER) cc_final: 0.6230 (ptmt) REVERT: A 543 SER cc_start: 0.7809 (OUTLIER) cc_final: 0.7409 (p) REVERT: A 544 ARG cc_start: 0.7561 (mtt90) cc_final: 0.7342 (mmm-85) REVERT: A 548 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7472 (tpt170) REVERT: B 143 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6932 (mm-40) REVERT: B 175 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6434 (pp20) REVERT: B 217 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8304 (t) REVERT: B 284 ASP cc_start: 0.7673 (t0) cc_final: 0.7411 (t0) REVERT: B 305 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6646 (tp30) REVERT: B 385 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7514 (ttm170) REVERT: B 511 LYS cc_start: 0.6588 (OUTLIER) cc_final: 0.6312 (ptmt) REVERT: B 515 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7652 (ttmm) REVERT: B 543 SER cc_start: 0.7722 (OUTLIER) cc_final: 0.7308 (p) REVERT: B 579 LYS cc_start: 0.8244 (ptmt) cc_final: 0.7536 (ptpp) REVERT: B 592 LYS cc_start: 0.7789 (pttt) cc_final: 0.6980 (ptmm) REVERT: C 174 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6886 (mtpt) REVERT: C 284 ASP cc_start: 0.7678 (t70) cc_final: 0.7467 (t0) REVERT: C 305 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6780 (tm-30) REVERT: C 385 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7414 (ttm110) REVERT: C 543 SER cc_start: 0.7735 (OUTLIER) cc_final: 0.7291 (p) REVERT: C 548 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7622 (tpt170) outliers start: 25 outliers final: 11 residues processed: 148 average time/residue: 0.7394 time to fit residues: 117.6732 Evaluate side-chains 155 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 548 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 356 ASN C 408 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.154471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.104911 restraints weight = 11933.170| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.56 r_work: 0.2991 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13815 Z= 0.149 Angle : 0.551 7.916 18666 Z= 0.269 Chirality : 0.043 0.135 1980 Planarity : 0.005 0.050 2340 Dihedral : 7.775 122.987 2064 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.79 % Allowed : 18.50 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.21), residues: 1602 helix: 1.55 (0.25), residues: 432 sheet: 0.09 (0.26), residues: 381 loop : 1.19 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 20 TYR 0.014 0.001 TYR C 336 PHE 0.015 0.002 PHE C 275 TRP 0.012 0.002 TRP C 575 HIS 0.004 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00342 (13755) covalent geometry : angle 0.52946 (18582) SS BOND : bond 0.00336 ( 15) SS BOND : angle 1.13246 ( 30) hydrogen bonds : bond 0.03454 ( 564) hydrogen bonds : angle 5.03010 ( 1593) metal coordination : bond 0.00329 ( 24) metal coordination : angle 2.93721 ( 36) Misc. bond : bond 0.00020 ( 15) link_NAG-ASN : bond 0.00140 ( 6) link_NAG-ASN : angle 2.37435 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5507.78 seconds wall clock time: 94 minutes 31.71 seconds (5671.71 seconds total)