Starting phenix.real_space_refine on Wed Nov 19 19:39:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mat_9063/11_2025/6mat_9063.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mat_9063/11_2025/6mat_9063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mat_9063/11_2025/6mat_9063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mat_9063/11_2025/6mat_9063.map" model { file = "/net/cci-nas-00/data/ceres_data/6mat_9063/11_2025/6mat_9063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mat_9063/11_2025/6mat_9063.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 33 5.49 5 S 124 5.16 5 C 16811 2.51 5 N 4824 2.21 5 O 5238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27030 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4454 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 4454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4454 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4454 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 4454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4454 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 4369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4369 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 537} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 4369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4369 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 537} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 135 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'UNK:plan-1': 27} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.61, per 1000 atoms: 0.24 Number of scatterers: 27030 At special positions: 0 Unit cell: (154.29, 154.29, 113.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 P 33 15.00 O 5238 8.00 N 4824 7.00 C 16811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.2 seconds 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6446 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 12 sheets defined 57.9% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 207 through 224 removed outlier: 4.166A pdb=" N PHE A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 278 through 294 Processing helix chain 'A' and resid 318 through 337 Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 373 through 386 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 407 through 423 Processing helix chain 'A' and resid 423 through 438 removed outlier: 3.822A pdb=" N ILE A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 460 removed outlier: 3.790A pdb=" N ARG A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 482 Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 506 through 523 Proline residue: A 520 - end of helix Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.543A pdb=" N PHE A 527 " --> pdb=" O ASN A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 Processing helix chain 'A' and resid 578 through 593 Processing helix chain 'A' and resid 616 through 631 Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.596A pdb=" N ARG A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'A' and resid 715 through 725 removed outlier: 4.220A pdb=" N LEU A 719 " --> pdb=" O THR A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 730 removed outlier: 3.548A pdb=" N GLY A 730 " --> pdb=" O LEU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 762 Processing helix chain 'A' and resid 776 through 787 removed outlier: 3.825A pdb=" N TRP A 780 " --> pdb=" O THR A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 800 Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.752A pdb=" N ASP B 203 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE B 204 " --> pdb=" O ILE B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 200 through 204' Processing helix chain 'B' and resid 207 through 224 removed outlier: 4.179A pdb=" N PHE B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 318 through 337 Processing helix chain 'B' and resid 356 through 363 Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 407 through 423 Processing helix chain 'B' and resid 423 through 438 removed outlier: 3.859A pdb=" N ILE B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 460 removed outlier: 3.786A pdb=" N ARG B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 482 Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 506 through 523 Proline residue: B 520 - end of helix Processing helix chain 'B' and resid 523 through 531 removed outlier: 3.541A pdb=" N PHE B 527 " --> pdb=" O ASN B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 560 Processing helix chain 'B' and resid 578 through 593 Processing helix chain 'B' and resid 616 through 631 Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.610A pdb=" N ARG B 655 " --> pdb=" O ASP B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 682 Processing helix chain 'B' and resid 715 through 725 removed outlier: 4.230A pdb=" N LEU B 719 " --> pdb=" O THR B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 730 removed outlier: 3.571A pdb=" N GLY B 730 " --> pdb=" O LEU B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 762 Processing helix chain 'B' and resid 776 through 787 removed outlier: 3.828A pdb=" N TRP B 780 " --> pdb=" O THR B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 800 Processing helix chain 'C' and resid 200 through 204 removed outlier: 3.773A pdb=" N ASP C 203 " --> pdb=" O SER C 200 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE C 204 " --> pdb=" O ILE C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 200 through 204' Processing helix chain 'C' and resid 207 through 224 removed outlier: 4.156A pdb=" N PHE C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Proline residue: C 221 - end of helix Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 248 through 261 Processing helix chain 'C' and resid 278 through 294 Processing helix chain 'C' and resid 316 through 337 removed outlier: 3.854A pdb=" N SER C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG C 321 " --> pdb=" O GLY C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 363 Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 407 through 423 Processing helix chain 'C' and resid 423 through 438 removed outlier: 3.770A pdb=" N ILE C 427 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 460 removed outlier: 3.818A pdb=" N ARG C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 482 Processing helix chain 'C' and resid 499 through 503 Processing helix chain 'C' and resid 506 through 523 Proline residue: C 520 - end of helix Processing helix chain 'C' and resid 523 through 531 removed outlier: 3.548A pdb=" N PHE C 527 " --> pdb=" O ASN C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 560 Processing helix chain 'C' and resid 578 through 593 Processing helix chain 'C' and resid 616 through 631 Processing helix chain 'C' and resid 651 through 656 removed outlier: 3.607A pdb=" N ARG C 655 " --> pdb=" O ASP C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 682 Processing helix chain 'C' and resid 715 through 725 removed outlier: 4.210A pdb=" N LEU C 719 " --> pdb=" O THR C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 removed outlier: 3.551A pdb=" N GLY C 730 " --> pdb=" O LEU C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 762 Processing helix chain 'C' and resid 776 through 787 removed outlier: 3.823A pdb=" N TRP C 780 " --> pdb=" O THR C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 800 Processing helix chain 'D' and resid 200 through 204 removed outlier: 3.750A pdb=" N ASP D 203 " --> pdb=" O SER D 200 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE D 204 " --> pdb=" O ILE D 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 200 through 204' Processing helix chain 'D' and resid 207 through 224 removed outlier: 4.162A pdb=" N PHE D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 248 through 261 Processing helix chain 'D' and resid 278 through 294 Processing helix chain 'D' and resid 316 through 337 removed outlier: 3.864A pdb=" N SER D 320 " --> pdb=" O LYS D 316 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG D 321 " --> pdb=" O GLY D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 363 Processing helix chain 'D' and resid 373 through 386 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 407 through 423 Processing helix chain 'D' and resid 423 through 438 removed outlier: 3.782A pdb=" N ILE D 427 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 460 removed outlier: 3.819A pdb=" N ARG D 451 " --> pdb=" O SER D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 482 Processing helix chain 'D' and resid 499 through 503 Processing helix chain 'D' and resid 506 through 523 Proline residue: D 520 - end of helix Processing helix chain 'D' and resid 523 through 531 removed outlier: 3.546A pdb=" N PHE D 527 " --> pdb=" O ASN D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 560 Processing helix chain 'D' and resid 578 through 593 Processing helix chain 'D' and resid 616 through 631 Processing helix chain 'D' and resid 651 through 656 removed outlier: 3.604A pdb=" N ARG D 655 " --> pdb=" O ASP D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 682 Processing helix chain 'D' and resid 715 through 725 removed outlier: 4.188A pdb=" N LEU D 719 " --> pdb=" O THR D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 730 removed outlier: 3.569A pdb=" N GLY D 730 " --> pdb=" O LEU D 726 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 762 Processing helix chain 'D' and resid 776 through 787 removed outlier: 3.837A pdb=" N TRP D 780 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 800 Processing helix chain 'E' and resid 200 through 204 removed outlier: 3.773A pdb=" N ASP E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE E 204 " --> pdb=" O ILE E 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 200 through 204' Processing helix chain 'E' and resid 207 through 224 removed outlier: 4.176A pdb=" N PHE E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Proline residue: E 221 - end of helix Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 248 through 261 Processing helix chain 'E' and resid 278 through 294 Processing helix chain 'E' and resid 318 through 337 Processing helix chain 'E' and resid 356 through 363 Processing helix chain 'E' and resid 373 through 386 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 407 through 423 Processing helix chain 'E' and resid 423 through 438 removed outlier: 3.839A pdb=" N ILE E 427 " --> pdb=" O PHE E 423 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA E 436 " --> pdb=" O ALA E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 460 removed outlier: 3.786A pdb=" N ARG E 451 " --> pdb=" O SER E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 482 Processing helix chain 'E' and resid 499 through 503 Processing helix chain 'E' and resid 506 through 523 Proline residue: E 520 - end of helix Processing helix chain 'E' and resid 523 through 531 removed outlier: 3.544A pdb=" N PHE E 527 " --> pdb=" O ASN E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 560 Processing helix chain 'E' and resid 577 through 593 removed outlier: 3.913A pdb=" N ARG E 581 " --> pdb=" O GLY E 577 " (cutoff:3.500A) Processing helix chain 'E' and resid 616 through 632 removed outlier: 3.635A pdb=" N VAL E 632 " --> pdb=" O GLU E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 651 through 656 removed outlier: 3.587A pdb=" N ARG E 655 " --> pdb=" O ASP E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 670 through 682 Processing helix chain 'E' and resid 715 through 725 removed outlier: 4.205A pdb=" N LEU E 719 " --> pdb=" O THR E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 730 removed outlier: 3.558A pdb=" N GLY E 730 " --> pdb=" O LEU E 726 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 762 Processing helix chain 'E' and resid 776 through 787 removed outlier: 3.829A pdb=" N TRP E 780 " --> pdb=" O THR E 776 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 224 removed outlier: 4.184A pdb=" N PHE F 220 " --> pdb=" O LYS F 216 " (cutoff:3.500A) Proline residue: F 221 - end of helix Processing helix chain 'F' and resid 224 through 232 Processing helix chain 'F' and resid 248 through 261 Processing helix chain 'F' and resid 278 through 294 Processing helix chain 'F' and resid 316 through 337 removed outlier: 3.870A pdb=" N SER F 320 " --> pdb=" O LYS F 316 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG F 321 " --> pdb=" O GLY F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 363 Processing helix chain 'F' and resid 373 through 386 Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 407 through 423 Processing helix chain 'F' and resid 423 through 438 removed outlier: 3.829A pdb=" N ILE F 427 " --> pdb=" O PHE F 423 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA F 436 " --> pdb=" O ALA F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 460 removed outlier: 3.773A pdb=" N ARG F 451 " --> pdb=" O SER F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 482 Processing helix chain 'F' and resid 499 through 503 Processing helix chain 'F' and resid 506 through 523 Proline residue: F 520 - end of helix Processing helix chain 'F' and resid 523 through 531 removed outlier: 3.545A pdb=" N PHE F 527 " --> pdb=" O ASN F 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 Processing helix chain 'F' and resid 577 through 593 removed outlier: 4.006A pdb=" N ARG F 581 " --> pdb=" O GLY F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 632 removed outlier: 3.562A pdb=" N VAL F 632 " --> pdb=" O GLU F 628 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 656 removed outlier: 3.571A pdb=" N ARG F 655 " --> pdb=" O ASP F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 670 through 682 Processing helix chain 'F' and resid 715 through 725 removed outlier: 4.213A pdb=" N LEU F 719 " --> pdb=" O THR F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 730 removed outlier: 3.566A pdb=" N GLY F 730 " --> pdb=" O LEU F 726 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 762 Processing helix chain 'F' and resid 776 through 787 removed outlier: 3.828A pdb=" N TRP F 780 " --> pdb=" O THR F 776 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.483A pdb=" N ALA A 263 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N PHE A 300 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 265 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ASP A 302 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 267 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS A 297 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU A 346 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE A 299 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ALA A 348 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 301 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 562 through 567 removed outlier: 6.624A pdb=" N ASN A 562 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE A 599 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE A 564 " --> pdb=" O PHE A 599 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP A 601 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 566 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS A 596 " --> pdb=" O TYR A 639 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE A 641 " --> pdb=" O CYS A 596 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU A 598 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ALA A 643 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE A 600 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLY A 537 " --> pdb=" O THR A 662 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE A 664 " --> pdb=" O GLY A 537 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU A 539 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.737A pdb=" N CYS B 297 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU B 346 " --> pdb=" O CYS B 297 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE B 299 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA B 348 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU B 301 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 562 through 567 removed outlier: 6.637A pdb=" N ASN B 562 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE B 599 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE B 564 " --> pdb=" O PHE B 599 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP B 601 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 566 " --> pdb=" O ASP B 601 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N CYS B 596 " --> pdb=" O TYR B 639 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE B 641 " --> pdb=" O CYS B 596 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU B 598 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ALA B 643 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE B 600 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLY B 537 " --> pdb=" O THR B 662 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE B 664 " --> pdb=" O GLY B 537 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU B 539 " --> pdb=" O ILE B 664 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.474A pdb=" N ALA C 263 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE C 300 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 265 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASP C 302 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL C 267 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N CYS C 297 " --> pdb=" O VAL C 344 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU C 346 " --> pdb=" O CYS C 297 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE C 299 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA C 348 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU C 301 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 562 through 567 removed outlier: 6.624A pdb=" N ASN C 562 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N PHE C 599 " --> pdb=" O ASN C 562 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE C 564 " --> pdb=" O PHE C 599 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASP C 601 " --> pdb=" O ILE C 564 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE C 566 " --> pdb=" O ASP C 601 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS C 596 " --> pdb=" O TYR C 639 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE C 641 " --> pdb=" O CYS C 596 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU C 598 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ALA C 643 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE C 600 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLY C 537 " --> pdb=" O THR C 662 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ILE C 664 " --> pdb=" O GLY C 537 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU C 539 " --> pdb=" O ILE C 664 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 263 through 268 removed outlier: 6.476A pdb=" N ALA D 263 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE D 300 " --> pdb=" O ALA D 263 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE D 265 " --> pdb=" O PHE D 300 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP D 302 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL D 267 " --> pdb=" O ASP D 302 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS D 297 " --> pdb=" O VAL D 344 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU D 346 " --> pdb=" O CYS D 297 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE D 299 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA D 348 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU D 301 " --> pdb=" O ALA D 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 562 through 567 removed outlier: 6.627A pdb=" N ASN D 562 " --> pdb=" O ILE D 597 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE D 599 " --> pdb=" O ASN D 562 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE D 564 " --> pdb=" O PHE D 599 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP D 601 " --> pdb=" O ILE D 564 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE D 566 " --> pdb=" O ASP D 601 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N CYS D 596 " --> pdb=" O TYR D 639 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE D 641 " --> pdb=" O CYS D 596 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU D 598 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ALA D 643 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE D 600 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLY D 537 " --> pdb=" O THR D 662 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE D 664 " --> pdb=" O GLY D 537 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU D 539 " --> pdb=" O ILE D 664 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.477A pdb=" N ALA E 263 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE E 300 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE E 265 " --> pdb=" O PHE E 300 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASP E 302 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL E 267 " --> pdb=" O ASP E 302 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS E 297 " --> pdb=" O VAL E 344 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU E 346 " --> pdb=" O CYS E 297 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE E 299 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ALA E 348 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU E 301 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 562 through 567 removed outlier: 6.656A pdb=" N ASN E 562 " --> pdb=" O ILE E 597 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE E 599 " --> pdb=" O ASN E 562 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE E 564 " --> pdb=" O PHE E 599 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP E 601 " --> pdb=" O ILE E 564 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE E 566 " --> pdb=" O ASP E 601 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N CYS E 596 " --> pdb=" O TYR E 639 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE E 641 " --> pdb=" O CYS E 596 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU E 598 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ALA E 643 " --> pdb=" O LEU E 598 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE E 600 " --> pdb=" O ALA E 643 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE E 538 " --> pdb=" O GLY E 642 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N THR E 644 " --> pdb=" O ILE E 538 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU E 540 " --> pdb=" O THR E 644 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLY E 537 " --> pdb=" O THR E 662 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ILE E 664 " --> pdb=" O GLY E 537 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU E 539 " --> pdb=" O ILE E 664 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 263 through 267 removed outlier: 6.468A pdb=" N ALA F 263 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N PHE F 300 " --> pdb=" O ALA F 263 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE F 265 " --> pdb=" O PHE F 300 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP F 302 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL F 267 " --> pdb=" O ASP F 302 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N CYS F 297 " --> pdb=" O VAL F 344 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU F 346 " --> pdb=" O CYS F 297 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE F 299 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA F 348 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU F 301 " --> pdb=" O ALA F 348 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 562 through 567 removed outlier: 6.662A pdb=" N ASN F 562 " --> pdb=" O ILE F 597 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE F 599 " --> pdb=" O ASN F 562 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE F 564 " --> pdb=" O PHE F 599 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP F 601 " --> pdb=" O ILE F 564 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE F 566 " --> pdb=" O ASP F 601 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N CYS F 596 " --> pdb=" O TYR F 639 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE F 641 " --> pdb=" O CYS F 596 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU F 598 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA F 643 " --> pdb=" O LEU F 598 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE F 600 " --> pdb=" O ALA F 643 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLY F 537 " --> pdb=" O THR F 662 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ILE F 664 " --> pdb=" O GLY F 537 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU F 539 " --> pdb=" O ILE F 664 " (cutoff:3.500A) 1365 hydrogen bonds defined for protein. 4041 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: 4.17 Time building geometry restraints manager: 2.71 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: 8907 1.34 - 1.47: 4117 1.47 - 1.59: 14194 1.59 - 1.72: 59 1.72 - 1.85: 206 Bond restraints: 27483 Sorted by residual: bond pdb=" C4 ATP B 902 " pdb=" C5 ATP B 902 " ideal model delta sigma weight residual 1.388 1.478 -0.090 1.00e-02 1.00e+04 8.06e+01 bond pdb=" C5 ATP B 902 " pdb=" C6 ATP B 902 " ideal model delta sigma weight residual 1.409 1.498 -0.089 1.00e-02 1.00e+04 7.98e+01 bond pdb=" C4 ATP C 901 " pdb=" C5 ATP C 901 " ideal model delta sigma weight residual 1.388 1.474 -0.086 1.00e-02 1.00e+04 7.43e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.474 -0.086 1.00e-02 1.00e+04 7.39e+01 bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.27e+01 ... (remaining 27478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 36119 4.29 - 8.58: 1007 8.58 - 12.87: 81 12.87 - 17.16: 28 17.16 - 21.45: 7 Bond angle restraints: 37242 Sorted by residual: angle pdb=" PB ATP C 902 " pdb=" O3B ATP C 902 " pdb=" PG ATP C 902 " ideal model delta sigma weight residual 139.87 118.42 21.45 1.00e+00 1.00e+00 4.60e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 118.91 20.96 1.00e+00 1.00e+00 4.39e+02 angle pdb=" PB ATP A 902 " pdb=" O3B ATP A 902 " pdb=" PG ATP A 902 " ideal model delta sigma weight residual 139.87 118.92 20.95 1.00e+00 1.00e+00 4.39e+02 angle pdb=" PB ATP B 902 " pdb=" O3B ATP B 902 " pdb=" PG ATP B 902 " ideal model delta sigma weight residual 139.87 119.45 20.42 1.00e+00 1.00e+00 4.17e+02 angle pdb=" PB ATP D 902 " pdb=" O3B ATP D 902 " pdb=" PG ATP D 902 " ideal model delta sigma weight residual 139.87 119.47 20.40 1.00e+00 1.00e+00 4.16e+02 ... (remaining 37237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 15321 18.02 - 36.04: 1082 36.04 - 54.06: 374 54.06 - 72.08: 146 72.08 - 90.09: 219 Dihedral angle restraints: 17142 sinusoidal: 7182 harmonic: 9960 Sorted by residual: dihedral pdb=" C THR F 337 " pdb=" N THR F 337 " pdb=" CA THR F 337 " pdb=" CB THR F 337 " ideal model delta harmonic sigma weight residual -122.00 -134.43 12.43 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" C THR A 337 " pdb=" N THR A 337 " pdb=" CA THR A 337 " pdb=" CB THR A 337 " ideal model delta harmonic sigma weight residual -122.00 -134.24 12.24 0 2.50e+00 1.60e-01 2.40e+01 dihedral pdb=" C THR B 337 " pdb=" N THR B 337 " pdb=" CA THR B 337 " pdb=" CB THR B 337 " ideal model delta harmonic sigma weight residual -122.00 -134.23 12.23 0 2.50e+00 1.60e-01 2.39e+01 ... (remaining 17139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 3414 0.143 - 0.286: 710 0.286 - 0.428: 84 0.428 - 0.571: 10 0.571 - 0.714: 1 Chirality restraints: 4219 Sorted by residual: chirality pdb=" CA PRO E 544 " pdb=" N PRO E 544 " pdb=" C PRO E 544 " pdb=" CB PRO E 544 " both_signs ideal model delta sigma weight residual False 2.72 2.00 0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CA SER C 636 " pdb=" N SER C 636 " pdb=" C SER C 636 " pdb=" CB SER C 636 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CA THR B 337 " pdb=" N THR B 337 " pdb=" C THR B 337 " pdb=" CB THR B 337 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.45 2.00e-01 2.50e+01 4.98e+00 ... (remaining 4216 not shown) Planarity restraints: 4825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 639 " -0.101 2.00e-02 2.50e+03 5.25e-02 5.51e+01 pdb=" CG TYR D 639 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR D 639 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR D 639 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR D 639 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR D 639 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR D 639 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 639 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 639 " 0.100 2.00e-02 2.50e+03 5.20e-02 5.41e+01 pdb=" CG TYR B 639 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 639 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR B 639 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR B 639 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR B 639 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR B 639 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 639 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 639 " -0.093 2.00e-02 2.50e+03 4.83e-02 4.67e+01 pdb=" CG TYR C 639 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR C 639 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR C 639 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR C 639 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR C 639 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR C 639 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 639 " -0.067 2.00e-02 2.50e+03 ... (remaining 4822 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 8043 2.90 - 3.40: 24745 3.40 - 3.90: 40945 3.90 - 4.40: 45255 4.40 - 4.90: 78396 Nonbonded interactions: 197384 Sorted by model distance: nonbonded pdb=" O PRO E 543 " pdb=" CA PRO E 544 " model vdw 2.397 2.776 nonbonded pdb=" O GLY A 258 " pdb=" NH2 ARG F 460 " model vdw 2.413 3.120 nonbonded pdb=" O ASN E 557 " pdb=" N LYS E 560 " model vdw 2.480 3.120 nonbonded pdb=" O ARG E 460 " pdb=" NH2 ARG F 223 " model vdw 2.482 3.120 nonbonded pdb=" NH2 ARG C 659 " pdb=" O1G ATP B 901 " model vdw 2.486 3.120 ... (remaining 197379 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 193 through 790 or resid 902)) selection = (chain 'B' and (resid 193 through 790 or resid 902)) selection = (chain 'C' and (resid 193 through 790 or resid 902)) selection = (chain 'D' and (resid 193 through 790 or resid 902)) selection = chain 'E' selection = (chain 'F' and (resid 193 through 790 or resid 902)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.450 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 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 : 0.012 0.090 27483 Z= 0.803 Angle : 1.798 21.450 37242 Z= 1.254 Chirality : 0.114 0.714 4219 Planarity : 0.010 0.111 4825 Dihedral : 19.221 90.095 10696 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 2.02 % Allowed : 6.36 % Favored : 91.62 % Rotamer: Outliers : 2.79 % Allowed : 8.90 % Favored : 88.31 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 6.52 % 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: -1.24 (0.13), residues: 3412 helix: 0.24 (0.10), residues: 1876 sheet: -0.37 (0.25), residues: 407 loop : -2.82 (0.16), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG F 460 TYR 0.101 0.009 TYR D 639 PHE 0.041 0.007 PHE D 527 TRP 0.066 0.009 TRP E 453 HIS 0.001 0.000 HIS F 254 Details of bonding type rmsd covalent geometry : bond 0.01233 (27483) covalent geometry : angle 1.79757 (37242) hydrogen bonds : bond 0.25465 ( 1365) hydrogen bonds : angle 6.41148 ( 4041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 913 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ILE cc_start: 0.9106 (mp) cc_final: 0.8411 (tp) REVERT: A 350 ASN cc_start: 0.7720 (m-40) cc_final: 0.7369 (t0) REVERT: A 485 PRO cc_start: 0.5604 (Cg_endo) cc_final: 0.4763 (Cg_exo) REVERT: A 495 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8351 (tp) REVERT: A 599 PHE cc_start: 0.8921 (t80) cc_final: 0.8042 (t80) REVERT: A 738 ASN cc_start: 0.9166 (t0) cc_final: 0.8951 (t0) REVERT: B 231 MET cc_start: 0.8937 (mtt) cc_final: 0.8506 (mtm) REVERT: B 240 LEU cc_start: 0.8904 (tp) cc_final: 0.8318 (mt) REVERT: B 292 ILE cc_start: 0.9186 (pt) cc_final: 0.8497 (mt) REVERT: B 325 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7404 (tp30) REVERT: B 380 ILE cc_start: 0.8954 (mt) cc_final: 0.8686 (mm) REVERT: B 500 TRP cc_start: 0.8230 (m100) cc_final: 0.7081 (m100) REVERT: B 627 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8473 (m) REVERT: B 639 TYR cc_start: 0.8178 (m-80) cc_final: 0.7827 (m-10) REVERT: B 656 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.6733 (tmm160) REVERT: B 664 ILE cc_start: 0.9098 (mt) cc_final: 0.8855 (mm) REVERT: B 731 PHE cc_start: 0.8331 (m-10) cc_final: 0.7764 (m-80) REVERT: B 780 TRP cc_start: 0.8244 (OUTLIER) cc_final: 0.7897 (m100) REVERT: B 798 MET cc_start: 0.8282 (mmm) cc_final: 0.7996 (mmt) REVERT: C 284 ILE cc_start: 0.8534 (mt) cc_final: 0.7999 (mt) REVERT: C 345 VAL cc_start: 0.9077 (t) cc_final: 0.8397 (t) REVERT: C 388 LEU cc_start: 0.8859 (mp) cc_final: 0.8467 (mp) REVERT: C 407 VAL cc_start: 0.6334 (OUTLIER) cc_final: 0.5916 (m) REVERT: C 656 ARG cc_start: 0.6515 (OUTLIER) cc_final: 0.6126 (tmm-80) REVERT: C 740 MET cc_start: 0.8987 (tmm) cc_final: 0.8767 (tmm) REVERT: D 204 ILE cc_start: 0.8854 (mp) cc_final: 0.8464 (mm) REVERT: D 264 PHE cc_start: 0.7852 (t80) cc_final: 0.6972 (t80) REVERT: D 292 ILE cc_start: 0.8833 (pt) cc_final: 0.8346 (mt) REVERT: D 354 PHE cc_start: 0.7851 (t80) cc_final: 0.7603 (t80) REVERT: D 355 LEU cc_start: 0.9181 (mt) cc_final: 0.8941 (mt) REVERT: D 495 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8805 (tp) REVERT: D 627 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8663 (m) REVERT: D 682 TYR cc_start: 0.8148 (t80) cc_final: 0.7777 (t80) REVERT: D 727 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6105 (mtm-85) REVERT: E 325 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: E 350 ASN cc_start: 0.8347 (m-40) cc_final: 0.7852 (p0) REVERT: E 402 MET cc_start: 0.7532 (mmm) cc_final: 0.6902 (ptm) REVERT: E 473 MET cc_start: 0.8530 (tpt) cc_final: 0.8277 (tpt) REVERT: E 488 LYS cc_start: 0.7928 (pttm) cc_final: 0.7235 (tppt) REVERT: E 495 ILE cc_start: -0.0492 (OUTLIER) cc_final: -0.1109 (tp) REVERT: E 597 ILE cc_start: 0.9288 (mp) cc_final: 0.9021 (mp) REVERT: E 599 PHE cc_start: 0.7901 (t80) cc_final: 0.7640 (t80) REVERT: F 369 MET cc_start: 0.5268 (mtp) cc_final: 0.4865 (mpp) REVERT: F 623 ASN cc_start: 0.7815 (m-40) cc_final: 0.7501 (m-40) REVERT: F 639 TYR cc_start: 0.7298 (m-80) cc_final: 0.6966 (m-10) REVERT: F 760 LYS cc_start: 0.7660 (mttt) cc_final: 0.7116 (pptt) outliers start: 80 outliers final: 15 residues processed: 970 average time/residue: 0.2161 time to fit residues: 310.1602 Evaluate side-chains 448 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 421 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN A 336 ASN A 350 ASN A 445 ASN A 502 HIS A 585 GLN A 602 GLN B 254 HIS ** B 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN B 484 GLN B 502 HIS B 602 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 HIS C 445 ASN C 450 GLN C 502 HIS C 557 ASN C 573 ASN ** C 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 GLN D 254 HIS D 328 ASN D 335 GLN D 395 ASN D 445 ASN D 502 HIS ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 ASN E 502 HIS E 523 ASN E 585 GLN F 395 ASN ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 445 ASN F 502 HIS ** F 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.091401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.077160 restraints weight = 116340.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.078814 restraints weight = 80674.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.080017 restraints weight = 60329.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.080860 restraints weight = 47748.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.081524 restraints weight = 39905.545| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27483 Z= 0.205 Angle : 0.808 13.555 37242 Z= 0.422 Chirality : 0.046 0.264 4219 Planarity : 0.008 0.134 4825 Dihedral : 11.873 89.827 4140 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.77 % Favored : 93.93 % Rotamer: Outliers : 0.24 % Allowed : 4.33 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.14), residues: 3412 helix: 1.53 (0.12), residues: 1845 sheet: 0.18 (0.25), residues: 420 loop : -2.41 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 351 TYR 0.017 0.002 TYR A 406 PHE 0.024 0.002 PHE E 600 TRP 0.027 0.002 TRP C 780 HIS 0.008 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00426 (27483) covalent geometry : angle 0.80839 (37242) hydrogen bonds : bond 0.07148 ( 1365) hydrogen bonds : angle 5.16206 ( 4041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 514 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.8600 (tmm) cc_final: 0.8121 (tmm) REVERT: A 388 LEU cc_start: 0.8577 (tp) cc_final: 0.8361 (tt) REVERT: A 601 ASP cc_start: 0.6621 (t0) cc_final: 0.6265 (t0) REVERT: A 738 ASN cc_start: 0.9053 (t0) cc_final: 0.8781 (t0) REVERT: A 740 MET cc_start: 0.8291 (tmm) cc_final: 0.8061 (tmm) REVERT: A 798 MET cc_start: 0.6673 (tmm) cc_final: 0.6439 (tmm) REVERT: B 231 MET cc_start: 0.8963 (mtt) cc_final: 0.8519 (mtt) REVERT: B 240 LEU cc_start: 0.8974 (tp) cc_final: 0.8456 (mt) REVERT: B 616 ASP cc_start: 0.8146 (p0) cc_final: 0.7572 (p0) REVERT: B 798 MET cc_start: 0.7808 (mmm) cc_final: 0.7575 (mmm) REVERT: C 327 MET cc_start: 0.8997 (tpp) cc_final: 0.8466 (mmm) REVERT: C 388 LEU cc_start: 0.8832 (mp) cc_final: 0.8539 (mp) REVERT: C 662 THR cc_start: 0.7902 (m) cc_final: 0.7556 (m) REVERT: C 740 MET cc_start: 0.8859 (tmm) cc_final: 0.8456 (tmm) REVERT: D 281 GLU cc_start: 0.9139 (mp0) cc_final: 0.8938 (mp0) REVERT: D 581 ARG cc_start: 0.8304 (ttp80) cc_final: 0.8063 (ttp80) REVERT: D 682 TYR cc_start: 0.8031 (t80) cc_final: 0.7570 (t80) REVERT: D 722 VAL cc_start: 0.9335 (t) cc_final: 0.9096 (p) REVERT: E 318 MET cc_start: 0.8423 (ppp) cc_final: 0.7913 (ppp) REVERT: E 369 MET cc_start: 0.8188 (ttm) cc_final: 0.7852 (ttm) REVERT: E 377 ARG cc_start: 0.8496 (mtm-85) cc_final: 0.7225 (mtt-85) REVERT: E 402 MET cc_start: 0.8335 (mmm) cc_final: 0.7288 (ptm) REVERT: E 427 ILE cc_start: 0.7080 (mp) cc_final: 0.6343 (mp) REVERT: E 488 LYS cc_start: 0.8058 (pttm) cc_final: 0.7451 (tppt) REVERT: E 599 PHE cc_start: 0.8423 (t80) cc_final: 0.7815 (t80) REVERT: F 235 TYR cc_start: 0.3909 (p90) cc_final: 0.3568 (p90) REVERT: F 300 PHE cc_start: 0.6471 (t80) cc_final: 0.6220 (t80) REVERT: F 362 ARG cc_start: 0.5869 (mmp80) cc_final: 0.4752 (tpt90) REVERT: F 369 MET cc_start: 0.4722 (mtp) cc_final: 0.3730 (tpp) REVERT: F 452 ASP cc_start: 0.8394 (m-30) cc_final: 0.8154 (m-30) REVERT: F 623 ASN cc_start: 0.9191 (m-40) cc_final: 0.8611 (m-40) REVERT: F 639 TYR cc_start: 0.8036 (m-80) cc_final: 0.7799 (m-10) REVERT: F 777 MET cc_start: 0.9046 (tpt) cc_final: 0.8787 (tpp) outliers start: 7 outliers final: 1 residues processed: 518 average time/residue: 0.2118 time to fit residues: 164.2600 Evaluate side-chains 308 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 95 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 165 optimal weight: 20.0000 chunk 334 optimal weight: 7.9990 chunk 269 optimal weight: 0.0570 chunk 257 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 170 optimal weight: 0.5980 chunk 290 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 overall best weight: 3.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 602 GLN B 745 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 HIS ** C 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 ASN F 557 ASN F 573 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.088447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.074087 restraints weight = 121895.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.075642 restraints weight = 85017.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.076743 restraints weight = 64242.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.077484 restraints weight = 51668.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.078110 restraints weight = 43923.253| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27483 Z= 0.177 Angle : 0.705 8.621 37242 Z= 0.365 Chirality : 0.043 0.185 4219 Planarity : 0.007 0.092 4825 Dihedral : 11.777 89.727 4140 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.13 % Favored : 93.64 % Rotamer: Outliers : 0.10 % Allowed : 4.85 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.49 (0.15), residues: 3412 helix: 1.69 (0.12), residues: 1844 sheet: 0.31 (0.25), residues: 422 loop : -2.03 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 361 TYR 0.026 0.002 TYR A 413 PHE 0.032 0.002 PHE A 731 TRP 0.022 0.003 TRP E 541 HIS 0.008 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00382 (27483) covalent geometry : angle 0.70521 (37242) hydrogen bonds : bond 0.05268 ( 1365) hydrogen bonds : angle 4.89321 ( 4041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 395 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.8682 (tp) cc_final: 0.8372 (tt) REVERT: A 677 ILE cc_start: 0.9520 (pt) cc_final: 0.9259 (tt) REVERT: A 738 ASN cc_start: 0.9116 (t0) cc_final: 0.8885 (t0) REVERT: A 740 MET cc_start: 0.8337 (tmm) cc_final: 0.8094 (tmm) REVERT: A 770 GLU cc_start: 0.6168 (tp30) cc_final: 0.5447 (tm-30) REVERT: B 231 MET cc_start: 0.9061 (mtt) cc_final: 0.8514 (mtt) REVERT: B 616 ASP cc_start: 0.8077 (p0) cc_final: 0.7512 (p0) REVERT: B 628 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 640 VAL cc_start: 0.9568 (t) cc_final: 0.9218 (m) REVERT: B 798 MET cc_start: 0.7731 (mmm) cc_final: 0.7413 (mmm) REVERT: C 406 TYR cc_start: 0.7553 (m-80) cc_final: 0.7202 (m-80) REVERT: C 740 MET cc_start: 0.8887 (tmm) cc_final: 0.8529 (tmm) REVERT: D 593 SER cc_start: 0.8536 (m) cc_final: 0.7722 (t) REVERT: E 318 MET cc_start: 0.8186 (ppp) cc_final: 0.7974 (ppp) REVERT: E 354 PHE cc_start: 0.8658 (t80) cc_final: 0.8448 (t80) REVERT: E 369 MET cc_start: 0.8105 (ttm) cc_final: 0.7799 (ttm) REVERT: E 402 MET cc_start: 0.8431 (mmm) cc_final: 0.7393 (ptm) REVERT: E 427 ILE cc_start: 0.7085 (mp) cc_final: 0.6496 (mp) REVERT: E 452 ASP cc_start: 0.8113 (m-30) cc_final: 0.7898 (m-30) REVERT: E 488 LYS cc_start: 0.8192 (pttm) cc_final: 0.7555 (tppt) REVERT: E 514 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7378 (mt-10) REVERT: E 599 PHE cc_start: 0.8491 (t80) cc_final: 0.7589 (t80) REVERT: E 740 MET cc_start: 0.8830 (ppp) cc_final: 0.8496 (ppp) REVERT: F 215 LEU cc_start: 0.8765 (tp) cc_final: 0.8557 (tp) REVERT: F 362 ARG cc_start: 0.6218 (mmp-170) cc_final: 0.5643 (tpt90) REVERT: F 369 MET cc_start: 0.4996 (mtp) cc_final: 0.3750 (tpp) REVERT: F 623 ASN cc_start: 0.9135 (m-40) cc_final: 0.8764 (m-40) REVERT: F 639 TYR cc_start: 0.8118 (m-80) cc_final: 0.7821 (m-10) REVERT: F 740 MET cc_start: 0.8511 (ppp) cc_final: 0.8214 (ppp) REVERT: F 777 MET cc_start: 0.8954 (tpt) cc_final: 0.8616 (tpp) outliers start: 3 outliers final: 0 residues processed: 396 average time/residue: 0.1960 time to fit residues: 120.2994 Evaluate side-chains 264 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 211 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 336 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 197 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS ** B 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN ** C 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 785 ASN D 303 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 785 ASN E 303 GLN E 424 GLN F 573 ASN F 745 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.087889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.073606 restraints weight = 120904.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.075041 restraints weight = 85754.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.076077 restraints weight = 65847.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.076845 restraints weight = 53687.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.077217 restraints weight = 45765.211| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27483 Z= 0.167 Angle : 0.665 10.361 37242 Z= 0.341 Chirality : 0.043 0.261 4219 Planarity : 0.006 0.090 4825 Dihedral : 11.571 88.583 4140 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.36 % Favored : 94.43 % Rotamer: Outliers : 0.07 % Allowed : 3.91 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.55 (0.15), residues: 3412 helix: 1.62 (0.12), residues: 1864 sheet: 0.50 (0.25), residues: 420 loop : -1.91 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 646 TYR 0.018 0.002 TYR F 413 PHE 0.020 0.002 PHE F 300 TRP 0.034 0.002 TRP F 780 HIS 0.009 0.001 HIS D 459 Details of bonding type rmsd covalent geometry : bond 0.00357 (27483) covalent geometry : angle 0.66476 (37242) hydrogen bonds : bond 0.04533 ( 1365) hydrogen bonds : angle 4.77784 ( 4041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 379 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.8507 (tmm) cc_final: 0.8266 (tmm) REVERT: A 413 TYR cc_start: 0.9142 (m-10) cc_final: 0.8872 (m-10) REVERT: A 576 VAL cc_start: 0.8351 (m) cc_final: 0.8034 (p) REVERT: A 603 MET cc_start: 0.8943 (mmp) cc_final: 0.8699 (mmp) REVERT: A 616 ASP cc_start: 0.7856 (p0) cc_final: 0.7607 (p0) REVERT: A 677 ILE cc_start: 0.9532 (pt) cc_final: 0.9256 (tt) REVERT: A 738 ASN cc_start: 0.8909 (t0) cc_final: 0.8686 (t0) REVERT: B 231 MET cc_start: 0.8908 (mtt) cc_final: 0.8397 (mtt) REVERT: B 304 ILE cc_start: 0.9401 (pt) cc_final: 0.9179 (mp) REVERT: B 318 MET cc_start: 0.7699 (mmm) cc_final: 0.7478 (mmm) REVERT: B 331 ASP cc_start: 0.8420 (m-30) cc_final: 0.8218 (m-30) REVERT: B 497 ASP cc_start: 0.6441 (p0) cc_final: 0.6227 (p0) REVERT: B 498 THR cc_start: 0.8583 (p) cc_final: 0.8317 (p) REVERT: B 616 ASP cc_start: 0.8149 (p0) cc_final: 0.7520 (p0) REVERT: B 628 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7616 (mm-30) REVERT: B 640 VAL cc_start: 0.9536 (t) cc_final: 0.9191 (m) REVERT: B 798 MET cc_start: 0.7845 (mmm) cc_final: 0.7367 (mmm) REVERT: C 406 TYR cc_start: 0.7413 (m-80) cc_final: 0.7050 (m-80) REVERT: D 281 GLU cc_start: 0.9058 (mp0) cc_final: 0.8140 (mp0) REVERT: D 593 SER cc_start: 0.8648 (m) cc_final: 0.8250 (t) REVERT: E 279 GLU cc_start: 0.8448 (tt0) cc_final: 0.7481 (tm-30) REVERT: E 318 MET cc_start: 0.8307 (ppp) cc_final: 0.8025 (ppp) REVERT: E 369 MET cc_start: 0.8033 (ttm) cc_final: 0.7672 (ttm) REVERT: E 402 MET cc_start: 0.8255 (mmm) cc_final: 0.7359 (ptm) REVERT: E 427 ILE cc_start: 0.7007 (mp) cc_final: 0.6636 (mm) REVERT: E 452 ASP cc_start: 0.8144 (m-30) cc_final: 0.7834 (m-30) REVERT: E 488 LYS cc_start: 0.8218 (pttm) cc_final: 0.7622 (tppt) REVERT: E 500 TRP cc_start: 0.8037 (m100) cc_final: 0.6886 (m100) REVERT: E 581 ARG cc_start: 0.8073 (ttt180) cc_final: 0.7820 (tpp-160) REVERT: E 599 PHE cc_start: 0.8275 (t80) cc_final: 0.7436 (t80) REVERT: E 616 ASP cc_start: 0.7137 (t0) cc_final: 0.6579 (t0) REVERT: E 740 MET cc_start: 0.8792 (ppp) cc_final: 0.8415 (ppp) REVERT: F 215 LEU cc_start: 0.8838 (tp) cc_final: 0.8638 (tp) REVERT: F 302 ASP cc_start: 0.8183 (p0) cc_final: 0.7352 (p0) REVERT: F 362 ARG cc_start: 0.6409 (mmp-170) cc_final: 0.5759 (tpt90) REVERT: F 369 MET cc_start: 0.4089 (mtp) cc_final: 0.3396 (tpp) REVERT: F 371 MET cc_start: 0.6123 (ppp) cc_final: 0.5816 (ppp) REVERT: F 413 TYR cc_start: 0.8417 (m-80) cc_final: 0.8217 (m-80) REVERT: F 567 LYS cc_start: 0.8597 (tmtt) cc_final: 0.8179 (tppp) REVERT: F 623 ASN cc_start: 0.9154 (m-40) cc_final: 0.8868 (m-40) REVERT: F 740 MET cc_start: 0.8519 (ppp) cc_final: 0.8244 (ppp) outliers start: 2 outliers final: 0 residues processed: 379 average time/residue: 0.1813 time to fit residues: 108.3326 Evaluate side-chains 262 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 322 optimal weight: 20.0000 chunk 180 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 318 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 280 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN A 562 ASN B 602 GLN B 785 ASN B 799 HIS ** C 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN D 523 ASN D 684 ASN ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 684 ASN F 350 ASN ** F 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.082425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068456 restraints weight = 125383.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.069859 restraints weight = 88752.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.070821 restraints weight = 68076.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.071541 restraints weight = 55653.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.072085 restraints weight = 47578.624| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.7052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 27483 Z= 0.263 Angle : 0.791 12.220 37242 Z= 0.406 Chirality : 0.045 0.281 4219 Planarity : 0.007 0.095 4825 Dihedral : 11.791 89.000 4140 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.80 % Favored : 92.97 % Rotamer: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3412 helix: 1.03 (0.12), residues: 1903 sheet: 0.43 (0.25), residues: 415 loop : -1.88 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 646 TYR 0.023 0.002 TYR C 665 PHE 0.022 0.003 PHE E 587 TRP 0.022 0.002 TRP A 500 HIS 0.012 0.002 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00575 (27483) covalent geometry : angle 0.79058 (37242) hydrogen bonds : bond 0.05040 ( 1365) hydrogen bonds : angle 5.26161 ( 4041) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 324 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 LEU cc_start: 0.9095 (tp) cc_final: 0.8877 (tt) REVERT: A 413 TYR cc_start: 0.9223 (m-10) cc_final: 0.8988 (m-10) REVERT: A 515 MET cc_start: 0.9026 (tmm) cc_final: 0.8643 (tmm) REVERT: A 616 ASP cc_start: 0.7865 (p0) cc_final: 0.7558 (p0) REVERT: A 638 ILE cc_start: 0.7304 (mp) cc_final: 0.7043 (mt) REVERT: A 675 VAL cc_start: 0.9466 (t) cc_final: 0.9237 (t) REVERT: B 231 MET cc_start: 0.8851 (mtt) cc_final: 0.8334 (mtt) REVERT: B 497 ASP cc_start: 0.7051 (p0) cc_final: 0.6638 (p0) REVERT: B 498 THR cc_start: 0.8689 (p) cc_final: 0.8372 (t) REVERT: B 640 VAL cc_start: 0.9588 (t) cc_final: 0.9275 (m) REVERT: B 798 MET cc_start: 0.7718 (mmm) cc_final: 0.7479 (mmp) REVERT: C 231 MET cc_start: 0.8223 (ptp) cc_final: 0.6743 (ptp) REVERT: C 233 TYR cc_start: 0.7039 (m-10) cc_final: 0.6704 (m-80) REVERT: C 264 PHE cc_start: 0.8727 (t80) cc_final: 0.8487 (t80) REVERT: C 406 TYR cc_start: 0.7950 (m-80) cc_final: 0.7592 (m-80) REVERT: C 728 CYS cc_start: 0.8602 (t) cc_final: 0.8272 (t) REVERT: D 281 GLU cc_start: 0.9005 (mp0) cc_final: 0.8508 (mp0) REVERT: E 318 MET cc_start: 0.8321 (ppp) cc_final: 0.8019 (ppp) REVERT: E 369 MET cc_start: 0.8012 (ttm) cc_final: 0.7605 (ttm) REVERT: E 402 MET cc_start: 0.8421 (mmm) cc_final: 0.6976 (ptm) REVERT: E 427 ILE cc_start: 0.6895 (mp) cc_final: 0.6675 (mm) REVERT: E 488 LYS cc_start: 0.8193 (pttm) cc_final: 0.7765 (tppt) REVERT: E 500 TRP cc_start: 0.8656 (m100) cc_final: 0.8120 (m100) REVERT: E 507 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7794 (pm20) REVERT: E 599 PHE cc_start: 0.8659 (t80) cc_final: 0.7692 (t80) REVERT: E 740 MET cc_start: 0.8665 (ppp) cc_final: 0.8252 (ppp) REVERT: F 300 PHE cc_start: 0.7634 (t80) cc_final: 0.7165 (t80) REVERT: F 302 ASP cc_start: 0.8099 (p0) cc_final: 0.7720 (p0) REVERT: F 362 ARG cc_start: 0.6421 (mmp-170) cc_final: 0.5797 (tpt90) REVERT: F 371 MET cc_start: 0.6113 (ppp) cc_final: 0.5811 (ppp) REVERT: F 623 ASN cc_start: 0.9177 (m-40) cc_final: 0.8863 (m-40) REVERT: F 646 ARG cc_start: 0.7217 (mtp180) cc_final: 0.6449 (tpt90) outliers start: 2 outliers final: 0 residues processed: 324 average time/residue: 0.1804 time to fit residues: 92.9837 Evaluate side-chains 232 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 18 optimal weight: 0.9980 chunk 248 optimal weight: 9.9990 chunk 316 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 310 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 chunk 247 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN A 254 HIS B 438 HIS ** C 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN C 741 GLN D 623 ASN D 738 ASN D 799 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.084547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.070504 restraints weight = 123545.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.071992 restraints weight = 86461.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.072967 restraints weight = 65518.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.073758 restraints weight = 53321.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.074309 restraints weight = 45262.569| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.7236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27483 Z= 0.140 Angle : 0.648 10.063 37242 Z= 0.333 Chirality : 0.042 0.204 4219 Planarity : 0.006 0.100 4825 Dihedral : 11.487 88.443 4140 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.39 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.41 (0.15), residues: 3412 helix: 1.31 (0.12), residues: 1907 sheet: 0.42 (0.25), residues: 415 loop : -1.68 (0.20), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 361 TYR 0.031 0.002 TYR D 752 PHE 0.021 0.002 PHE B 731 TRP 0.019 0.002 TRP C 219 HIS 0.006 0.001 HIS C 459 Details of bonding type rmsd covalent geometry : bond 0.00303 (27483) covalent geometry : angle 0.64815 (37242) hydrogen bonds : bond 0.04368 ( 1365) hydrogen bonds : angle 4.84152 ( 4041) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASP cc_start: 0.7868 (p0) cc_final: 0.7617 (p0) REVERT: B 231 MET cc_start: 0.8843 (mtt) cc_final: 0.8371 (mtt) REVERT: B 304 ILE cc_start: 0.9393 (pt) cc_final: 0.9131 (mp) REVERT: B 497 ASP cc_start: 0.7077 (p0) cc_final: 0.6666 (p0) REVERT: B 498 THR cc_start: 0.8636 (p) cc_final: 0.8278 (t) REVERT: B 640 VAL cc_start: 0.9520 (t) cc_final: 0.9205 (m) REVERT: B 728 CYS cc_start: 0.8010 (t) cc_final: 0.7769 (t) REVERT: B 798 MET cc_start: 0.7873 (mmm) cc_final: 0.7426 (mmp) REVERT: C 354 PHE cc_start: 0.7838 (m-80) cc_final: 0.7581 (m-80) REVERT: C 369 MET cc_start: 0.8918 (mmt) cc_final: 0.8695 (mmt) REVERT: C 406 TYR cc_start: 0.7633 (m-80) cc_final: 0.7242 (m-80) REVERT: C 728 CYS cc_start: 0.8530 (t) cc_final: 0.8187 (t) REVERT: D 281 GLU cc_start: 0.8861 (mp0) cc_final: 0.8431 (mp0) REVERT: E 279 GLU cc_start: 0.8612 (tt0) cc_final: 0.7514 (tm-30) REVERT: E 318 MET cc_start: 0.8207 (ppp) cc_final: 0.7961 (ppp) REVERT: E 369 MET cc_start: 0.7939 (ttm) cc_final: 0.7441 (ttm) REVERT: E 402 MET cc_start: 0.8319 (mmm) cc_final: 0.6967 (ptm) REVERT: E 488 LYS cc_start: 0.8245 (pttm) cc_final: 0.7637 (tppt) REVERT: E 500 TRP cc_start: 0.8530 (m100) cc_final: 0.8088 (m100) REVERT: E 507 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7871 (pm20) REVERT: E 599 PHE cc_start: 0.8428 (t80) cc_final: 0.7546 (t80) REVERT: E 740 MET cc_start: 0.8664 (ppp) cc_final: 0.8205 (ppp) REVERT: F 215 LEU cc_start: 0.9010 (tp) cc_final: 0.8778 (tp) REVERT: F 300 PHE cc_start: 0.7347 (t80) cc_final: 0.6953 (t80) REVERT: F 302 ASP cc_start: 0.8122 (p0) cc_final: 0.7624 (p0) REVERT: F 362 ARG cc_start: 0.6782 (mmp-170) cc_final: 0.6110 (tpt90) REVERT: F 371 MET cc_start: 0.6192 (ppp) cc_final: 0.5828 (ppp) REVERT: F 646 ARG cc_start: 0.6948 (mtp180) cc_final: 0.6275 (tpt90) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1870 time to fit residues: 101.1158 Evaluate side-chains 242 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 305 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 263 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 chunk 324 optimal weight: 0.9990 chunk 265 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 212 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS ** C 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 ASN F 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.084978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.071025 restraints weight = 122365.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072454 restraints weight = 86175.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.073500 restraints weight = 65797.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.074189 restraints weight = 53100.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.074778 restraints weight = 45455.129| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.7411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27483 Z= 0.134 Angle : 0.644 11.536 37242 Z= 0.329 Chirality : 0.042 0.202 4219 Planarity : 0.006 0.098 4825 Dihedral : 11.206 87.610 4140 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.77 % Favored : 94.08 % Rotamer: Outliers : 0.03 % Allowed : 1.29 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.50 (0.15), residues: 3412 helix: 1.36 (0.12), residues: 1901 sheet: 0.51 (0.25), residues: 413 loop : -1.56 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 361 TYR 0.030 0.001 TYR D 752 PHE 0.021 0.002 PHE A 264 TRP 0.021 0.002 TRP C 219 HIS 0.005 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00284 (27483) covalent geometry : angle 0.64385 (37242) hydrogen bonds : bond 0.04160 ( 1365) hydrogen bonds : angle 4.83641 ( 4041) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.7793 (ttm) cc_final: 0.7391 (ptm) REVERT: A 601 ASP cc_start: 0.9026 (p0) cc_final: 0.7612 (t0) REVERT: A 616 ASP cc_start: 0.7871 (p0) cc_final: 0.7545 (p0) REVERT: A 798 MET cc_start: 0.6628 (tmm) cc_final: 0.6426 (tmm) REVERT: B 231 MET cc_start: 0.8691 (mtt) cc_final: 0.8145 (mtt) REVERT: B 304 ILE cc_start: 0.9337 (pt) cc_final: 0.9127 (mp) REVERT: B 497 ASP cc_start: 0.7238 (p0) cc_final: 0.6880 (p0) REVERT: B 498 THR cc_start: 0.8589 (p) cc_final: 0.8197 (t) REVERT: B 600 PHE cc_start: 0.9188 (m-10) cc_final: 0.8855 (m-10) REVERT: B 628 GLU cc_start: 0.7596 (mp0) cc_final: 0.7325 (mp0) REVERT: B 640 VAL cc_start: 0.9516 (t) cc_final: 0.9185 (m) REVERT: B 798 MET cc_start: 0.7864 (mmm) cc_final: 0.7542 (mmp) REVERT: C 318 MET cc_start: 0.8029 (tpt) cc_final: 0.7583 (tpt) REVERT: C 728 CYS cc_start: 0.8520 (t) cc_final: 0.8135 (t) REVERT: D 281 GLU cc_start: 0.8904 (mp0) cc_final: 0.8455 (mp0) REVERT: D 406 TYR cc_start: 0.7551 (m-80) cc_final: 0.7277 (m-80) REVERT: D 752 TYR cc_start: 0.7680 (m-80) cc_final: 0.7002 (m-80) REVERT: E 279 GLU cc_start: 0.8569 (tt0) cc_final: 0.7525 (tm-30) REVERT: E 369 MET cc_start: 0.7776 (ttm) cc_final: 0.7340 (ttm) REVERT: E 402 MET cc_start: 0.8413 (mmm) cc_final: 0.7283 (ptm) REVERT: E 488 LYS cc_start: 0.8179 (pttm) cc_final: 0.7607 (tppt) REVERT: E 507 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7776 (pm20) REVERT: E 538 ILE cc_start: 0.8567 (mt) cc_final: 0.8259 (mp) REVERT: E 599 PHE cc_start: 0.8223 (t80) cc_final: 0.7390 (t80) REVERT: E 740 MET cc_start: 0.8663 (ppp) cc_final: 0.8180 (ppp) REVERT: E 782 LYS cc_start: 0.9227 (pttp) cc_final: 0.8990 (ptmm) REVERT: F 215 LEU cc_start: 0.8962 (tp) cc_final: 0.8677 (tp) REVERT: F 231 MET cc_start: 0.8246 (mmp) cc_final: 0.8015 (mmm) REVERT: F 300 PHE cc_start: 0.6898 (t80) cc_final: 0.6679 (t80) REVERT: F 302 ASP cc_start: 0.8000 (p0) cc_final: 0.7478 (p0) REVERT: F 362 ARG cc_start: 0.6879 (mmp-170) cc_final: 0.6174 (tpt90) REVERT: F 371 MET cc_start: 0.6797 (ppp) cc_final: 0.6428 (ppp) outliers start: 1 outliers final: 0 residues processed: 330 average time/residue: 0.1761 time to fit residues: 92.9657 Evaluate side-chains 227 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 84 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 334 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 337 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN C 741 GLN D 645 ASN D 799 HIS E 342 ASN F 283 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.083887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.070344 restraints weight = 123088.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.071620 restraints weight = 89098.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.072636 restraints weight = 63790.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.072982 restraints weight = 53581.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.073178 restraints weight = 48279.308| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.7637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27483 Z= 0.148 Angle : 0.641 10.301 37242 Z= 0.327 Chirality : 0.042 0.171 4219 Planarity : 0.006 0.106 4825 Dihedral : 11.104 89.200 4140 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.63 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.56 (0.15), residues: 3412 helix: 1.40 (0.12), residues: 1894 sheet: 0.47 (0.25), residues: 414 loop : -1.50 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 635 TYR 0.024 0.002 TYR D 752 PHE 0.037 0.002 PHE A 492 TRP 0.022 0.002 TRP C 219 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00326 (27483) covalent geometry : angle 0.64060 (37242) hydrogen bonds : bond 0.04134 ( 1365) hydrogen bonds : angle 4.76762 ( 4041) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.7773 (ttm) cc_final: 0.7369 (ptm) REVERT: A 601 ASP cc_start: 0.8941 (p0) cc_final: 0.7470 (t0) REVERT: A 616 ASP cc_start: 0.8099 (p0) cc_final: 0.7718 (p0) REVERT: A 638 ILE cc_start: 0.7222 (mp) cc_final: 0.6972 (mt) REVERT: A 798 MET cc_start: 0.6797 (tmm) cc_final: 0.6509 (tmm) REVERT: B 231 MET cc_start: 0.8889 (mtt) cc_final: 0.8345 (mtt) REVERT: B 304 ILE cc_start: 0.9345 (pt) cc_final: 0.9117 (mp) REVERT: B 497 ASP cc_start: 0.7343 (p0) cc_final: 0.7004 (p0) REVERT: B 498 THR cc_start: 0.8590 (p) cc_final: 0.8222 (t) REVERT: B 600 PHE cc_start: 0.9168 (m-10) cc_final: 0.8823 (m-10) REVERT: B 628 GLU cc_start: 0.7512 (mp0) cc_final: 0.7186 (mp0) REVERT: B 640 VAL cc_start: 0.9489 (t) cc_final: 0.9166 (m) REVERT: B 798 MET cc_start: 0.7789 (mmm) cc_final: 0.7488 (mmp) REVERT: C 318 MET cc_start: 0.8186 (tpt) cc_final: 0.7722 (tpt) REVERT: C 406 TYR cc_start: 0.7454 (m-80) cc_final: 0.7250 (m-80) REVERT: C 728 CYS cc_start: 0.8588 (t) cc_final: 0.8196 (t) REVERT: D 281 GLU cc_start: 0.9049 (mp0) cc_final: 0.8057 (mp0) REVERT: D 498 THR cc_start: 0.7249 (p) cc_final: 0.7032 (p) REVERT: D 752 TYR cc_start: 0.7780 (m-80) cc_final: 0.7071 (m-80) REVERT: E 279 GLU cc_start: 0.8686 (tt0) cc_final: 0.7612 (tm-30) REVERT: E 369 MET cc_start: 0.7659 (ttm) cc_final: 0.7264 (ttm) REVERT: E 402 MET cc_start: 0.8377 (mmm) cc_final: 0.7264 (ptm) REVERT: E 488 LYS cc_start: 0.8208 (pttm) cc_final: 0.7600 (tppt) REVERT: E 599 PHE cc_start: 0.8334 (t80) cc_final: 0.7561 (t80) REVERT: E 740 MET cc_start: 0.8643 (ppp) cc_final: 0.8180 (ppp) REVERT: F 300 PHE cc_start: 0.6694 (t80) cc_final: 0.6417 (t80) REVERT: F 302 ASP cc_start: 0.7908 (p0) cc_final: 0.7373 (p0) REVERT: F 362 ARG cc_start: 0.6785 (mmp-170) cc_final: 0.6195 (tpt90) REVERT: F 371 MET cc_start: 0.6991 (ppp) cc_final: 0.6694 (ppp) REVERT: F 646 ARG cc_start: 0.6950 (mtp180) cc_final: 0.6299 (tpt90) REVERT: F 782 LYS cc_start: 0.9226 (mmpt) cc_final: 0.8975 (ptmm) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.1741 time to fit residues: 89.1211 Evaluate side-chains 226 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 59 optimal weight: 0.7980 chunk 301 optimal weight: 2.9990 chunk 327 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 131 optimal weight: 20.0000 chunk 297 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 ASN ** F 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.082456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.068607 restraints weight = 124888.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.069965 restraints weight = 87855.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.070958 restraints weight = 67275.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.071624 restraints weight = 54681.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.072192 restraints weight = 46958.585| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.7950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27483 Z= 0.173 Angle : 0.670 10.344 37242 Z= 0.344 Chirality : 0.042 0.170 4219 Planarity : 0.006 0.106 4825 Dihedral : 10.951 87.805 4140 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.92 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.42 (0.15), residues: 3412 helix: 1.25 (0.12), residues: 1905 sheet: 0.46 (0.26), residues: 410 loop : -1.50 (0.20), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 361 TYR 0.044 0.002 TYR A 752 PHE 0.026 0.002 PHE E 587 TRP 0.025 0.002 TRP C 780 HIS 0.005 0.001 HIS F 242 Details of bonding type rmsd covalent geometry : bond 0.00380 (27483) covalent geometry : angle 0.66953 (37242) hydrogen bonds : bond 0.04253 ( 1365) hydrogen bonds : angle 4.91122 ( 4041) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.7882 (ttm) cc_final: 0.7383 (ptm) REVERT: A 596 CYS cc_start: 0.7549 (p) cc_final: 0.7201 (p) REVERT: A 798 MET cc_start: 0.6797 (tmm) cc_final: 0.6278 (tmm) REVERT: B 231 MET cc_start: 0.8987 (mtt) cc_final: 0.8402 (mtt) REVERT: B 390 LEU cc_start: 0.8616 (mt) cc_final: 0.8412 (mt) REVERT: B 497 ASP cc_start: 0.7676 (p0) cc_final: 0.7364 (p0) REVERT: B 498 THR cc_start: 0.8611 (p) cc_final: 0.8302 (t) REVERT: B 600 PHE cc_start: 0.9216 (m-10) cc_final: 0.8897 (m-10) REVERT: B 640 VAL cc_start: 0.9522 (t) cc_final: 0.9190 (m) REVERT: B 798 MET cc_start: 0.7824 (mmm) cc_final: 0.7524 (mmp) REVERT: C 231 MET cc_start: 0.8677 (ptp) cc_final: 0.8105 (ptt) REVERT: C 318 MET cc_start: 0.8263 (tpt) cc_final: 0.7771 (tpt) REVERT: C 406 TYR cc_start: 0.7548 (m-80) cc_final: 0.7328 (m-80) REVERT: C 728 CYS cc_start: 0.8613 (t) cc_final: 0.8190 (t) REVERT: D 281 GLU cc_start: 0.9083 (mp0) cc_final: 0.8072 (mp0) REVERT: D 498 THR cc_start: 0.7129 (p) cc_final: 0.6925 (p) REVERT: D 752 TYR cc_start: 0.7796 (m-80) cc_final: 0.7071 (m-80) REVERT: E 279 GLU cc_start: 0.8724 (tt0) cc_final: 0.7666 (tm-30) REVERT: E 369 MET cc_start: 0.7744 (ttm) cc_final: 0.7423 (ttm) REVERT: E 402 MET cc_start: 0.8415 (mmm) cc_final: 0.7246 (ptm) REVERT: E 488 LYS cc_start: 0.7998 (pttm) cc_final: 0.7451 (tppt) REVERT: E 581 ARG cc_start: 0.8178 (tpp-160) cc_final: 0.7749 (tpp-160) REVERT: E 599 PHE cc_start: 0.8354 (t80) cc_final: 0.7597 (t80) REVERT: E 740 MET cc_start: 0.8637 (ppp) cc_final: 0.8164 (ppp) REVERT: F 215 LEU cc_start: 0.9008 (tp) cc_final: 0.8804 (tp) REVERT: F 300 PHE cc_start: 0.7333 (t80) cc_final: 0.7043 (t80) REVERT: F 362 ARG cc_start: 0.6952 (mmp-170) cc_final: 0.6060 (ttp80) REVERT: F 371 MET cc_start: 0.6561 (ppp) cc_final: 0.6238 (ppp) REVERT: F 570 GLU cc_start: 0.8396 (pt0) cc_final: 0.8179 (pt0) REVERT: F 639 TYR cc_start: 0.7762 (m-80) cc_final: 0.7532 (m-80) REVERT: F 646 ARG cc_start: 0.6771 (mtp180) cc_final: 0.6041 (mmm160) REVERT: F 782 LYS cc_start: 0.9197 (mmpt) cc_final: 0.8895 (ptmm) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1820 time to fit residues: 90.3250 Evaluate side-chains 231 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 268 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 310 optimal weight: 20.0000 chunk 148 optimal weight: 0.9980 chunk 228 optimal weight: 20.0000 chunk 275 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 267 optimal weight: 5.9990 chunk 165 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 756 GLN D 645 ASN F 283 ASN F 379 GLN ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.082496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.068673 restraints weight = 123708.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.070113 restraints weight = 86915.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.071061 restraints weight = 65937.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.071795 restraints weight = 53737.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072353 restraints weight = 45704.742| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.8154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27483 Z= 0.150 Angle : 0.650 13.417 37242 Z= 0.330 Chirality : 0.042 0.173 4219 Planarity : 0.006 0.105 4825 Dihedral : 10.684 82.095 4140 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.42 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.47 (0.15), residues: 3412 helix: 1.28 (0.12), residues: 1908 sheet: 0.41 (0.25), residues: 406 loop : -1.44 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 361 TYR 0.021 0.002 TYR D 752 PHE 0.023 0.002 PHE E 587 TRP 0.027 0.002 TRP C 453 HIS 0.005 0.001 HIS F 242 Details of bonding type rmsd covalent geometry : bond 0.00333 (27483) covalent geometry : angle 0.64966 (37242) hydrogen bonds : bond 0.04090 ( 1365) hydrogen bonds : angle 4.82258 ( 4041) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.7934 (ttm) cc_final: 0.7621 (ptm) REVERT: A 596 CYS cc_start: 0.7500 (p) cc_final: 0.7246 (p) REVERT: A 798 MET cc_start: 0.6793 (tmm) cc_final: 0.6271 (tmm) REVERT: B 231 MET cc_start: 0.8735 (mtt) cc_final: 0.8217 (mtt) REVERT: B 497 ASP cc_start: 0.7795 (p0) cc_final: 0.7370 (p0) REVERT: B 498 THR cc_start: 0.8596 (p) cc_final: 0.8304 (t) REVERT: B 600 PHE cc_start: 0.9129 (m-10) cc_final: 0.8822 (m-10) REVERT: B 616 ASP cc_start: 0.8033 (p0) cc_final: 0.7339 (p0) REVERT: B 628 GLU cc_start: 0.7569 (mp0) cc_final: 0.7089 (mp0) REVERT: B 640 VAL cc_start: 0.9496 (t) cc_final: 0.9177 (m) REVERT: B 798 MET cc_start: 0.7792 (mmm) cc_final: 0.7483 (mmp) REVERT: C 318 MET cc_start: 0.8192 (tpt) cc_final: 0.7677 (tpt) REVERT: C 728 CYS cc_start: 0.8546 (t) cc_final: 0.8150 (t) REVERT: D 281 GLU cc_start: 0.8924 (mp0) cc_final: 0.7849 (mp0) REVERT: D 339 LEU cc_start: 0.7119 (tt) cc_final: 0.6677 (mp) REVERT: D 498 THR cc_start: 0.7196 (p) cc_final: 0.6974 (p) REVERT: D 752 TYR cc_start: 0.7751 (m-80) cc_final: 0.7042 (m-80) REVERT: E 279 GLU cc_start: 0.8712 (tt0) cc_final: 0.7718 (tm-30) REVERT: E 369 MET cc_start: 0.7630 (ttm) cc_final: 0.7339 (ttm) REVERT: E 402 MET cc_start: 0.8473 (mmm) cc_final: 0.7455 (ptm) REVERT: E 489 ARG cc_start: 0.7971 (pmt170) cc_final: 0.6996 (mpt180) REVERT: E 581 ARG cc_start: 0.8201 (tpp-160) cc_final: 0.7783 (tpp-160) REVERT: E 599 PHE cc_start: 0.8217 (t80) cc_final: 0.7527 (t80) REVERT: E 740 MET cc_start: 0.8687 (ppp) cc_final: 0.8208 (ppp) REVERT: F 215 LEU cc_start: 0.8916 (tp) cc_final: 0.8632 (tp) REVERT: F 362 ARG cc_start: 0.6961 (mmp-170) cc_final: 0.6022 (ttp80) REVERT: F 371 MET cc_start: 0.6970 (ppp) cc_final: 0.6648 (ppp) REVERT: F 646 ARG cc_start: 0.6872 (mtp180) cc_final: 0.6315 (mmm160) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.1833 time to fit residues: 91.8222 Evaluate side-chains 237 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 136 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 chunk 317 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 75 optimal weight: 0.0970 chunk 7 optimal weight: 0.0570 chunk 237 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 HIS ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 ASN ** E 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 ASN F 379 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.083186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.069730 restraints weight = 122441.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.071184 restraints weight = 87249.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.072376 restraints weight = 60978.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.072528 restraints weight = 51944.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.072679 restraints weight = 46423.886| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.8273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27483 Z= 0.127 Angle : 0.635 10.279 37242 Z= 0.323 Chirality : 0.041 0.175 4219 Planarity : 0.006 0.101 4825 Dihedral : 10.444 86.718 4140 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.59 (0.15), residues: 3412 helix: 1.36 (0.12), residues: 1908 sheet: 0.53 (0.25), residues: 405 loop : -1.38 (0.20), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 361 TYR 0.023 0.001 TYR D 752 PHE 0.022 0.002 PHE E 587 TRP 0.027 0.001 TRP C 219 HIS 0.005 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00280 (27483) covalent geometry : angle 0.63525 (37242) hydrogen bonds : bond 0.03903 ( 1365) hydrogen bonds : angle 4.73477 ( 4041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4197.46 seconds wall clock time: 73 minutes 38.79 seconds (4418.79 seconds total)