Starting phenix.real_space_refine on Mon Sep 14 00:46:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6mat_9063/09_2026/6mat_9063.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mat_9063/09_2026/6mat_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_9063/09_2026/6mat_9063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mat_9063/09_2026/6mat_9063.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6mat_9063/09_2026/6mat_9063.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6mat_9063/09_2026/6mat_9063.cif" model { file = "/net/cci-nas-00/data/ceres_data/6mat_9063/09_2026/6mat_9063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mat_9063/09_2026/6mat_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 6.16, per 1000 atoms: 0.23 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: 2.23 Conformation dependent library (CDL) restraints added in 1.1 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: 0.51 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: 4.42 Time building geometry restraints manager: 2.97 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: 15228 18.02 - 36.04: 940 36.04 - 54.06: 296 54.06 - 72.08: 136 72.08 - 90.09: 201 Dihedral angle restraints: 16801 sinusoidal: 6841 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 16798 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: 0.520 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: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.390 Find NCS groups from input model: 0.720 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: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 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 : 18.407 90.095 10355 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/Z covalent geometry : bond 0.01233 / 0.80 (27483) covalent geometry : angle 1.79757 / 1.25 (37242) hydrogen bonds : bond 0.25465 / 17.24 ( 1365) hydrogen bonds : angle 6.41148 / 4.58 ( 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 : 1.163 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: 0.4762 (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: 0.9165 (t0) cc_final: 0.8950 (t0) REVERT: B 231 MET cc_start: 0.8937 (mtt) cc_final: 0.8507 (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: 0.9097 (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: 0.7851 (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: 0.7853 (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: 0.7502 (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: 0.2088 time to fit residues: 302.9183 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 : 1.054 ------------------------------------------------------------------------------- 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... 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 C 254 HIS C 445 ASN C 450 GLN C 502 HIS C 573 ASN ** C 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 GLN D 254 HIS D 328 ASN 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 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 ASN E 502 HIS E 523 ASN ** F 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.091197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.076959 restraints weight = 117424.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.078548 restraints weight = 82122.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.079722 restraints weight = 62061.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.080583 restraints weight = 49349.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.081137 restraints weight = 41150.287| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27483 Z= 0.199 Angle : 0.799 10.257 37242 Z= 0.414 Chirality : 0.046 0.271 4219 Planarity : 0.007 0.094 4825 Dihedral : 6.414 87.634 3799 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.66 % Favored : 94.08 % Rotamer: Outliers : 0.28 % Allowed : 4.57 % Favored : 95.15 % 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: 0.18 (0.14), residues: 3412 helix: 1.57 (0.12), residues: 1833 sheet: 0.19 (0.25), residues: 420 loop : -2.40 (0.17), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 362 TYR 0.017 0.002 TYR A 406 PHE 0.020 0.002 PHE E 600 TRP 0.025 0.003 TRP C 780 HIS 0.010 0.001 HIS E 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 (27483) covalent geometry : angle 0.79890 / 0.41 (37242) hydrogen bonds : bond 0.06495 / 4.40 ( 1365) hydrogen bonds : angle 5.08366 / 3.63 ( 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 523 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 515 time to evaluate : 1.052 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 388 LEU cc_start: 0.8628 (tp) cc_final: 0.8377 (tt) REVERT: A 473 MET cc_start: 0.7856 (tpt) cc_final: 0.7637 (tpp) REVERT: A 500 TRP cc_start: 0.8431 (m100) cc_final: 0.8191 (m100) REVERT: A 601 ASP cc_start: 0.6593 (t0) cc_final: 0.6309 (t0) REVERT: A 738 ASN cc_start: 0.9107 (t0) cc_final: 0.8823 (t0) REVERT: A 740 MET cc_start: 0.8316 (tmm) cc_final: 0.8104 (tmm) REVERT: B 231 MET cc_start: 0.8974 (mtt) cc_final: 0.8370 (mtm) REVERT: B 240 LEU cc_start: 0.9005 (tp) cc_final: 0.8454 (mt) REVERT: B 616 ASP cc_start: 0.8132 (p0) cc_final: 0.7593 (p0) REVERT: B 798 MET cc_start: 0.7825 (mmm) cc_final: 0.7558 (mmm) REVERT: C 388 LEU cc_start: 0.8846 (mp) cc_final: 0.8553 (mp) REVERT: C 662 THR cc_start: 0.7894 (m) cc_final: 0.7556 (m) REVERT: C 740 MET cc_start: 0.8901 (tmm) cc_final: 0.8520 (tmm) REVERT: D 281 GLU cc_start: 0.9174 (mp0) cc_final: 0.8972 (mp0) REVERT: D 677 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8705 (tt) REVERT: D 682 TYR cc_start: 0.7977 (t80) cc_final: 0.7489 (t80) REVERT: E 285 ARG cc_start: 0.8566 (mpt-90) cc_final: 0.8225 (mmm-85) REVERT: E 318 MET cc_start: 0.8426 (ppp) cc_final: 0.7925 (ppp) REVERT: E 369 MET cc_start: 0.8037 (ttm) cc_final: 0.7656 (ttm) REVERT: E 377 ARG cc_start: 0.8526 (mtm-85) cc_final: 0.7201 (mtt-85) REVERT: E 402 MET cc_start: 0.8351 (mmm) cc_final: 0.7297 (ptm) REVERT: E 427 ILE cc_start: 0.7110 (mp) cc_final: 0.6352 (mp) REVERT: E 488 LYS cc_start: 0.8061 (pttm) cc_final: 0.7445 (tppt) REVERT: E 599 PHE cc_start: 0.8530 (t80) cc_final: 0.7874 (t80) REVERT: F 235 TYR cc_start: 0.3923 (p90) cc_final: 0.3551 (p90) REVERT: F 300 PHE cc_start: 0.6508 (t80) cc_final: 0.6285 (t80) REVERT: F 362 ARG cc_start: 0.5733 (mmp80) cc_final: 0.4661 (tpt90) REVERT: F 369 MET cc_start: 0.4975 (mtp) cc_final: 0.3859 (tpp) REVERT: F 452 ASP cc_start: 0.8429 (m-30) cc_final: 0.8172 (m-30) REVERT: F 623 ASN cc_start: 0.9202 (m-40) cc_final: 0.8627 (m-40) REVERT: F 639 TYR cc_start: 0.8072 (m-80) cc_final: 0.7771 (m-10) REVERT: F 777 MET cc_start: 0.9050 (tpt) cc_final: 0.8829 (tpp) outliers start: 8 outliers final: 0 residues processed: 521 average time/residue: 0.2041 time to fit residues: 160.9865 Evaluate side-chains 300 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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: 6.9990 chunk 182 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 165 optimal weight: 20.0000 chunk 334 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 chunk 210 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 290 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 HIS B 602 GLN B 745 GLN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 HIS ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 ASN ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 ASN E 424 GLN E 585 GLN F 395 ASN F 557 ASN F 573 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.086456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.072009 restraints weight = 124001.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.073560 restraints weight = 87147.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.074625 restraints weight = 65647.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.075395 restraints weight = 52965.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.075951 restraints weight = 44892.595| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 27483 Z= 0.211 Angle : 0.749 9.004 37242 Z= 0.386 Chirality : 0.044 0.232 4219 Planarity : 0.007 0.088 4825 Dihedral : 6.465 88.209 3799 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.59 % Favored : 93.17 % Rotamer: Outliers : 0.17 % Allowed : 5.58 % Favored : 94.24 % 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: 0.30 (0.15), residues: 3412 helix: 1.44 (0.12), residues: 1859 sheet: 0.37 (0.25), residues: 421 loop : -2.03 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 361 TYR 0.023 0.002 TYR A 413 PHE 0.033 0.002 PHE A 731 TRP 0.026 0.002 TRP E 541 HIS 0.007 0.002 HIS F 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (27483) covalent geometry : angle 0.74948 / 0.39 (37242) hydrogen bonds : bond 0.05298 / 3.62 ( 1365) hydrogen bonds : angle 4.97560 / 3.53 ( 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 391 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 386 time to evaluate : 1.072 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 388 LEU cc_start: 0.8761 (tp) cc_final: 0.8499 (tt) REVERT: A 413 TYR cc_start: 0.9110 (m-10) cc_final: 0.8801 (m-10) REVERT: A 576 VAL cc_start: 0.8382 (m) cc_final: 0.8071 (p) REVERT: A 677 ILE cc_start: 0.9570 (pt) cc_final: 0.9238 (tt) REVERT: A 738 ASN cc_start: 0.9152 (t0) cc_final: 0.8893 (t0) REVERT: A 740 MET cc_start: 0.8380 (tmm) cc_final: 0.8107 (tmm) REVERT: A 770 GLU cc_start: 0.6322 (tp30) cc_final: 0.5574 (tm-30) REVERT: B 231 MET cc_start: 0.9068 (mtt) cc_final: 0.8396 (mtt) REVERT: B 616 ASP cc_start: 0.8099 (p0) cc_final: 0.7480 (p0) REVERT: B 628 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7772 (mm-30) REVERT: B 640 VAL cc_start: 0.9591 (t) cc_final: 0.9269 (m) REVERT: B 798 MET cc_start: 0.7739 (mmm) cc_final: 0.7234 (mmm) REVERT: C 231 MET cc_start: 0.8179 (ptp) cc_final: 0.6846 (ptp) REVERT: C 406 TYR cc_start: 0.7795 (m-80) cc_final: 0.7586 (m-80) REVERT: E 285 ARG cc_start: 0.8499 (mpt-90) cc_final: 0.8064 (mmm-85) REVERT: E 318 MET cc_start: 0.8148 (ppp) cc_final: 0.7841 (ppp) REVERT: E 354 PHE cc_start: 0.8634 (t80) cc_final: 0.8431 (t80) REVERT: E 369 MET cc_start: 0.8116 (ttm) cc_final: 0.7781 (ttm) REVERT: E 402 MET cc_start: 0.8439 (mmm) cc_final: 0.7266 (ptm) REVERT: E 427 ILE cc_start: 0.7153 (mp) cc_final: 0.6537 (mm) REVERT: E 452 ASP cc_start: 0.8025 (m-30) cc_final: 0.7750 (m-30) REVERT: E 488 LYS cc_start: 0.8218 (pttm) cc_final: 0.7781 (tppt) REVERT: E 500 TRP cc_start: 0.8045 (m100) cc_final: 0.6935 (m100) REVERT: E 599 PHE cc_start: 0.8451 (t80) cc_final: 0.7763 (t80) REVERT: E 740 MET cc_start: 0.8809 (ppp) cc_final: 0.8427 (ppp) REVERT: E 780 TRP cc_start: 0.9051 (m100) cc_final: 0.8713 (m-90) REVERT: F 215 LEU cc_start: 0.8842 (tp) cc_final: 0.8630 (tp) REVERT: F 525 GLU cc_start: 0.7835 (pm20) cc_final: 0.7460 (pm20) REVERT: F 623 ASN cc_start: 0.9141 (m-40) cc_final: 0.8767 (m-40) REVERT: F 740 MET cc_start: 0.8520 (ppp) cc_final: 0.8246 (ppp) REVERT: F 777 MET cc_start: 0.8862 (tpt) cc_final: 0.8538 (tpp) outliers start: 5 outliers final: 0 residues processed: 389 average time/residue: 0.1817 time to fit residues: 110.2010 Evaluate side-chains 268 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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: 10.0000 chunk 7 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 245 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 145 optimal weight: 0.1980 chunk 172 optimal weight: 8.9990 chunk 336 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 HIS A 450 GLN B 602 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 799 HIS C 303 GLN C 785 ASN D 448 GLN D 738 ASN D 785 ASN E 303 GLN F 350 ASN ** F 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 573 ASN F 745 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.086004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.071845 restraints weight = 121943.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.073238 restraints weight = 85915.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.074266 restraints weight = 65949.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.075006 restraints weight = 53782.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.075537 restraints weight = 45858.117| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.6426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27483 Z= 0.186 Angle : 0.681 8.359 37242 Z= 0.349 Chirality : 0.043 0.182 4219 Planarity : 0.006 0.093 4825 Dihedral : 6.445 81.681 3799 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.60 % Favored : 94.17 % Rotamer: Outliers : 0.07 % Allowed : 3.35 % Favored : 96.58 % 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: 1.46 (0.12), residues: 1876 sheet: 0.47 (0.25), residues: 417 loop : -1.90 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG D 510 TYR 0.019 0.002 TYR A 752 PHE 0.022 0.002 PHE F 527 TRP 0.043 0.002 TRP D 500 HIS 0.007 0.001 HIS F 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (27483) covalent geometry : angle 0.68113 / 0.35 (37242) hydrogen bonds : bond 0.04622 / 3.15 ( 1365) hydrogen bonds : angle 4.86082 / 3.45 ( 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 366 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 364 time to evaluate : 1.066 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: 0.8933 (tmm) cc_final: 0.8276 (tmm) REVERT: A 616 ASP cc_start: 0.7878 (p0) cc_final: 0.7627 (p0) REVERT: A 677 ILE cc_start: 0.9540 (pt) cc_final: 0.9311 (tt) REVERT: A 738 ASN cc_start: 0.8964 (t0) cc_final: 0.8703 (t0) REVERT: B 231 MET cc_start: 0.8907 (mtt) cc_final: 0.8363 (mtt) REVERT: B 290 GLU cc_start: 0.8802 (mp0) cc_final: 0.8413 (mp0) REVERT: B 355 LEU cc_start: 0.9153 (mt) cc_final: 0.8867 (mp) REVERT: B 497 ASP cc_start: 0.6487 (p0) cc_final: 0.6250 (p0) REVERT: B 498 THR cc_start: 0.8640 (p) cc_final: 0.8258 (t) REVERT: B 628 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7594 (mm-30) REVERT: B 635 ARG cc_start: 0.7802 (ttt180) cc_final: 0.7479 (ttt180) REVERT: B 640 VAL cc_start: 0.9560 (t) cc_final: 0.9225 (m) REVERT: B 798 MET cc_start: 0.7639 (mmm) cc_final: 0.7374 (mmm) REVERT: C 231 MET cc_start: 0.8139 (ptp) cc_final: 0.6861 (ptp) REVERT: C 264 PHE cc_start: 0.8634 (t80) cc_final: 0.8394 (t80) REVERT: C 406 TYR cc_start: 0.7878 (m-80) cc_final: 0.7560 (m-80) REVERT: C 728 CYS cc_start: 0.8432 (t) cc_final: 0.8167 (t) REVERT: D 281 GLU cc_start: 0.8992 (mp0) cc_final: 0.8120 (mp0) REVERT: E 279 GLU cc_start: 0.8449 (tt0) cc_final: 0.7459 (tm-30) REVERT: E 285 ARG cc_start: 0.8651 (mpt-90) cc_final: 0.8267 (mmt-90) REVERT: E 318 MET cc_start: 0.8309 (ppp) cc_final: 0.8018 (ppp) REVERT: E 369 MET cc_start: 0.8024 (ttm) cc_final: 0.7590 (ttm) REVERT: E 402 MET cc_start: 0.8436 (mmm) cc_final: 0.7220 (ptm) REVERT: E 427 ILE cc_start: 0.7002 (mp) cc_final: 0.6678 (mm) REVERT: E 488 LYS cc_start: 0.8230 (pttm) cc_final: 0.7644 (tppt) REVERT: E 500 TRP cc_start: 0.8206 (m100) cc_final: 0.6910 (m100) REVERT: E 599 PHE cc_start: 0.8512 (t80) cc_final: 0.7564 (t80) REVERT: E 740 MET cc_start: 0.8738 (ppp) cc_final: 0.8297 (ppp) REVERT: F 215 LEU cc_start: 0.8809 (tp) cc_final: 0.8598 (tp) REVERT: F 231 MET cc_start: 0.8237 (mmp) cc_final: 0.8034 (mmm) REVERT: F 302 ASP cc_start: 0.8111 (p0) cc_final: 0.7643 (p0) REVERT: F 362 ARG cc_start: 0.6409 (mmp-170) cc_final: 0.5741 (tpt90) REVERT: F 371 MET cc_start: 0.6241 (ppp) cc_final: 0.5806 (ppp) REVERT: F 623 ASN cc_start: 0.9120 (m-40) cc_final: 0.8850 (m-40) REVERT: F 646 ARG cc_start: 0.6855 (mtp180) cc_final: 0.6396 (tpt90) REVERT: F 740 MET cc_start: 0.8541 (ppp) cc_final: 0.8264 (ppp) outliers start: 2 outliers final: 0 residues processed: 364 average time/residue: 0.1899 time to fit residues: 107.8134 Evaluate side-chains 255 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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: 9.9990 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 280 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 222 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 HIS B 785 ASN B 799 HIS C 484 GLN F 283 ASN ** F 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.084362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.070376 restraints weight = 122525.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.071833 restraints weight = 86121.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.072881 restraints weight = 65433.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.073588 restraints weight = 52714.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.074140 restraints weight = 45045.787| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.6895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27483 Z= 0.181 Angle : 0.663 10.751 37242 Z= 0.340 Chirality : 0.042 0.186 4219 Planarity : 0.006 0.097 4825 Dihedral : 6.386 75.825 3799 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.01 % Favored : 93.76 % 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: 0.43 (0.15), residues: 3412 helix: 1.38 (0.12), residues: 1891 sheet: 0.49 (0.25), residues: 415 loop : -1.76 (0.20), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 332 TYR 0.023 0.002 TYR E 413 PHE 0.020 0.002 PHE F 527 TRP 0.019 0.002 TRP F 780 HIS 0.008 0.001 HIS C 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (27483) covalent geometry : angle 0.66291 / 0.34 (37242) hydrogen bonds : bond 0.04497 / 3.06 ( 1365) hydrogen bonds : angle 4.86631 / 3.45 ( 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 334 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 332 time to evaluate : 1.060 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 413 TYR cc_start: 0.9186 (m-10) cc_final: 0.8861 (m-10) REVERT: A 515 MET cc_start: 0.8970 (tmm) cc_final: 0.8226 (tmm) REVERT: A 616 ASP cc_start: 0.7892 (p0) cc_final: 0.7596 (p0) REVERT: A 673 ASP cc_start: 0.7931 (m-30) cc_final: 0.7578 (m-30) REVERT: A 677 ILE cc_start: 0.9559 (pt) cc_final: 0.9336 (tt) REVERT: A 738 ASN cc_start: 0.9211 (t0) cc_final: 0.8970 (t0) REVERT: A 798 MET cc_start: 0.6921 (tmm) cc_final: 0.6626 (tmm) REVERT: B 231 MET cc_start: 0.8872 (mtt) cc_final: 0.8363 (mtt) REVERT: B 355 LEU cc_start: 0.9172 (mt) cc_final: 0.8879 (mp) REVERT: B 497 ASP cc_start: 0.6537 (p0) cc_final: 0.6156 (p0) REVERT: B 498 THR cc_start: 0.8692 (p) cc_final: 0.8352 (t) REVERT: B 513 LEU cc_start: 0.9563 (mt) cc_final: 0.9322 (mt) REVERT: B 640 VAL cc_start: 0.9592 (t) cc_final: 0.9239 (m) REVERT: B 798 MET cc_start: 0.7909 (mmm) cc_final: 0.7508 (mmp) REVERT: C 300 PHE cc_start: 0.8562 (t80) cc_final: 0.8310 (t80) REVERT: C 406 TYR cc_start: 0.8091 (m-80) cc_final: 0.7853 (m-80) REVERT: C 728 CYS cc_start: 0.8520 (t) cc_final: 0.8171 (t) REVERT: D 281 GLU cc_start: 0.8956 (mp0) cc_final: 0.8494 (mp0) REVERT: D 473 MET cc_start: 0.8003 (mmm) cc_final: 0.7785 (mmm) REVERT: E 279 GLU cc_start: 0.8577 (tt0) cc_final: 0.7403 (tm-30) REVERT: E 285 ARG cc_start: 0.8665 (mpt-90) cc_final: 0.8256 (mmt-90) REVERT: E 318 MET cc_start: 0.8312 (ppp) cc_final: 0.8014 (ppp) REVERT: E 369 MET cc_start: 0.8040 (ttm) cc_final: 0.7452 (ttm) REVERT: E 402 MET cc_start: 0.8292 (mmm) cc_final: 0.6930 (ptm) REVERT: E 427 ILE cc_start: 0.7038 (mp) cc_final: 0.6777 (mm) REVERT: E 488 LYS cc_start: 0.8133 (pttm) cc_final: 0.7564 (tppt) REVERT: E 500 TRP cc_start: 0.8490 (m100) cc_final: 0.8047 (m100) REVERT: E 507 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7815 (pm20) REVERT: E 538 ILE cc_start: 0.8449 (mt) cc_final: 0.8117 (mp) REVERT: E 599 PHE cc_start: 0.8459 (t80) cc_final: 0.7563 (t80) REVERT: E 740 MET cc_start: 0.8656 (ppp) cc_final: 0.8218 (ppp) REVERT: F 215 LEU cc_start: 0.8885 (tp) cc_final: 0.8656 (tp) REVERT: F 300 PHE cc_start: 0.6959 (t80) cc_final: 0.6483 (t80) REVERT: F 302 ASP cc_start: 0.7975 (p0) cc_final: 0.7365 (p0) REVERT: F 362 ARG cc_start: 0.6429 (mmp-170) cc_final: 0.5811 (tpt90) REVERT: F 371 MET cc_start: 0.6352 (ppp) cc_final: 0.5842 (ppp) REVERT: F 525 GLU cc_start: 0.7822 (pm20) cc_final: 0.7611 (pm20) REVERT: F 623 ASN cc_start: 0.9149 (m-40) cc_final: 0.8880 (m-40) REVERT: F 646 ARG cc_start: 0.7135 (mtp180) cc_final: 0.6455 (tpt90) outliers start: 2 outliers final: 0 residues processed: 332 average time/residue: 0.1761 time to fit residues: 93.2271 Evaluate side-chains 241 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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: 6.9990 chunk 248 optimal weight: 7.9990 chunk 316 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 310 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 ASN A 254 HIS A 562 ASN B 438 HIS C 741 GLN C 756 GLN D 623 ASN E 342 ASN E 684 ASN ** F 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.081911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.068228 restraints weight = 124613.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.069643 restraints weight = 87173.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.070647 restraints weight = 66043.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.071330 restraints weight = 53266.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.071898 restraints weight = 45343.096| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.7480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 27483 Z= 0.232 Angle : 0.715 8.946 37242 Z= 0.371 Chirality : 0.043 0.187 4219 Planarity : 0.007 0.102 4825 Dihedral : 6.684 75.947 3799 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.39 % Favored : 93.46 % Rotamer: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.96 % 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: 0.17 (0.15), residues: 3412 helix: 1.13 (0.12), residues: 1898 sheet: 0.36 (0.25), residues: 413 loop : -1.80 (0.20), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 361 TYR 0.020 0.002 TYR C 665 PHE 0.021 0.002 PHE C 600 TRP 0.021 0.002 TRP D 453 HIS 0.007 0.002 HIS C 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.23 (27483) covalent geometry : angle 0.71460 / 0.37 (37242) hydrogen bonds : bond 0.04635 / 3.17 ( 1365) hydrogen bonds : angle 5.02365 / 3.55 ( 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 315 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 1.040 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: A 365 VAL cc_start: 0.8177 (t) cc_final: 0.7612 (p) REVERT: A 413 TYR cc_start: 0.9091 (m-10) cc_final: 0.8775 (m-10) REVERT: A 616 ASP cc_start: 0.7955 (p0) cc_final: 0.7668 (p0) REVERT: A 638 ILE cc_start: 0.7623 (mp) cc_final: 0.7351 (mt) REVERT: A 798 MET cc_start: 0.7225 (tmm) cc_final: 0.6825 (tmm) REVERT: B 231 MET cc_start: 0.8835 (mtt) cc_final: 0.8272 (mtt) REVERT: B 240 LEU cc_start: 0.9301 (tp) cc_final: 0.9023 (tt) REVERT: B 290 GLU cc_start: 0.8951 (mp0) cc_final: 0.8628 (mp0) REVERT: B 355 LEU cc_start: 0.9107 (mt) cc_final: 0.8811 (mp) REVERT: B 497 ASP cc_start: 0.6932 (p0) cc_final: 0.6535 (p0) REVERT: B 498 THR cc_start: 0.8599 (p) cc_final: 0.8310 (t) REVERT: B 635 ARG cc_start: 0.7790 (ttt180) cc_final: 0.7499 (ttt90) REVERT: B 640 VAL cc_start: 0.9610 (t) cc_final: 0.9227 (m) REVERT: B 798 MET cc_start: 0.7832 (mmm) cc_final: 0.7479 (mmp) REVERT: C 231 MET cc_start: 0.8326 (ptp) cc_final: 0.7109 (ptp) REVERT: C 233 TYR cc_start: 0.6938 (m-10) cc_final: 0.6652 (m-80) REVERT: C 300 PHE cc_start: 0.8406 (t80) cc_final: 0.8164 (t80) REVERT: C 728 CYS cc_start: 0.8489 (t) cc_final: 0.8160 (t) REVERT: D 240 LEU cc_start: 0.9299 (tp) cc_final: 0.9064 (tp) REVERT: D 281 GLU cc_start: 0.8939 (mp0) cc_final: 0.8524 (mp0) REVERT: D 369 MET cc_start: 0.8071 (ttp) cc_final: 0.7756 (ttp) REVERT: E 279 GLU cc_start: 0.8690 (tt0) cc_final: 0.7564 (tm-30) REVERT: E 318 MET cc_start: 0.8122 (ppp) cc_final: 0.7846 (ppp) REVERT: E 325 GLU cc_start: 0.8181 (tp30) cc_final: 0.7922 (tp30) REVERT: E 369 MET cc_start: 0.7950 (ttm) cc_final: 0.7561 (ttm) REVERT: E 402 MET cc_start: 0.8353 (mmm) cc_final: 0.7019 (ptm) REVERT: E 489 ARG cc_start: 0.8178 (pmt170) cc_final: 0.7061 (mpt180) REVERT: E 500 TRP cc_start: 0.8655 (m100) cc_final: 0.8168 (m100) REVERT: E 599 PHE cc_start: 0.8479 (t80) cc_final: 0.7588 (t80) REVERT: E 740 MET cc_start: 0.8701 (ppp) cc_final: 0.8188 (ppp) REVERT: F 215 LEU cc_start: 0.8876 (tp) cc_final: 0.8651 (tp) REVERT: F 300 PHE cc_start: 0.6944 (t80) cc_final: 0.6696 (t80) REVERT: F 302 ASP cc_start: 0.8153 (p0) cc_final: 0.7605 (p0) REVERT: F 362 ARG cc_start: 0.6564 (mmp-170) cc_final: 0.5984 (tpt90) REVERT: F 371 MET cc_start: 0.6462 (ppp) cc_final: 0.5984 (ppp) REVERT: F 525 GLU cc_start: 0.7921 (pm20) cc_final: 0.7691 (pm20) REVERT: F 623 ASN cc_start: 0.9178 (m-40) cc_final: 0.8955 (m-40) REVERT: F 646 ARG cc_start: 0.6843 (mtp180) cc_final: 0.5999 (mmm160) outliers start: 1 outliers final: 0 residues processed: 314 average time/residue: 0.1792 time to fit residues: 88.9453 Evaluate side-chains 229 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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: 7.9990 chunk 130 optimal weight: 0.2980 chunk 235 optimal weight: 5.9990 chunk 291 optimal weight: 10.0000 chunk 263 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 324 optimal weight: 7.9990 chunk 265 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 426 ASN D 557 ASN D 645 ASN F 283 ASN F 684 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.082780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.068962 restraints weight = 123232.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.070378 restraints weight = 86151.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071385 restraints weight = 65262.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.072125 restraints weight = 52832.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.072657 restraints weight = 44735.723| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.7692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27483 Z= 0.160 Angle : 0.650 8.633 37242 Z= 0.333 Chirality : 0.042 0.174 4219 Planarity : 0.006 0.101 4825 Dihedral : 6.545 80.437 3799 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.95 % Favored : 93.87 % Rotamer: Outliers : 0.03 % Allowed : 1.36 % Favored : 98.60 % 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: 0.36 (0.15), residues: 3412 helix: 1.31 (0.12), residues: 1886 sheet: 0.30 (0.25), residues: 410 loop : -1.67 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 361 TYR 0.031 0.002 TYR D 752 PHE 0.021 0.002 PHE A 423 TRP 0.020 0.002 TRP C 219 HIS 0.007 0.001 HIS C 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (27483) covalent geometry : angle 0.65015 / 0.33 (37242) hydrogen bonds : bond 0.04298 / 2.94 ( 1365) hydrogen bonds : angle 4.85742 / 3.44 ( 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 322 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 321 time to evaluate : 1.112 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: A 365 VAL cc_start: 0.8293 (t) cc_final: 0.7968 (m) REVERT: A 413 TYR cc_start: 0.9075 (m-10) cc_final: 0.8786 (m-10) REVERT: A 616 ASP cc_start: 0.8013 (p0) cc_final: 0.7694 (p0) REVERT: A 638 ILE cc_start: 0.7552 (mp) cc_final: 0.7244 (mt) REVERT: A 798 MET cc_start: 0.7232 (tmm) cc_final: 0.6794 (tmm) REVERT: B 231 MET cc_start: 0.8945 (mtt) cc_final: 0.8307 (mtt) REVERT: B 290 GLU cc_start: 0.8926 (mp0) cc_final: 0.8538 (mp0) REVERT: B 355 LEU cc_start: 0.9214 (mt) cc_final: 0.8896 (mp) REVERT: B 497 ASP cc_start: 0.7370 (p0) cc_final: 0.7034 (p0) REVERT: B 498 THR cc_start: 0.8645 (p) cc_final: 0.8384 (t) REVERT: B 600 PHE cc_start: 0.9106 (m-10) cc_final: 0.8828 (m-10) REVERT: B 640 VAL cc_start: 0.9572 (t) cc_final: 0.9218 (m) REVERT: B 798 MET cc_start: 0.7829 (mmm) cc_final: 0.7454 (mmm) REVERT: C 231 MET cc_start: 0.8427 (ptp) cc_final: 0.7248 (ptp) REVERT: C 233 TYR cc_start: 0.6993 (m-10) cc_final: 0.6694 (m-80) REVERT: C 300 PHE cc_start: 0.8430 (t80) cc_final: 0.8207 (t80) REVERT: C 728 CYS cc_start: 0.8570 (t) cc_final: 0.8166 (t) REVERT: D 281 GLU cc_start: 0.8941 (mp0) cc_final: 0.8516 (mp0) REVERT: E 279 GLU cc_start: 0.8666 (tt0) cc_final: 0.7582 (tm-30) REVERT: E 318 MET cc_start: 0.8082 (ppp) cc_final: 0.7835 (ppp) REVERT: E 369 MET cc_start: 0.7785 (ttm) cc_final: 0.7444 (ttm) REVERT: E 371 MET cc_start: 0.6603 (ptp) cc_final: 0.6361 (ptm) REVERT: E 402 MET cc_start: 0.8327 (mmm) cc_final: 0.7035 (ptm) REVERT: E 500 TRP cc_start: 0.8635 (m100) cc_final: 0.8114 (m100) REVERT: E 599 PHE cc_start: 0.8375 (t80) cc_final: 0.7579 (t80) REVERT: E 740 MET cc_start: 0.8710 (ppp) cc_final: 0.8197 (ppp) REVERT: F 215 LEU cc_start: 0.8892 (tp) cc_final: 0.8532 (tp) REVERT: F 302 ASP cc_start: 0.8158 (p0) cc_final: 0.7703 (p0) REVERT: F 362 ARG cc_start: 0.6542 (mmp-170) cc_final: 0.5950 (tpt90) REVERT: F 371 MET cc_start: 0.6727 (ppp) cc_final: 0.6278 (ppp) REVERT: F 623 ASN cc_start: 0.9180 (m-40) cc_final: 0.8961 (m-40) REVERT: F 646 ARG cc_start: 0.6876 (mtp180) cc_final: 0.6134 (mmm160) outliers start: 1 outliers final: 0 residues processed: 321 average time/residue: 0.1564 time to fit residues: 80.8109 Evaluate side-chains 235 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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: 20.0000 chunk 42 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 337 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 799 HIS F 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.081750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.068083 restraints weight = 124834.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.069501 restraints weight = 86900.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.070521 restraints weight = 65732.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.071266 restraints weight = 52907.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.071765 restraints weight = 44698.874| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.7976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27483 Z= 0.172 Angle : 0.651 10.156 37242 Z= 0.332 Chirality : 0.042 0.171 4219 Planarity : 0.006 0.103 4825 Dihedral : 6.589 86.492 3799 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.36 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 0.30 (0.15), residues: 3412 helix: 1.22 (0.12), residues: 1909 sheet: 0.27 (0.25), residues: 410 loop : -1.65 (0.20), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 361 TYR 0.031 0.002 TYR C 406 PHE 0.039 0.002 PHE A 492 TRP 0.023 0.002 TRP C 219 HIS 0.011 0.002 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (27483) covalent geometry : angle 0.65114 / 0.33 (37242) hydrogen bonds : bond 0.04277 / 2.92 ( 1365) hydrogen bonds : angle 4.86327 / 3.43 ( 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 312 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.988 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 365 VAL cc_start: 0.8460 (t) cc_final: 0.8132 (m) REVERT: A 413 TYR cc_start: 0.9025 (m-10) cc_final: 0.8769 (m-10) REVERT: A 596 CYS cc_start: 0.7106 (p) cc_final: 0.6855 (p) REVERT: A 616 ASP cc_start: 0.8196 (p0) cc_final: 0.7721 (p0) REVERT: A 638 ILE cc_start: 0.7855 (mp) cc_final: 0.7567 (mt) REVERT: A 798 MET cc_start: 0.7280 (tmm) cc_final: 0.6814 (tmm) REVERT: B 231 MET cc_start: 0.8890 (mtt) cc_final: 0.8194 (mtt) REVERT: B 355 LEU cc_start: 0.9200 (mt) cc_final: 0.8890 (mp) REVERT: B 497 ASP cc_start: 0.7527 (p0) cc_final: 0.7251 (p0) REVERT: B 498 THR cc_start: 0.8615 (p) cc_final: 0.8380 (t) REVERT: B 600 PHE cc_start: 0.9118 (m-10) cc_final: 0.8787 (m-10) REVERT: B 640 VAL cc_start: 0.9573 (t) cc_final: 0.9227 (m) REVERT: B 798 MET cc_start: 0.7848 (mmm) cc_final: 0.7568 (mmp) REVERT: C 231 MET cc_start: 0.8493 (ptp) cc_final: 0.7486 (ptp) REVERT: C 233 TYR cc_start: 0.7067 (m-10) cc_final: 0.6661 (m-80) REVERT: C 300 PHE cc_start: 0.8349 (t80) cc_final: 0.8065 (t80) REVERT: C 318 MET cc_start: 0.8236 (tpt) cc_final: 0.7712 (tpt) REVERT: C 728 CYS cc_start: 0.8521 (t) cc_final: 0.8132 (t) REVERT: D 281 GLU cc_start: 0.9018 (mp0) cc_final: 0.8043 (mp0) REVERT: E 279 GLU cc_start: 0.8677 (tt0) cc_final: 0.7631 (tm-30) REVERT: E 318 MET cc_start: 0.8051 (ppp) cc_final: 0.7837 (ppp) REVERT: E 369 MET cc_start: 0.7741 (ttm) cc_final: 0.7462 (ttm) REVERT: E 371 MET cc_start: 0.6627 (ptp) cc_final: 0.6404 (ptm) REVERT: E 402 MET cc_start: 0.8367 (mmm) cc_final: 0.7195 (ptm) REVERT: E 599 PHE cc_start: 0.8362 (t80) cc_final: 0.7561 (t80) REVERT: E 740 MET cc_start: 0.8678 (ppp) cc_final: 0.8180 (ppp) REVERT: F 215 LEU cc_start: 0.8916 (tp) cc_final: 0.8582 (tp) REVERT: F 282 LYS cc_start: 0.5237 (tttm) cc_final: 0.4871 (tttm) REVERT: F 300 PHE cc_start: 0.7093 (t80) cc_final: 0.6649 (t80) REVERT: F 371 MET cc_start: 0.6528 (ppp) cc_final: 0.6097 (ppp) REVERT: F 646 ARG cc_start: 0.6712 (mtp180) cc_final: 0.6129 (mmm160) REVERT: F 782 LYS cc_start: 0.9199 (mmpt) cc_final: 0.8925 (ptmm) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.1762 time to fit residues: 88.1197 Evaluate side-chains 230 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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: 3.9990 chunk 301 optimal weight: 3.9990 chunk 327 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 76 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 131 optimal weight: 0.0270 chunk 297 optimal weight: 9.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 HIS C 741 GLN D 645 ASN F 283 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.083496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.069610 restraints weight = 121445.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.071032 restraints weight = 85401.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.072053 restraints weight = 64964.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.072797 restraints weight = 52485.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.073298 restraints weight = 44619.248| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.8043 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= 0.124 Angle : 0.628 8.556 37242 Z= 0.318 Chirality : 0.042 0.195 4219 Planarity : 0.006 0.100 4825 Dihedral : 6.403 88.477 3799 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.13 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: 0.52 (0.15), residues: 3412 helix: 1.40 (0.12), residues: 1892 sheet: 0.35 (0.25), residues: 406 loop : -1.50 (0.20), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 683 TYR 0.027 0.001 TYR D 752 PHE 0.023 0.001 PHE F 354 TRP 0.025 0.002 TRP C 219 HIS 0.007 0.001 HIS C 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (27483) covalent geometry : angle 0.62784 / 0.32 (37242) hydrogen bonds : bond 0.03930 / 2.69 ( 1365) hydrogen bonds : angle 4.72435 / 3.32 ( 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 327 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.123 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: A 365 VAL cc_start: 0.8312 (t) cc_final: 0.7864 (m) REVERT: A 369 MET cc_start: 0.8169 (ttm) cc_final: 0.7892 (ptm) REVERT: A 473 MET cc_start: 0.7546 (tpt) cc_final: 0.7159 (tpp) REVERT: A 489 ARG cc_start: 0.7798 (ptt-90) cc_final: 0.7576 (mtm110) REVERT: A 596 CYS cc_start: 0.7068 (p) cc_final: 0.6868 (p) REVERT: A 616 ASP cc_start: 0.8176 (p0) cc_final: 0.7663 (p0) REVERT: A 638 ILE cc_start: 0.7830 (mp) cc_final: 0.7523 (mt) REVERT: A 798 MET cc_start: 0.7387 (tmm) cc_final: 0.6997 (tmm) REVERT: B 231 MET cc_start: 0.8878 (mtt) cc_final: 0.8351 (mtt) REVERT: B 355 LEU cc_start: 0.9173 (mt) cc_final: 0.8866 (mp) REVERT: B 497 ASP cc_start: 0.7658 (p0) cc_final: 0.7372 (p0) REVERT: B 498 THR cc_start: 0.8642 (p) cc_final: 0.8425 (t) REVERT: B 527 PHE cc_start: 0.7494 (m-80) cc_final: 0.6743 (m-80) REVERT: B 600 PHE cc_start: 0.9148 (m-10) cc_final: 0.8849 (m-10) REVERT: B 616 ASP cc_start: 0.8097 (p0) cc_final: 0.7410 (p0) REVERT: B 640 VAL cc_start: 0.9547 (t) cc_final: 0.9182 (m) REVERT: B 798 MET cc_start: 0.7761 (mmm) cc_final: 0.7460 (mmp) REVERT: C 231 MET cc_start: 0.8422 (ptp) cc_final: 0.7371 (ptp) REVERT: C 289 ASP cc_start: 0.7786 (m-30) cc_final: 0.7556 (m-30) REVERT: C 318 MET cc_start: 0.8082 (tpt) cc_final: 0.7502 (tpt) REVERT: C 406 TYR cc_start: 0.7715 (m-80) cc_final: 0.7500 (m-80) REVERT: C 497 ASP cc_start: 0.8538 (p0) cc_final: 0.8337 (m-30) REVERT: C 728 CYS cc_start: 0.8476 (t) cc_final: 0.8082 (t) REVERT: D 281 GLU cc_start: 0.8962 (mp0) cc_final: 0.8107 (mp0) REVERT: D 752 TYR cc_start: 0.7722 (m-80) cc_final: 0.7020 (m-80) REVERT: E 279 GLU cc_start: 0.8669 (tt0) cc_final: 0.7704 (tm-30) REVERT: E 369 MET cc_start: 0.7632 (ttm) cc_final: 0.7358 (ttm) REVERT: E 402 MET cc_start: 0.8375 (mmm) cc_final: 0.7337 (ptm) REVERT: E 599 PHE cc_start: 0.8296 (t80) cc_final: 0.7625 (t80) REVERT: E 660 LEU cc_start: 0.8001 (mt) cc_final: 0.7711 (mt) REVERT: E 740 MET cc_start: 0.8680 (ppp) cc_final: 0.8177 (ppp) REVERT: F 215 LEU cc_start: 0.8872 (tp) cc_final: 0.8519 (tp) REVERT: F 300 PHE cc_start: 0.6734 (t80) cc_final: 0.6303 (t80) REVERT: F 369 MET cc_start: 0.3462 (mpp) cc_final: 0.3118 (mpp) REVERT: F 371 MET cc_start: 0.6861 (ppp) cc_final: 0.6281 (ppp) REVERT: F 646 ARG cc_start: 0.6611 (mtp180) cc_final: 0.6186 (mmm160) REVERT: F 782 LYS cc_start: 0.9202 (mmpt) cc_final: 0.8997 (ptmm) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1779 time to fit residues: 93.6060 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 : 1.059 ------------------------------------------------------------------------------- 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: 0.0570 chunk 94 optimal weight: 6.9990 chunk 310 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 228 optimal weight: 0.0050 chunk 275 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 267 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 218 optimal weight: 0.8980 overall best weight: 1.7714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 HIS ** A 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 ASN 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 = 0.3584 r_free = 0.3584 target = 0.083339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.069506 restraints weight = 121715.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.070926 restraints weight = 84758.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.071940 restraints weight = 64295.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.072680 restraints weight = 51981.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.073182 restraints weight = 44017.289| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.8166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27483 Z= 0.128 Angle : 0.643 11.193 37242 Z= 0.327 Chirality : 0.042 0.183 4219 Planarity : 0.006 0.099 4825 Dihedral : 6.320 88.637 3799 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.54 % Favored : 94.37 % 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: 0.52 (0.15), residues: 3412 helix: 1.36 (0.12), residues: 1892 sheet: 0.41 (0.25), residues: 406 loop : -1.45 (0.20), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 635 TYR 0.026 0.002 TYR D 752 PHE 0.024 0.002 PHE C 300 TRP 0.024 0.002 TRP C 219 HIS 0.008 0.001 HIS C 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (27483) covalent geometry : angle 0.64323 / 0.33 (37242) hydrogen bonds : bond 0.03924 / 2.70 ( 1365) hydrogen bonds : angle 4.74085 / 3.33 ( 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 320 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.088 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 365 VAL cc_start: 0.8202 (t) cc_final: 0.7789 (m) REVERT: A 369 MET cc_start: 0.8210 (ttm) cc_final: 0.7922 (ptm) REVERT: A 473 MET cc_start: 0.7249 (tpt) cc_final: 0.6949 (tpp) REVERT: A 596 CYS cc_start: 0.7439 (p) cc_final: 0.7235 (p) REVERT: A 638 ILE cc_start: 0.7789 (mp) cc_final: 0.7432 (mt) REVERT: A 798 MET cc_start: 0.7391 (tmm) cc_final: 0.6975 (tmm) REVERT: B 231 MET cc_start: 0.8880 (mtt) cc_final: 0.8304 (mtt) REVERT: B 355 LEU cc_start: 0.9183 (mt) cc_final: 0.8903 (mp) REVERT: B 497 ASP cc_start: 0.7669 (p0) cc_final: 0.7417 (p0) REVERT: B 498 THR cc_start: 0.8594 (p) cc_final: 0.8362 (t) REVERT: B 527 PHE cc_start: 0.7365 (m-80) cc_final: 0.6812 (m-80) REVERT: B 600 PHE cc_start: 0.9121 (m-10) cc_final: 0.8796 (m-10) REVERT: B 616 ASP cc_start: 0.8108 (p0) cc_final: 0.7396 (p0) REVERT: B 640 VAL cc_start: 0.9499 (t) cc_final: 0.9196 (m) REVERT: B 798 MET cc_start: 0.7706 (mmm) cc_final: 0.7428 (mmp) REVERT: C 231 MET cc_start: 0.8555 (ptp) cc_final: 0.7644 (ptp) REVERT: C 318 MET cc_start: 0.8000 (tpt) cc_final: 0.7472 (tpt) REVERT: C 728 CYS cc_start: 0.8391 (t) cc_final: 0.8013 (t) REVERT: D 281 GLU cc_start: 0.8862 (mp0) cc_final: 0.8053 (mp0) REVERT: D 339 LEU cc_start: 0.7143 (tt) cc_final: 0.6546 (mp) REVERT: D 752 TYR cc_start: 0.7672 (m-80) cc_final: 0.7027 (m-80) REVERT: E 356 ASP cc_start: 0.8598 (t0) cc_final: 0.8322 (t0) REVERT: E 361 ARG cc_start: 0.8596 (mmt90) cc_final: 0.8177 (mmm-85) REVERT: E 369 MET cc_start: 0.7621 (ttm) cc_final: 0.7405 (ttm) REVERT: E 402 MET cc_start: 0.8383 (mmm) cc_final: 0.7510 (ptm) REVERT: E 599 PHE cc_start: 0.8167 (t80) cc_final: 0.7520 (t80) REVERT: E 660 LEU cc_start: 0.8044 (mt) cc_final: 0.7699 (mt) REVERT: E 740 MET cc_start: 0.8675 (ppp) cc_final: 0.8428 (ppp) REVERT: F 215 LEU cc_start: 0.8956 (tp) cc_final: 0.8618 (tp) REVERT: F 282 LYS cc_start: 0.4769 (tttm) cc_final: 0.4399 (tttm) REVERT: F 300 PHE cc_start: 0.6724 (t80) cc_final: 0.6288 (t80) REVERT: F 369 MET cc_start: 0.3972 (mpp) cc_final: 0.3769 (mpp) REVERT: F 371 MET cc_start: 0.6865 (ppp) cc_final: 0.6308 (ppp) REVERT: F 646 ARG cc_start: 0.6675 (mtp180) cc_final: 0.6311 (mmm160) REVERT: F 777 MET cc_start: 0.8748 (tpp) cc_final: 0.8183 (tpp) REVERT: F 782 LYS cc_start: 0.9211 (mmpt) cc_final: 0.8941 (ptmm) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.1679 time to fit residues: 87.6977 Evaluate side-chains 238 residues out of total 2872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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: 0.9990 chunk 23 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 237 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 HIS ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 283 ASN F 379 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.081224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.067657 restraints weight = 123915.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.069048 restraints weight = 87724.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.070027 restraints weight = 66824.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.070737 restraints weight = 54181.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.071271 restraints weight = 46184.347| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.8392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27483 Z= 0.171 Angle : 0.667 9.576 37242 Z= 0.342 Chirality : 0.042 0.192 4219 Planarity : 0.006 0.103 4825 Dihedral : 6.477 87.999 3799 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.27 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: 0.37 (0.15), residues: 3412 helix: 1.24 (0.12), residues: 1905 sheet: 0.36 (0.24), residues: 403 loop : -1.55 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 635 TYR 0.038 0.002 TYR A 752 PHE 0.019 0.002 PHE C 300 TRP 0.025 0.002 TRP C 219 HIS 0.007 0.001 HIS C 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (27483) covalent geometry : angle 0.66714 / 0.34 (37242) hydrogen bonds : bond 0.04170 / 2.86 ( 1365) hydrogen bonds : angle 4.89213 / 3.45 ( 4041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4114.72 seconds wall clock time: 72 minutes 16.13 seconds (4336.13 seconds total)