Starting phenix.real_space_refine on Wed Aug 27 03:00:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lw1_23544/08_2025/7lw1_23544_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lw1_23544/08_2025/7lw1_23544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lw1_23544/08_2025/7lw1_23544_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lw1_23544/08_2025/7lw1_23544_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lw1_23544/08_2025/7lw1_23544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lw1_23544/08_2025/7lw1_23544.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.334 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 20 5.49 5 S 148 5.16 5 C 14464 2.51 5 N 4052 2.21 5 O 4404 1.98 5 H 22704 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.14s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45792 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 11355 Classifications: {'peptide': 744} Link IDs: {'PTRANS': 20, 'TRANS': 723} Chain: "D" Number of atoms: 11355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 11355 Classifications: {'peptide': 744} Link IDs: {'PTRANS': 20, 'TRANS': 723} Chain: "E" Number of atoms: 11355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 11355 Classifications: {'peptide': 744} Link IDs: {'PTRANS': 20, 'TRANS': 723} Chain: "F" Number of atoms: 11355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 11355 Classifications: {'peptide': 744} Link IDs: {'PTRANS': 20, 'TRANS': 723} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'ADP': 1, 'F6P': 1, 'FBP': 1, 'YG1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'ADP': 1, 'F6P': 1, 'FBP': 1, 'YG1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'ADP': 1, 'F6P': 1, 'FBP': 1, 'YG1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'ADP': 1, 'F6P': 1, 'FBP': 1, 'YG1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1' ADP A 804 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP A 804 " occ=0.50 residue: pdb=" C1' ADP D 804 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP D 804 " occ=0.50 residue: pdb=" C1' ADP E 804 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP E 804 " occ=0.50 residue: pdb=" C1' ADP F 804 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP F 804 " occ=0.50 Time building chain proxies: 6.71, per 1000 atoms: 0.15 Number of scatterers: 45792 At special positions: 0 Unit cell: (158.55, 127.05, 129.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 148 16.00 P 20 15.00 O 4404 8.00 N 4052 7.00 C 14464 6.00 H 22704 1.00 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: 3.14 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5312 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 20 sheets defined 52.7% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 29 through 44 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 94 through 109 removed outlier: 3.902A pdb=" N ALA A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 131 removed outlier: 3.643A pdb=" N ALA A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 177 through 200 removed outlier: 4.366A pdb=" N THR A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 238 through 253 removed outlier: 4.053A pdb=" N PHE A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 306 through 327 Processing helix chain 'A' and resid 348 through 364 removed outlier: 3.662A pdb=" N VAL A 358 " --> pdb=" O MET A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 375 removed outlier: 4.070A pdb=" N GLY A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 391 Processing helix chain 'A' and resid 413 through 428 Processing helix chain 'A' and resid 437 through 444 Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.860A pdb=" N VAL A 455 " --> pdb=" O TRP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 475 removed outlier: 3.912A pdb=" N GLY A 475 " --> pdb=" O LEU A 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 475' Processing helix chain 'A' and resid 476 through 488 removed outlier: 3.840A pdb=" N GLU A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.501A pdb=" N LEU A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS A 518 " --> pdb=" O GLU A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 514 through 518' Processing helix chain 'A' and resid 540 through 562 removed outlier: 3.576A pdb=" N SER A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 554 " --> pdb=" O GLU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 600 through 615 removed outlier: 3.742A pdb=" N MET A 615 " --> pdb=" O MET A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 668 through 692 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 723 through 727 removed outlier: 3.961A pdb=" N LYS A 727 " --> pdb=" O GLU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 742 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.908A pdb=" N MET A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 94 through 109 removed outlier: 3.902A pdb=" N ALA D 100 " --> pdb=" O GLU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 131 removed outlier: 3.643A pdb=" N ALA D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 142 Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 177 through 200 removed outlier: 4.365A pdb=" N THR D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 224 Processing helix chain 'D' and resid 238 through 253 removed outlier: 4.053A pdb=" N PHE D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 306 through 327 Processing helix chain 'D' and resid 348 through 364 removed outlier: 3.661A pdb=" N VAL D 358 " --> pdb=" O MET D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 375 removed outlier: 4.071A pdb=" N GLY D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 391 Processing helix chain 'D' and resid 413 through 428 Processing helix chain 'D' and resid 437 through 444 Processing helix chain 'D' and resid 452 through 456 removed outlier: 3.861A pdb=" N VAL D 455 " --> pdb=" O TRP D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 475 removed outlier: 3.912A pdb=" N GLY D 475 " --> pdb=" O LEU D 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 472 through 475' Processing helix chain 'D' and resid 476 through 488 removed outlier: 3.840A pdb=" N GLU D 482 " --> pdb=" O GLU D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 509 Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.501A pdb=" N LEU D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS D 518 " --> pdb=" O GLU D 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 514 through 518' Processing helix chain 'D' and resid 540 through 562 removed outlier: 3.576A pdb=" N SER D 551 " --> pdb=" O ALA D 547 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D 554 " --> pdb=" O GLU D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 588 Processing helix chain 'D' and resid 600 through 615 removed outlier: 3.742A pdb=" N MET D 615 " --> pdb=" O MET D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 647 Processing helix chain 'D' and resid 659 through 664 Processing helix chain 'D' and resid 668 through 692 Processing helix chain 'D' and resid 703 through 705 No H-bonds generated for 'chain 'D' and resid 703 through 705' Processing helix chain 'D' and resid 723 through 727 removed outlier: 3.961A pdb=" N LYS D 727 " --> pdb=" O GLU D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 742 Processing helix chain 'D' and resid 743 through 752 removed outlier: 3.908A pdb=" N MET D 747 " --> pdb=" O SER D 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 94 through 109 removed outlier: 3.902A pdb=" N ALA E 100 " --> pdb=" O GLU E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 131 removed outlier: 3.643A pdb=" N ALA E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 142 Processing helix chain 'E' and resid 146 through 153 Processing helix chain 'E' and resid 177 through 200 removed outlier: 4.366A pdb=" N THR E 194 " --> pdb=" O ASP E 190 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 224 Processing helix chain 'E' and resid 238 through 253 removed outlier: 4.053A pdb=" N PHE E 242 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 288 Processing helix chain 'E' and resid 297 through 302 Processing helix chain 'E' and resid 306 through 327 Processing helix chain 'E' and resid 348 through 364 removed outlier: 3.662A pdb=" N VAL E 358 " --> pdb=" O MET E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 375 removed outlier: 4.071A pdb=" N GLY E 375 " --> pdb=" O THR E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 391 Processing helix chain 'E' and resid 413 through 428 Processing helix chain 'E' and resid 437 through 444 Processing helix chain 'E' and resid 452 through 456 removed outlier: 3.860A pdb=" N VAL E 455 " --> pdb=" O TRP E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 475 removed outlier: 3.912A pdb=" N GLY E 475 " --> pdb=" O LEU E 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 472 through 475' Processing helix chain 'E' and resid 476 through 488 removed outlier: 3.840A pdb=" N GLU E 482 " --> pdb=" O GLU E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 509 Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.501A pdb=" N LEU E 517 " --> pdb=" O TYR E 514 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS E 518 " --> pdb=" O GLU E 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 514 through 518' Processing helix chain 'E' and resid 540 through 562 removed outlier: 3.577A pdb=" N SER E 551 " --> pdb=" O ALA E 547 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG E 554 " --> pdb=" O GLU E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 588 Processing helix chain 'E' and resid 600 through 615 removed outlier: 3.741A pdb=" N MET E 615 " --> pdb=" O MET E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 647 Processing helix chain 'E' and resid 659 through 664 Processing helix chain 'E' and resid 668 through 692 Processing helix chain 'E' and resid 703 through 705 No H-bonds generated for 'chain 'E' and resid 703 through 705' Processing helix chain 'E' and resid 723 through 727 removed outlier: 3.961A pdb=" N LYS E 727 " --> pdb=" O GLU E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 739 through 742 Processing helix chain 'E' and resid 743 through 752 removed outlier: 3.908A pdb=" N MET E 747 " --> pdb=" O SER E 743 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 44 Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 94 through 109 removed outlier: 3.902A pdb=" N ALA F 100 " --> pdb=" O GLU F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 131 removed outlier: 3.643A pdb=" N ALA F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 142 Processing helix chain 'F' and resid 146 through 153 Processing helix chain 'F' and resid 177 through 200 removed outlier: 4.365A pdb=" N THR F 194 " --> pdb=" O ASP F 190 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR F 195 " --> pdb=" O ALA F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 224 Processing helix chain 'F' and resid 238 through 253 removed outlier: 4.053A pdb=" N PHE F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG F 251 " --> pdb=" O LEU F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 288 Processing helix chain 'F' and resid 297 through 302 Processing helix chain 'F' and resid 306 through 327 Processing helix chain 'F' and resid 348 through 364 removed outlier: 3.662A pdb=" N VAL F 358 " --> pdb=" O MET F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 375 removed outlier: 4.070A pdb=" N GLY F 375 " --> pdb=" O THR F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 391 Processing helix chain 'F' and resid 413 through 428 Processing helix chain 'F' and resid 437 through 444 Processing helix chain 'F' and resid 452 through 456 removed outlier: 3.860A pdb=" N VAL F 455 " --> pdb=" O TRP F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 475 removed outlier: 3.912A pdb=" N GLY F 475 " --> pdb=" O LEU F 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 472 through 475' Processing helix chain 'F' and resid 476 through 488 removed outlier: 3.840A pdb=" N GLU F 482 " --> pdb=" O GLU F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 497 through 509 Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.500A pdb=" N LEU F 517 " --> pdb=" O TYR F 514 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS F 518 " --> pdb=" O GLU F 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 514 through 518' Processing helix chain 'F' and resid 540 through 562 removed outlier: 3.576A pdb=" N SER F 551 " --> pdb=" O ALA F 547 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG F 554 " --> pdb=" O GLU F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 588 Processing helix chain 'F' and resid 600 through 615 removed outlier: 3.742A pdb=" N MET F 615 " --> pdb=" O MET F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 635 through 647 Processing helix chain 'F' and resid 659 through 664 Processing helix chain 'F' and resid 668 through 692 Processing helix chain 'F' and resid 703 through 705 No H-bonds generated for 'chain 'F' and resid 703 through 705' Processing helix chain 'F' and resid 723 through 727 removed outlier: 3.961A pdb=" N LYS F 727 " --> pdb=" O GLU F 724 " (cutoff:3.500A) Processing helix chain 'F' and resid 739 through 742 Processing helix chain 'F' and resid 743 through 752 removed outlier: 3.908A pdb=" N MET F 747 " --> pdb=" O SER F 743 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 67 removed outlier: 4.946A pdb=" N THR A 22 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA A 17 " --> pdb=" O ASN A 112 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N CYS A 114 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY A 19 " --> pdb=" O CYS A 114 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE A 116 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU A 21 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 113 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU A 161 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL A 115 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS A 334 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 162 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU A 338 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN A 342 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 229 removed outlier: 6.493A pdb=" N TRP A 227 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ALA A 263 " --> pdb=" O TRP A 227 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE A 229 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE A 203 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE A 262 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU A 205 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 447 through 449 removed outlier: 6.362A pdb=" N LEU A 402 " --> pdb=" O TYR A 433 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL A 435 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 404 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER A 401 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N LEU A 493 " --> pdb=" O SER A 401 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA A 403 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL A 495 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU A 405 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N MET A 521 " --> pdb=" O CYS A 708 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE A 710 " --> pdb=" O MET A 521 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL A 523 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N LEU A 712 " --> pdb=" O VAL A 523 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 591 through 593 removed outlier: 6.318A pdb=" N ALA A 591 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASN A 627 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR A 593 " --> pdb=" O ASN A 627 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG A 565 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL A 624 " --> pdb=" O ARG A 565 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE A 567 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ARG A 626 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL A 569 " --> pdb=" O ARG A 626 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 729 through 730 Processing sheet with id=AA6, first strand: chain 'D' and resid 65 through 67 removed outlier: 4.947A pdb=" N THR D 22 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA D 17 " --> pdb=" O ASN D 112 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N CYS D 114 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY D 19 " --> pdb=" O CYS D 114 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE D 116 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 21 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU D 113 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU D 161 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL D 115 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS D 334 " --> pdb=" O ILE D 158 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL D 162 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU D 338 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN D 342 " --> pdb=" O SER D 339 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.493A pdb=" N TRP D 227 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ALA D 263 " --> pdb=" O TRP D 227 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE D 229 " --> pdb=" O ALA D 263 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE D 203 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE D 262 " --> pdb=" O PHE D 203 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU D 205 " --> pdb=" O ILE D 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 447 through 449 removed outlier: 6.362A pdb=" N LEU D 402 " --> pdb=" O TYR D 433 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL D 435 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE D 404 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER D 401 " --> pdb=" O ALA D 491 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N LEU D 493 " --> pdb=" O SER D 401 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA D 403 " --> pdb=" O LEU D 493 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL D 495 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU D 405 " --> pdb=" O VAL D 495 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET D 521 " --> pdb=" O CYS D 708 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE D 710 " --> pdb=" O MET D 521 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL D 523 " --> pdb=" O ILE D 710 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N LEU D 712 " --> pdb=" O VAL D 523 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 591 through 593 removed outlier: 6.318A pdb=" N ALA D 591 " --> pdb=" O LEU D 625 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASN D 627 " --> pdb=" O ALA D 591 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR D 593 " --> pdb=" O ASN D 627 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG D 565 " --> pdb=" O GLY D 622 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL D 624 " --> pdb=" O ARG D 565 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE D 567 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG D 626 " --> pdb=" O PHE D 567 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL D 569 " --> pdb=" O ARG D 626 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 729 through 730 Processing sheet with id=AB2, first strand: chain 'E' and resid 65 through 67 removed outlier: 4.947A pdb=" N THR E 22 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA E 17 " --> pdb=" O ASN E 112 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N CYS E 114 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY E 19 " --> pdb=" O CYS E 114 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ILE E 116 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU E 21 " --> pdb=" O ILE E 116 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU E 113 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU E 161 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL E 115 " --> pdb=" O LEU E 161 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS E 334 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL E 162 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N LEU E 338 " --> pdb=" O VAL E 162 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN E 342 " --> pdb=" O SER E 339 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 227 through 229 removed outlier: 6.493A pdb=" N TRP E 227 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ALA E 263 " --> pdb=" O TRP E 227 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N PHE E 229 " --> pdb=" O ALA E 263 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 447 through 449 removed outlier: 6.362A pdb=" N LEU E 402 " --> pdb=" O TYR E 433 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL E 435 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE E 404 " --> pdb=" O VAL E 435 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER E 401 " --> pdb=" O ALA E 491 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LEU E 493 " --> pdb=" O SER E 401 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA E 403 " --> pdb=" O LEU E 493 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL E 495 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU E 405 " --> pdb=" O VAL E 495 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N MET E 521 " --> pdb=" O CYS E 708 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE E 710 " --> pdb=" O MET E 521 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL E 523 " --> pdb=" O ILE E 710 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N LEU E 712 " --> pdb=" O VAL E 523 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 591 through 593 removed outlier: 6.317A pdb=" N ALA E 591 " --> pdb=" O LEU E 625 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASN E 627 " --> pdb=" O ALA E 591 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR E 593 " --> pdb=" O ASN E 627 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG E 565 " --> pdb=" O GLY E 622 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL E 624 " --> pdb=" O ARG E 565 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE E 567 " --> pdb=" O VAL E 624 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG E 626 " --> pdb=" O PHE E 567 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL E 569 " --> pdb=" O ARG E 626 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 729 through 730 Processing sheet with id=AB7, first strand: chain 'F' and resid 65 through 67 removed outlier: 4.947A pdb=" N THR F 22 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA F 17 " --> pdb=" O ASN F 112 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N CYS F 114 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY F 19 " --> pdb=" O CYS F 114 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE F 116 " --> pdb=" O GLY F 19 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU F 21 " --> pdb=" O ILE F 116 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU F 113 " --> pdb=" O ALA F 159 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU F 161 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL F 115 " --> pdb=" O LEU F 161 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS F 334 " --> pdb=" O ILE F 158 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL F 162 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N LEU F 338 " --> pdb=" O VAL F 162 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN F 342 " --> pdb=" O SER F 339 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 227 through 229 removed outlier: 6.493A pdb=" N TRP F 227 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ALA F 263 " --> pdb=" O TRP F 227 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE F 229 " --> pdb=" O ALA F 263 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE F 203 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE F 262 " --> pdb=" O PHE F 203 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU F 205 " --> pdb=" O ILE F 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 447 through 449 removed outlier: 6.363A pdb=" N LEU F 402 " --> pdb=" O TYR F 433 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL F 435 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE F 404 " --> pdb=" O VAL F 435 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER F 401 " --> pdb=" O ALA F 491 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N LEU F 493 " --> pdb=" O SER F 401 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA F 403 " --> pdb=" O LEU F 493 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL F 495 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU F 405 " --> pdb=" O VAL F 495 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N MET F 521 " --> pdb=" O CYS F 708 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE F 710 " --> pdb=" O MET F 521 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL F 523 " --> pdb=" O ILE F 710 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N LEU F 712 " --> pdb=" O VAL F 523 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 591 through 593 removed outlier: 6.318A pdb=" N ALA F 591 " --> pdb=" O LEU F 625 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ASN F 627 " --> pdb=" O ALA F 591 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TYR F 593 " --> pdb=" O ASN F 627 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 565 " --> pdb=" O GLY F 622 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL F 624 " --> pdb=" O ARG F 565 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE F 567 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG F 626 " --> pdb=" O PHE F 567 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL F 569 " --> pdb=" O ARG F 626 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 729 through 730 1161 hydrogen bonds defined for protein. 3363 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: 10.43 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 15394 1.09 - 1.27: 11082 1.27 - 1.45: 6743 1.45 - 1.64: 12761 1.64 - 1.82: 240 Bond restraints: 46220 Sorted by residual: bond pdb=" C5 FBP A 802 " pdb=" O5 FBP A 802 " ideal model delta sigma weight residual 1.608 1.417 0.191 2.00e-02 2.50e+03 9.08e+01 bond pdb=" C5 FBP D 802 " pdb=" O5 FBP D 802 " ideal model delta sigma weight residual 1.608 1.417 0.191 2.00e-02 2.50e+03 9.08e+01 bond pdb=" C5 FBP F 802 " pdb=" O5 FBP F 802 " ideal model delta sigma weight residual 1.608 1.417 0.191 2.00e-02 2.50e+03 9.08e+01 bond pdb=" C5 FBP E 802 " pdb=" O5 FBP E 802 " ideal model delta sigma weight residual 1.608 1.417 0.191 2.00e-02 2.50e+03 9.07e+01 bond pdb=" C2 F6P E 803 " pdb=" O5 F6P E 803 " ideal model delta sigma weight residual 1.600 1.418 0.182 2.00e-02 2.50e+03 8.24e+01 ... (remaining 46215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.98: 81984 6.98 - 13.95: 1172 13.95 - 20.93: 40 20.93 - 27.90: 44 27.90 - 34.88: 40 Bond angle restraints: 83280 Sorted by residual: angle pdb=" CG2 VAL E 162 " pdb=" CB VAL E 162 " pdb=" HB VAL E 162 " ideal model delta sigma weight residual 108.00 73.12 34.88 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CG2 VAL D 162 " pdb=" CB VAL D 162 " pdb=" HB VAL D 162 " ideal model delta sigma weight residual 108.00 73.16 34.84 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CG2 VAL A 162 " pdb=" CB VAL A 162 " pdb=" HB VAL A 162 " ideal model delta sigma weight residual 108.00 73.16 34.84 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CG2 VAL F 162 " pdb=" CB VAL F 162 " pdb=" HB VAL F 162 " ideal model delta sigma weight residual 108.00 73.19 34.81 3.00e+00 1.11e-01 1.35e+02 angle pdb=" CA VAL E 709 " pdb=" CB VAL E 709 " pdb=" CG1 VAL E 709 " ideal model delta sigma weight residual 110.40 129.88 -19.48 1.70e+00 3.46e-01 1.31e+02 ... (remaining 83275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 20661 35.70 - 71.41: 959 71.41 - 107.11: 70 107.11 - 142.81: 5 142.81 - 178.52: 5 Dihedral angle restraints: 21700 sinusoidal: 12052 harmonic: 9648 Sorted by residual: dihedral pdb=" O1B ADP E 804 " pdb=" O3A ADP E 804 " pdb=" PB ADP E 804 " pdb=" PA ADP E 804 " ideal model delta sinusoidal sigma weight residual 300.00 143.89 156.11 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O1B ADP A 804 " pdb=" O3A ADP A 804 " pdb=" PB ADP A 804 " pdb=" PA ADP A 804 " ideal model delta sinusoidal sigma weight residual 300.00 143.89 156.11 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' ADP E 804 " pdb=" O5' ADP E 804 " pdb=" PA ADP E 804 " pdb=" O2A ADP E 804 " ideal model delta sinusoidal sigma weight residual 300.00 157.54 142.46 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 21697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.240: 3433 0.240 - 0.480: 111 0.480 - 0.720: 0 0.720 - 0.960: 12 0.960 - 1.200: 4 Chirality restraints: 3560 Sorted by residual: chirality pdb=" CB VAL E 709 " pdb=" CA VAL E 709 " pdb=" CG1 VAL E 709 " pdb=" CG2 VAL E 709 " both_signs ideal model delta sigma weight residual False -2.63 -1.43 -1.20 2.00e-01 2.50e+01 3.60e+01 chirality pdb=" CB VAL D 709 " pdb=" CA VAL D 709 " pdb=" CG1 VAL D 709 " pdb=" CG2 VAL D 709 " both_signs ideal model delta sigma weight residual False -2.63 -1.43 -1.20 2.00e-01 2.50e+01 3.60e+01 chirality pdb=" CB VAL F 709 " pdb=" CA VAL F 709 " pdb=" CG1 VAL F 709 " pdb=" CG2 VAL F 709 " both_signs ideal model delta sigma weight residual False -2.63 -1.43 -1.20 2.00e-01 2.50e+01 3.60e+01 ... (remaining 3557 not shown) Planarity restraints: 6956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 654 " -0.135 9.50e-02 1.11e+02 1.15e-01 2.53e+02 pdb=" NE ARG F 654 " -0.079 2.00e-02 2.50e+03 pdb=" CZ ARG F 654 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG F 654 " 0.058 2.00e-02 2.50e+03 pdb=" NH2 ARG F 654 " 0.017 2.00e-02 2.50e+03 pdb="HH11 ARG F 654 " 0.151 2.00e-02 2.50e+03 pdb="HH12 ARG F 654 " -0.233 2.00e-02 2.50e+03 pdb="HH21 ARG F 654 " -0.019 2.00e-02 2.50e+03 pdb="HH22 ARG F 654 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 654 " 0.135 9.50e-02 1.11e+02 1.15e-01 2.53e+02 pdb=" NE ARG D 654 " 0.079 2.00e-02 2.50e+03 pdb=" CZ ARG D 654 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D 654 " -0.058 2.00e-02 2.50e+03 pdb=" NH2 ARG D 654 " -0.017 2.00e-02 2.50e+03 pdb="HH11 ARG D 654 " -0.151 2.00e-02 2.50e+03 pdb="HH12 ARG D 654 " 0.233 2.00e-02 2.50e+03 pdb="HH21 ARG D 654 " 0.019 2.00e-02 2.50e+03 pdb="HH22 ARG D 654 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 654 " -0.135 9.50e-02 1.11e+02 1.15e-01 2.53e+02 pdb=" NE ARG E 654 " -0.080 2.00e-02 2.50e+03 pdb=" CZ ARG E 654 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG E 654 " 0.058 2.00e-02 2.50e+03 pdb=" NH2 ARG E 654 " 0.017 2.00e-02 2.50e+03 pdb="HH11 ARG E 654 " 0.151 2.00e-02 2.50e+03 pdb="HH12 ARG E 654 " -0.233 2.00e-02 2.50e+03 pdb="HH21 ARG E 654 " -0.019 2.00e-02 2.50e+03 pdb="HH22 ARG E 654 " 0.113 2.00e-02 2.50e+03 ... (remaining 6953 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.03: 1260 2.03 - 2.67: 59655 2.67 - 3.31: 144380 3.31 - 3.96: 193781 3.96 - 4.60: 288934 Nonbonded interactions: 688010 Sorted by model distance: nonbonded pdb="HH22 ARG F 734 " pdb=" O5P FBP F 802 " model vdw 1.384 2.450 nonbonded pdb="HH22 ARG E 734 " pdb=" O4P FBP E 802 " model vdw 1.384 2.450 nonbonded pdb="HH22 ARG A 734 " pdb=" O4P FBP A 802 " model vdw 1.384 2.450 nonbonded pdb="HH22 ARG D 734 " pdb=" O5P FBP D 802 " model vdw 1.385 2.450 nonbonded pdb=" HG SER D 121 " pdb=" O1B ADP D 804 " model vdw 1.393 2.450 ... (remaining 688005 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.320 Extract box with map and model: 0.450 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 37.420 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 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 : 0.014 0.191 23516 Z= 0.851 Angle : 2.111 19.484 31844 Z= 1.354 Chirality : 0.123 1.200 3560 Planarity : 0.016 0.163 4064 Dihedral : 16.963 178.516 8744 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.45 % Favored : 95.42 % Rotamer: Outliers : 1.00 % Allowed : 4.68 % Favored : 94.31 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.68 (0.14), residues: 2968 helix: -1.86 (0.11), residues: 1412 sheet: -0.04 (0.25), residues: 348 loop : -0.17 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG D 39 TYR 0.195 0.024 TYR E 754 PHE 0.088 0.016 PHE D 169 TRP 0.109 0.024 TRP D 458 HIS 0.011 0.004 HIS D 211 Details of bonding type rmsd covalent geometry : bond 0.01441 (23516) covalent geometry : angle 2.11075 (31844) hydrogen bonds : bond 0.17014 ( 1161) hydrogen bonds : angle 8.07498 ( 3363) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 594 time to evaluate : 1.195 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8159 (t80) cc_final: 0.7877 (t80) REVERT: A 293 VAL cc_start: 0.8842 (p) cc_final: 0.8559 (p) REVERT: A 346 LEU cc_start: 0.8035 (mt) cc_final: 0.7794 (mt) REVERT: A 349 MET cc_start: 0.6160 (mmm) cc_final: 0.5687 (mmm) REVERT: A 353 GLN cc_start: 0.7120 (mm-40) cc_final: 0.6743 (mm-40) REVERT: A 448 GLN cc_start: 0.7833 (pt0) cc_final: 0.7505 (pt0) REVERT: A 743 SER cc_start: 0.8585 (p) cc_final: 0.8328 (m) REVERT: D 43 TYR cc_start: 0.8142 (t80) cc_final: 0.7912 (t80) REVERT: D 293 VAL cc_start: 0.8846 (p) cc_final: 0.8496 (p) REVERT: D 346 LEU cc_start: 0.8045 (mt) cc_final: 0.7811 (mt) REVERT: D 349 MET cc_start: 0.6196 (mmm) cc_final: 0.5774 (mmm) REVERT: D 353 GLN cc_start: 0.7165 (mm-40) cc_final: 0.6768 (mm-40) REVERT: D 448 GLN cc_start: 0.7861 (pt0) cc_final: 0.7495 (pt0) REVERT: E 43 TYR cc_start: 0.8136 (t80) cc_final: 0.7919 (t80) REVERT: E 56 GLU cc_start: 0.6647 (tm-30) cc_final: 0.6121 (tm-30) REVERT: E 293 VAL cc_start: 0.8847 (p) cc_final: 0.8568 (p) REVERT: E 346 LEU cc_start: 0.8069 (mt) cc_final: 0.7816 (mt) REVERT: E 349 MET cc_start: 0.6178 (mmm) cc_final: 0.5701 (mmm) REVERT: E 353 GLN cc_start: 0.7127 (mm-40) cc_final: 0.6736 (mm-40) REVERT: E 448 GLN cc_start: 0.7799 (pt0) cc_final: 0.7473 (pt0) REVERT: E 602 HIS cc_start: 0.6717 (t70) cc_final: 0.6477 (t-170) REVERT: F 43 TYR cc_start: 0.8150 (t80) cc_final: 0.7844 (t80) REVERT: F 293 VAL cc_start: 0.8848 (p) cc_final: 0.8557 (p) REVERT: F 346 LEU cc_start: 0.8062 (mt) cc_final: 0.7828 (mt) REVERT: F 349 MET cc_start: 0.6196 (mmm) cc_final: 0.5746 (mmm) REVERT: F 353 GLN cc_start: 0.7120 (mm-40) cc_final: 0.6767 (mm-40) REVERT: F 448 GLN cc_start: 0.7828 (pt0) cc_final: 0.7476 (pt0) REVERT: F 732 GLU cc_start: 0.6662 (tt0) cc_final: 0.6451 (tt0) REVERT: F 743 SER cc_start: 0.8560 (p) cc_final: 0.8318 (m) outliers start: 24 outliers final: 8 residues processed: 618 average time/residue: 1.0569 time to fit residues: 776.4799 Evaluate side-chains 450 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 442 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 363 ASP Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain F residue 601 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 285 GLN A 406 ASN A 476 GLN A 607 ASN A 620 GLN A 641 ASN D 383 ASN D 406 ASN D 476 GLN D 607 ASN D 620 GLN D 641 ASN E 67 GLN E 75 ASN E 406 ASN E 476 GLN E 607 ASN E 620 GLN E 641 ASN E 660 HIS F 75 ASN F 383 ASN F 406 ASN F 476 GLN F 607 ASN F 641 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.157578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.128199 restraints weight = 74445.715| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.65 r_work: 0.3231 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23516 Z= 0.185 Angle : 0.812 10.963 31844 Z= 0.425 Chirality : 0.104 1.426 3560 Planarity : 0.005 0.057 4064 Dihedral : 12.783 158.943 3559 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.17 % Allowed : 12.79 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: -0.43 (0.15), residues: 2968 helix: -0.17 (0.13), residues: 1440 sheet: -0.39 (0.23), residues: 424 loop : -0.10 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 470 TYR 0.018 0.002 TYR D 674 PHE 0.015 0.002 PHE A 651 TRP 0.010 0.001 TRP D 685 HIS 0.011 0.002 HIS E 660 Details of bonding type rmsd covalent geometry : bond 0.00405 (23516) covalent geometry : angle 0.81215 (31844) hydrogen bonds : bond 0.05371 ( 1161) hydrogen bonds : angle 5.37032 ( 3363) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 481 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 MET cc_start: 0.8125 (mtp) cc_final: 0.7679 (mtp) REVERT: A 293 VAL cc_start: 0.8861 (p) cc_final: 0.8580 (p) REVERT: A 346 LEU cc_start: 0.8010 (mt) cc_final: 0.7767 (mt) REVERT: A 349 MET cc_start: 0.7152 (mmm) cc_final: 0.6557 (mmm) REVERT: A 353 GLN cc_start: 0.7395 (mm-40) cc_final: 0.6801 (mm-40) REVERT: A 448 GLN cc_start: 0.8079 (pt0) cc_final: 0.7737 (pt0) REVERT: A 468 THR cc_start: 0.7750 (t) cc_final: 0.7353 (t) REVERT: A 476 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7562 (mm-40) REVERT: A 482 GLU cc_start: 0.7298 (tp30) cc_final: 0.6948 (mm-30) REVERT: A 485 ARG cc_start: 0.7088 (ttm170) cc_final: 0.6767 (ttm-80) REVERT: A 486 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7436 (mp) REVERT: A 490 HIS cc_start: 0.8336 (m90) cc_final: 0.7784 (m170) REVERT: A 615 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.7099 (mpt) REVERT: A 743 SER cc_start: 0.9058 (p) cc_final: 0.8720 (m) REVERT: D 208 MET cc_start: 0.8152 (mtp) cc_final: 0.7739 (mtp) REVERT: D 293 VAL cc_start: 0.8874 (p) cc_final: 0.8598 (p) REVERT: D 346 LEU cc_start: 0.8123 (mt) cc_final: 0.7893 (mt) REVERT: D 349 MET cc_start: 0.7178 (mmm) cc_final: 0.6552 (mmm) REVERT: D 353 GLN cc_start: 0.7434 (mm-40) cc_final: 0.6842 (mm-40) REVERT: D 448 GLN cc_start: 0.8098 (pt0) cc_final: 0.7751 (pt0) REVERT: D 468 THR cc_start: 0.7778 (t) cc_final: 0.7403 (t) REVERT: D 482 GLU cc_start: 0.7314 (tp30) cc_final: 0.6962 (mm-30) REVERT: D 485 ARG cc_start: 0.7121 (ttm170) cc_final: 0.6863 (ttm110) REVERT: D 486 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7477 (mp) REVERT: D 490 HIS cc_start: 0.8324 (m90) cc_final: 0.7770 (m170) REVERT: D 564 ARG cc_start: 0.8443 (mtt-85) cc_final: 0.8212 (mtt-85) REVERT: D 601 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8584 (pp) REVERT: D 615 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.7263 (mpt) REVERT: D 727 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8186 (ptpp) REVERT: D 743 SER cc_start: 0.8987 (p) cc_final: 0.8653 (m) REVERT: E 43 TYR cc_start: 0.8338 (t80) cc_final: 0.8077 (t80) REVERT: E 208 MET cc_start: 0.8162 (mtp) cc_final: 0.7956 (mtp) REVERT: E 226 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: E 293 VAL cc_start: 0.8881 (p) cc_final: 0.8590 (p) REVERT: E 316 MET cc_start: 0.8730 (mmp) cc_final: 0.8490 (mmp) REVERT: E 346 LEU cc_start: 0.8073 (mt) cc_final: 0.7840 (mt) REVERT: E 349 MET cc_start: 0.7113 (mmm) cc_final: 0.6455 (mmt) REVERT: E 353 GLN cc_start: 0.7376 (mm-40) cc_final: 0.6771 (mm-40) REVERT: E 448 GLN cc_start: 0.8038 (pt0) cc_final: 0.7705 (pt0) REVERT: E 476 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7554 (mm-40) REVERT: E 482 GLU cc_start: 0.7374 (tp30) cc_final: 0.7022 (mm-30) REVERT: E 486 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7414 (mp) REVERT: E 490 HIS cc_start: 0.8315 (m90) cc_final: 0.7777 (m170) REVERT: E 564 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.8230 (mtt-85) REVERT: E 601 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8526 (pp) REVERT: E 602 HIS cc_start: 0.7729 (t70) cc_final: 0.7476 (t70) REVERT: E 615 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.7193 (mpt) REVERT: E 727 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8215 (ptpp) REVERT: F 208 MET cc_start: 0.8095 (mtp) cc_final: 0.7674 (mtp) REVERT: F 293 VAL cc_start: 0.8857 (p) cc_final: 0.8567 (p) REVERT: F 346 LEU cc_start: 0.8085 (mt) cc_final: 0.7866 (mt) REVERT: F 353 GLN cc_start: 0.7390 (mm-40) cc_final: 0.6826 (mm-40) REVERT: F 448 GLN cc_start: 0.8073 (pt0) cc_final: 0.7725 (pt0) REVERT: F 468 THR cc_start: 0.7761 (t) cc_final: 0.7383 (t) REVERT: F 490 HIS cc_start: 0.8348 (m90) cc_final: 0.7812 (m170) REVERT: F 615 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.7309 (mpt) REVERT: F 743 SER cc_start: 0.8983 (p) cc_final: 0.8646 (m) outliers start: 52 outliers final: 13 residues processed: 512 average time/residue: 0.9821 time to fit residues: 611.0280 Evaluate side-chains 460 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 435 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 727 LYS Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 727 LYS Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 615 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 34 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 153 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 213 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 660 HIS D 476 GLN D 660 HIS F 476 GLN F 660 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.152792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.122846 restraints weight = 74611.072| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.67 r_work: 0.3170 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23516 Z= 0.203 Angle : 0.722 11.346 31844 Z= 0.372 Chirality : 0.107 1.518 3560 Planarity : 0.004 0.055 4064 Dihedral : 11.754 165.983 3549 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.26 % Allowed : 15.51 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.02 (0.15), residues: 2968 helix: 0.42 (0.13), residues: 1472 sheet: -0.82 (0.23), residues: 456 loop : 0.01 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 554 TYR 0.012 0.001 TYR F 385 PHE 0.017 0.002 PHE A 651 TRP 0.006 0.001 TRP A 685 HIS 0.008 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00440 (23516) covalent geometry : angle 0.72234 (31844) hydrogen bonds : bond 0.04586 ( 1161) hydrogen bonds : angle 4.80175 ( 3363) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 471 time to evaluate : 1.018 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: A 226 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7973 (m-30) REVERT: A 293 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8588 (p) REVERT: A 346 LEU cc_start: 0.8170 (mt) cc_final: 0.7927 (mt) REVERT: A 353 GLN cc_start: 0.7400 (mm-40) cc_final: 0.6678 (tm130) REVERT: A 365 LYS cc_start: 0.7354 (mmtm) cc_final: 0.6890 (mmmm) REVERT: A 448 GLN cc_start: 0.8205 (pt0) cc_final: 0.7831 (pt0) REVERT: A 468 THR cc_start: 0.7751 (t) cc_final: 0.7228 (t) REVERT: A 476 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7550 (mm-40) REVERT: A 482 GLU cc_start: 0.7371 (tp30) cc_final: 0.7036 (mm-30) REVERT: A 485 ARG cc_start: 0.7192 (ttm170) cc_final: 0.6975 (ttm-80) REVERT: A 486 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7480 (mp) REVERT: A 564 ARG cc_start: 0.8483 (mtt-85) cc_final: 0.8216 (mtt-85) REVERT: A 615 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.7250 (mpt) REVERT: A 743 SER cc_start: 0.9088 (p) cc_final: 0.8772 (m) REVERT: D 226 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.8034 (m-30) REVERT: D 285 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7093 (tm130) REVERT: D 293 VAL cc_start: 0.8886 (OUTLIER) cc_final: 0.8596 (p) REVERT: D 346 LEU cc_start: 0.8182 (mt) cc_final: 0.7963 (mt) REVERT: D 353 GLN cc_start: 0.7428 (mm-40) cc_final: 0.6857 (mm-40) REVERT: D 365 LYS cc_start: 0.7394 (mmtm) cc_final: 0.6951 (mmmm) REVERT: D 448 GLN cc_start: 0.8219 (pt0) cc_final: 0.7854 (pt0) REVERT: D 468 THR cc_start: 0.7739 (t) cc_final: 0.7241 (t) REVERT: D 476 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7495 (mm-40) REVERT: D 482 GLU cc_start: 0.7393 (tp30) cc_final: 0.7021 (mm-30) REVERT: D 486 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7504 (mp) REVERT: D 564 ARG cc_start: 0.8526 (mtt-85) cc_final: 0.8256 (mtt-85) REVERT: D 615 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.7212 (mpt) REVERT: E 226 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: E 285 GLN cc_start: 0.7562 (tm-30) cc_final: 0.7130 (tm130) REVERT: E 293 VAL cc_start: 0.8907 (p) cc_final: 0.8614 (p) REVERT: E 346 LEU cc_start: 0.8165 (mt) cc_final: 0.7930 (mt) REVERT: E 349 MET cc_start: 0.6912 (mmm) cc_final: 0.6317 (mmt) REVERT: E 353 GLN cc_start: 0.7413 (mm-40) cc_final: 0.6801 (mm110) REVERT: E 365 LYS cc_start: 0.7341 (mmtm) cc_final: 0.6930 (mmmm) REVERT: E 448 GLN cc_start: 0.8167 (pt0) cc_final: 0.7812 (pt0) REVERT: E 478 GLU cc_start: 0.7633 (tp30) cc_final: 0.7289 (tp30) REVERT: E 482 GLU cc_start: 0.7453 (tp30) cc_final: 0.7084 (mm-30) REVERT: E 486 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7490 (mp) REVERT: E 564 ARG cc_start: 0.8526 (mtt-85) cc_final: 0.8248 (mtt-85) REVERT: E 615 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.7260 (mpt) REVERT: F 226 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: F 243 MET cc_start: 0.8381 (ttp) cc_final: 0.8097 (ttt) REVERT: F 269 ARG cc_start: 0.6873 (tpt170) cc_final: 0.6510 (mmt180) REVERT: F 285 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7193 (tm130) REVERT: F 293 VAL cc_start: 0.8896 (p) cc_final: 0.8593 (p) REVERT: F 346 LEU cc_start: 0.8163 (mt) cc_final: 0.7943 (mt) REVERT: F 353 GLN cc_start: 0.7404 (mm-40) cc_final: 0.6819 (mm110) REVERT: F 448 GLN cc_start: 0.8179 (pt0) cc_final: 0.7815 (pt0) REVERT: F 468 THR cc_start: 0.7755 (t) cc_final: 0.7230 (t) REVERT: F 482 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7323 (mm-30) REVERT: F 486 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7528 (mp) REVERT: F 564 ARG cc_start: 0.8550 (mtt-85) cc_final: 0.8265 (mtt-85) REVERT: F 615 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.7243 (mpt) outliers start: 54 outliers final: 19 residues processed: 490 average time/residue: 0.9089 time to fit residues: 535.8420 Evaluate side-chains 473 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 439 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 482 GLU Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 615 MET Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 293 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 180 optimal weight: 0.0670 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN E 75 ASN F 341 ASN F 383 ASN F 476 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.152164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.122195 restraints weight = 74756.793| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.66 r_work: 0.3171 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23516 Z= 0.179 Angle : 0.685 11.471 31844 Z= 0.349 Chirality : 0.107 1.536 3560 Planarity : 0.004 0.047 4064 Dihedral : 10.898 167.535 3546 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.59 % Allowed : 16.51 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.37 (0.15), residues: 2968 helix: 0.86 (0.13), residues: 1452 sheet: -0.87 (0.23), residues: 432 loop : 0.11 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 513 TYR 0.012 0.001 TYR F 43 PHE 0.014 0.001 PHE A 651 TRP 0.007 0.001 TRP E 685 HIS 0.004 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00392 (23516) covalent geometry : angle 0.68452 (31844) hydrogen bonds : bond 0.04237 ( 1161) hydrogen bonds : angle 4.61177 ( 3363) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 462 time to evaluate : 1.067 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 226 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7961 (m-30) REVERT: A 243 MET cc_start: 0.8434 (ttp) cc_final: 0.8111 (ttt) REVERT: A 293 VAL cc_start: 0.8878 (p) cc_final: 0.8620 (p) REVERT: A 346 LEU cc_start: 0.8139 (mt) cc_final: 0.7905 (mt) REVERT: A 353 GLN cc_start: 0.7363 (mm-40) cc_final: 0.6671 (tm130) REVERT: A 448 GLN cc_start: 0.8329 (pt0) cc_final: 0.7938 (pt0) REVERT: A 476 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7595 (mm-40) REVERT: A 564 ARG cc_start: 0.8557 (mtt-85) cc_final: 0.8202 (mtt-85) REVERT: A 615 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.7287 (mpt) REVERT: D 226 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8108 (m-30) REVERT: D 243 MET cc_start: 0.8447 (ttp) cc_final: 0.8125 (ttt) REVERT: D 293 VAL cc_start: 0.8886 (p) cc_final: 0.8632 (p) REVERT: D 316 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8357 (mmt) REVERT: D 346 LEU cc_start: 0.8174 (mt) cc_final: 0.7962 (mt) REVERT: D 353 GLN cc_start: 0.7405 (mm-40) cc_final: 0.6781 (mm110) REVERT: D 365 LYS cc_start: 0.7398 (mmtm) cc_final: 0.6963 (mmmm) REVERT: D 448 GLN cc_start: 0.8337 (pt0) cc_final: 0.7958 (pt0) REVERT: D 468 THR cc_start: 0.7621 (t) cc_final: 0.7096 (t) REVERT: D 476 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7452 (mm-40) REVERT: D 482 GLU cc_start: 0.7446 (tp30) cc_final: 0.7062 (mm-30) REVERT: D 486 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7510 (mp) REVERT: D 564 ARG cc_start: 0.8545 (mtt-85) cc_final: 0.8240 (mtt-85) REVERT: D 615 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.7255 (mpt) REVERT: E 226 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8030 (m-30) REVERT: E 243 MET cc_start: 0.8415 (ttp) cc_final: 0.8110 (ttt) REVERT: E 285 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7187 (tm130) REVERT: E 293 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8613 (p) REVERT: E 322 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.6660 (mpp) REVERT: E 346 LEU cc_start: 0.8165 (mt) cc_final: 0.7930 (mt) REVERT: E 349 MET cc_start: 0.6830 (mmm) cc_final: 0.6225 (mmt) REVERT: E 353 GLN cc_start: 0.7372 (mm-40) cc_final: 0.6716 (mm110) REVERT: E 365 LYS cc_start: 0.7324 (mmtm) cc_final: 0.6926 (mmmm) REVERT: E 448 GLN cc_start: 0.8292 (pt0) cc_final: 0.7906 (pt0) REVERT: E 564 ARG cc_start: 0.8540 (mtt-85) cc_final: 0.8198 (mtt-85) REVERT: E 615 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.7304 (mpt) REVERT: F 157 ASN cc_start: 0.8198 (m-40) cc_final: 0.7789 (m-40) REVERT: F 226 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7883 (m-30) REVERT: F 243 MET cc_start: 0.8342 (ttp) cc_final: 0.8082 (ttt) REVERT: F 285 GLN cc_start: 0.7670 (tm-30) cc_final: 0.7249 (tm130) REVERT: F 293 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8611 (p) REVERT: F 316 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8396 (mmt) REVERT: F 322 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.6660 (mpp) REVERT: F 346 LEU cc_start: 0.8178 (mt) cc_final: 0.7959 (mt) REVERT: F 349 MET cc_start: 0.6883 (mmm) cc_final: 0.6275 (mmm) REVERT: F 353 GLN cc_start: 0.7364 (mm-40) cc_final: 0.6758 (mm110) REVERT: F 448 GLN cc_start: 0.8316 (pt0) cc_final: 0.7917 (pt0) REVERT: F 468 THR cc_start: 0.7679 (t) cc_final: 0.7153 (t) REVERT: F 482 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: F 486 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7491 (mp) REVERT: F 564 ARG cc_start: 0.8540 (mtt-85) cc_final: 0.8202 (mtt-85) REVERT: F 615 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.7310 (mpt) outliers start: 62 outliers final: 17 residues processed: 485 average time/residue: 0.8836 time to fit residues: 513.7069 Evaluate side-chains 478 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 444 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 482 GLU Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 615 MET Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 156 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 247 optimal weight: 0.3980 chunk 251 optimal weight: 1.9990 chunk 208 optimal weight: 0.0970 chunk 74 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 253 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN D 341 ASN E 341 ASN F 341 ASN F 383 ASN F 476 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.152017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.122151 restraints weight = 74233.199| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.65 r_work: 0.3170 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23516 Z= 0.167 Angle : 0.666 11.531 31844 Z= 0.338 Chirality : 0.106 1.541 3560 Planarity : 0.004 0.037 4064 Dihedral : 10.308 169.665 3546 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.38 % Allowed : 17.52 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.60 (0.15), residues: 2968 helix: 1.16 (0.13), residues: 1456 sheet: -0.88 (0.22), residues: 496 loop : 0.17 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 513 TYR 0.013 0.001 TYR E 43 PHE 0.013 0.001 PHE A 651 TRP 0.007 0.001 TRP A 685 HIS 0.003 0.001 HIS E 298 Details of bonding type rmsd covalent geometry : bond 0.00366 (23516) covalent geometry : angle 0.66593 (31844) hydrogen bonds : bond 0.04041 ( 1161) hydrogen bonds : angle 4.47924 ( 3363) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 468 time to evaluate : 0.951 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 53 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7763 (mm-30) REVERT: A 60 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7089 (mt-10) REVERT: A 226 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: A 243 MET cc_start: 0.8415 (ttp) cc_final: 0.8013 (ttt) REVERT: A 293 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8601 (p) REVERT: A 346 LEU cc_start: 0.8170 (mt) cc_final: 0.7936 (mt) REVERT: A 353 GLN cc_start: 0.7464 (mm-40) cc_final: 0.6750 (tm130) REVERT: A 448 GLN cc_start: 0.8321 (pt0) cc_final: 0.7931 (pt0) REVERT: A 564 ARG cc_start: 0.8510 (mtt-85) cc_final: 0.8117 (mtt-85) REVERT: A 615 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.7235 (mpt) REVERT: D 226 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8121 (m-30) REVERT: D 243 MET cc_start: 0.8465 (ttp) cc_final: 0.8102 (ttt) REVERT: D 293 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8611 (p) REVERT: D 316 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8353 (mmt) REVERT: D 346 LEU cc_start: 0.8186 (mt) cc_final: 0.7969 (mt) REVERT: D 349 MET cc_start: 0.6877 (mmm) cc_final: 0.6282 (mmm) REVERT: D 353 GLN cc_start: 0.7510 (mm-40) cc_final: 0.6859 (mm110) REVERT: D 365 LYS cc_start: 0.7396 (mmtm) cc_final: 0.6979 (mmmm) REVERT: D 448 GLN cc_start: 0.8347 (pt0) cc_final: 0.7948 (pt0) REVERT: D 476 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7492 (mm-40) REVERT: D 490 HIS cc_start: 0.8578 (m90) cc_final: 0.8092 (m90) REVERT: D 508 VAL cc_start: 0.8553 (t) cc_final: 0.8351 (t) REVERT: D 564 ARG cc_start: 0.8568 (mtt-85) cc_final: 0.8191 (mtt-85) REVERT: D 615 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.7222 (mpt) REVERT: E 226 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8039 (m-30) REVERT: E 243 MET cc_start: 0.8387 (ttp) cc_final: 0.8002 (ttt) REVERT: E 285 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7208 (tm130) REVERT: E 293 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8598 (p) REVERT: E 318 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7607 (ttm) REVERT: E 322 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6758 (mpp) REVERT: E 346 LEU cc_start: 0.8139 (mt) cc_final: 0.7900 (mt) REVERT: E 349 MET cc_start: 0.6884 (mmm) cc_final: 0.6323 (mmt) REVERT: E 353 GLN cc_start: 0.7350 (mm-40) cc_final: 0.6712 (mm110) REVERT: E 365 LYS cc_start: 0.7359 (mmtm) cc_final: 0.7044 (mmmt) REVERT: E 448 GLN cc_start: 0.8283 (pt0) cc_final: 0.7897 (pt0) REVERT: E 564 ARG cc_start: 0.8563 (mtt-85) cc_final: 0.8137 (mtt-85) REVERT: E 615 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.7411 (mpt) REVERT: F 226 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7931 (m-30) REVERT: F 243 MET cc_start: 0.8323 (ttp) cc_final: 0.8020 (ttt) REVERT: F 285 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7233 (tm130) REVERT: F 293 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8592 (p) REVERT: F 316 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8388 (mmt) REVERT: F 318 MET cc_start: 0.7865 (ttm) cc_final: 0.7602 (ttm) REVERT: F 322 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6746 (mpp) REVERT: F 346 LEU cc_start: 0.8172 (mt) cc_final: 0.7946 (mt) REVERT: F 349 MET cc_start: 0.6895 (mmm) cc_final: 0.6299 (mmm) REVERT: F 353 GLN cc_start: 0.7454 (mm-40) cc_final: 0.6826 (mm110) REVERT: F 448 GLN cc_start: 0.8330 (pt0) cc_final: 0.7930 (pt0) REVERT: F 490 HIS cc_start: 0.8577 (m90) cc_final: 0.8085 (m90) REVERT: F 508 VAL cc_start: 0.8533 (t) cc_final: 0.8331 (t) REVERT: F 564 ARG cc_start: 0.8554 (mtt-85) cc_final: 0.8154 (mtt-85) REVERT: F 615 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.7404 (mpt) outliers start: 57 outliers final: 14 residues processed: 491 average time/residue: 0.6581 time to fit residues: 392.3215 Evaluate side-chains 481 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 450 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 615 MET Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 103 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 286 optimal weight: 1.9990 chunk 260 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 295 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 341 ASN E 341 ASN F 383 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.150224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.120179 restraints weight = 74928.814| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.67 r_work: 0.3144 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 23516 Z= 0.222 Angle : 0.692 11.666 31844 Z= 0.352 Chirality : 0.108 1.546 3560 Planarity : 0.004 0.066 4064 Dihedral : 10.063 171.177 3546 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.72 % Allowed : 17.81 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.60 (0.15), residues: 2968 helix: 1.20 (0.13), residues: 1468 sheet: -0.76 (0.23), residues: 480 loop : -0.01 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 485 TYR 0.010 0.001 TYR F 674 PHE 0.013 0.002 PHE F 599 TRP 0.007 0.001 TRP E 685 HIS 0.004 0.001 HIS E 298 Details of bonding type rmsd covalent geometry : bond 0.00490 (23516) covalent geometry : angle 0.69247 (31844) hydrogen bonds : bond 0.04085 ( 1161) hydrogen bonds : angle 4.49123 ( 3363) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 457 time to evaluate : 0.690 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 129 ARG cc_start: 0.7636 (ttt-90) cc_final: 0.7430 (ttt-90) REVERT: A 226 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: A 243 MET cc_start: 0.8415 (ttp) cc_final: 0.8069 (ttt) REVERT: A 293 VAL cc_start: 0.8871 (OUTLIER) cc_final: 0.8609 (p) REVERT: A 346 LEU cc_start: 0.8100 (mt) cc_final: 0.7878 (mt) REVERT: A 353 GLN cc_start: 0.7417 (mm-40) cc_final: 0.6694 (tm130) REVERT: A 448 GLN cc_start: 0.8364 (pt0) cc_final: 0.7970 (pt0) REVERT: A 486 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7440 (mp) REVERT: A 564 ARG cc_start: 0.8563 (mtt-85) cc_final: 0.8153 (mtt-85) REVERT: A 615 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.7322 (mpt) REVERT: D 226 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: D 243 MET cc_start: 0.8473 (ttp) cc_final: 0.8130 (ttt) REVERT: D 293 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8625 (p) REVERT: D 316 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8362 (mmt) REVERT: D 346 LEU cc_start: 0.8104 (mt) cc_final: 0.7896 (mt) REVERT: D 349 MET cc_start: 0.6919 (mmm) cc_final: 0.6416 (mmm) REVERT: D 353 GLN cc_start: 0.7468 (mm-40) cc_final: 0.6829 (mm-40) REVERT: D 448 GLN cc_start: 0.8359 (pt0) cc_final: 0.7949 (pt0) REVERT: D 476 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7516 (mm-40) REVERT: D 486 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7496 (mp) REVERT: D 564 ARG cc_start: 0.8541 (mtt-85) cc_final: 0.8152 (mtt-85) REVERT: D 615 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.7352 (mpt) REVERT: E 60 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7025 (mt-10) REVERT: E 226 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: E 243 MET cc_start: 0.8339 (ttp) cc_final: 0.7974 (ttt) REVERT: E 285 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7226 (tm130) REVERT: E 293 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8607 (p) REVERT: E 318 MET cc_start: 0.7949 (ttm) cc_final: 0.7710 (ttm) REVERT: E 322 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.6694 (mpp) REVERT: E 346 LEU cc_start: 0.8088 (mt) cc_final: 0.7861 (mt) REVERT: E 349 MET cc_start: 0.6885 (mmm) cc_final: 0.6313 (mmt) REVERT: E 353 GLN cc_start: 0.7354 (mm-40) cc_final: 0.6692 (mm110) REVERT: E 365 LYS cc_start: 0.7369 (mmtm) cc_final: 0.7065 (mmmt) REVERT: E 448 GLN cc_start: 0.8307 (pt0) cc_final: 0.7919 (pt0) REVERT: E 486 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7459 (mp) REVERT: E 564 ARG cc_start: 0.8556 (mtt-85) cc_final: 0.8151 (mtt-85) REVERT: E 615 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.7325 (mpt) REVERT: F 60 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7028 (mt-10) REVERT: F 226 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: F 243 MET cc_start: 0.8391 (ttp) cc_final: 0.7835 (ttt) REVERT: F 285 GLN cc_start: 0.7683 (tm-30) cc_final: 0.7243 (tm130) REVERT: F 293 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8599 (p) REVERT: F 316 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8402 (mmt) REVERT: F 318 MET cc_start: 0.7936 (ttm) cc_final: 0.7636 (ttm) REVERT: F 322 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6710 (mpp) REVERT: F 346 LEU cc_start: 0.8107 (mt) cc_final: 0.7896 (mt) REVERT: F 349 MET cc_start: 0.6925 (mmm) cc_final: 0.6332 (mmm) REVERT: F 353 GLN cc_start: 0.7432 (mm-40) cc_final: 0.6788 (mm110) REVERT: F 448 GLN cc_start: 0.8315 (pt0) cc_final: 0.7909 (pt0) REVERT: F 486 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7468 (mp) REVERT: F 564 ARG cc_start: 0.8553 (mtt-85) cc_final: 0.8117 (mtt-85) REVERT: F 615 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.7375 (mpt) outliers start: 65 outliers final: 27 residues processed: 491 average time/residue: 0.6451 time to fit residues: 383.8092 Evaluate side-chains 492 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 445 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 615 MET Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.148404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.118361 restraints weight = 74627.311| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.66 r_work: 0.3123 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 23516 Z= 0.280 Angle : 0.721 11.692 31844 Z= 0.369 Chirality : 0.110 1.545 3560 Planarity : 0.004 0.043 4064 Dihedral : 10.074 172.930 3546 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.47 % Allowed : 18.23 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.40 (0.15), residues: 2968 helix: 0.97 (0.13), residues: 1492 sheet: -0.69 (0.23), residues: 480 loop : -0.12 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 513 TYR 0.012 0.002 TYR A 514 PHE 0.015 0.002 PHE A 651 TRP 0.008 0.002 TRP D 685 HIS 0.004 0.001 HIS D 298 Details of bonding type rmsd covalent geometry : bond 0.00621 (23516) covalent geometry : angle 0.72109 (31844) hydrogen bonds : bond 0.04197 ( 1161) hydrogen bonds : angle 4.57504 ( 3363) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 465 time to evaluate : 0.697 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: A 60 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7054 (mt-10) REVERT: A 226 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8105 (m-30) REVERT: A 243 MET cc_start: 0.8432 (ttp) cc_final: 0.8095 (ttt) REVERT: A 293 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8637 (p) REVERT: A 346 LEU cc_start: 0.8088 (mt) cc_final: 0.7873 (mt) REVERT: A 353 GLN cc_start: 0.7426 (mm-40) cc_final: 0.6759 (tp40) REVERT: A 365 LYS cc_start: 0.7430 (mmtm) cc_final: 0.7046 (mmmm) REVERT: A 448 GLN cc_start: 0.8330 (pt0) cc_final: 0.7927 (pt0) REVERT: A 564 ARG cc_start: 0.8615 (mtt-85) cc_final: 0.8200 (mtt-85) REVERT: A 615 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.7250 (mpt) REVERT: A 656 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.9008 (t0) REVERT: D 60 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7117 (mt-10) REVERT: D 226 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8119 (m-30) REVERT: D 243 MET cc_start: 0.8488 (ttp) cc_final: 0.8105 (ttt) REVERT: D 285 GLN cc_start: 0.7471 (tm-30) cc_final: 0.7163 (tm130) REVERT: D 293 VAL cc_start: 0.8914 (OUTLIER) cc_final: 0.8666 (p) REVERT: D 316 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8437 (mmt) REVERT: D 349 MET cc_start: 0.6933 (mmm) cc_final: 0.6449 (mmm) REVERT: D 353 GLN cc_start: 0.7463 (mm-40) cc_final: 0.6833 (mm-40) REVERT: D 365 LYS cc_start: 0.7462 (mmtm) cc_final: 0.6962 (mmmm) REVERT: D 448 GLN cc_start: 0.8311 (pt0) cc_final: 0.7880 (pt0) REVERT: D 476 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7556 (mm-40) REVERT: D 564 ARG cc_start: 0.8589 (mtt-85) cc_final: 0.8185 (mtt-85) REVERT: D 615 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.7356 (mpt) REVERT: D 656 ASN cc_start: 0.9232 (OUTLIER) cc_final: 0.9024 (t0) REVERT: E 60 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7029 (mt-10) REVERT: E 226 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: E 243 MET cc_start: 0.8363 (ttp) cc_final: 0.8040 (ttt) REVERT: E 285 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7211 (tm130) REVERT: E 293 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8607 (p) REVERT: E 318 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7732 (ttm) REVERT: E 322 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.6707 (mpp) REVERT: E 346 LEU cc_start: 0.8101 (mt) cc_final: 0.7889 (mt) REVERT: E 349 MET cc_start: 0.6891 (mmm) cc_final: 0.6289 (mmt) REVERT: E 353 GLN cc_start: 0.7359 (mm-40) cc_final: 0.6701 (mm110) REVERT: E 365 LYS cc_start: 0.7390 (mmtm) cc_final: 0.6997 (mmmt) REVERT: E 448 GLN cc_start: 0.8241 (pt0) cc_final: 0.7844 (pt0) REVERT: E 615 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.7377 (mpt) REVERT: E 656 ASN cc_start: 0.9191 (OUTLIER) cc_final: 0.8979 (t0) REVERT: F 60 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7084 (mt-10) REVERT: F 226 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: F 243 MET cc_start: 0.8341 (ttp) cc_final: 0.8101 (ttp) REVERT: F 285 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7309 (tm130) REVERT: F 293 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8630 (p) REVERT: F 316 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8435 (mmt) REVERT: F 318 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7708 (ttm) REVERT: F 322 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6708 (mpp) REVERT: F 346 LEU cc_start: 0.8115 (mt) cc_final: 0.7911 (mt) REVERT: F 349 MET cc_start: 0.6914 (mmm) cc_final: 0.6328 (mmm) REVERT: F 353 GLN cc_start: 0.7417 (mm-40) cc_final: 0.6788 (mm110) REVERT: F 448 GLN cc_start: 0.8270 (pt0) cc_final: 0.7839 (pt0) REVERT: F 564 ARG cc_start: 0.8600 (mtt-85) cc_final: 0.8193 (mtt-85) REVERT: F 615 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.7411 (mpt) outliers start: 83 outliers final: 40 residues processed: 511 average time/residue: 0.6719 time to fit residues: 412.7237 Evaluate side-chains 517 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 454 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 499 GLU Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 656 ASN Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 285 GLN Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain E residue 656 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 169 PHE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 285 GLN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 318 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 363 ASP Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 615 MET Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 235 optimal weight: 7.9990 chunk 199 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 240 optimal weight: 0.7980 chunk 272 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 ASN E 75 ASN F 383 ASN F 453 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.149824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.119815 restraints weight = 74657.508| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.66 r_work: 0.3141 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23516 Z= 0.193 Angle : 0.681 11.625 31844 Z= 0.346 Chirality : 0.108 1.549 3560 Planarity : 0.004 0.054 4064 Dihedral : 9.483 172.548 3546 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.09 % Allowed : 18.98 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.66 (0.16), residues: 2968 helix: 1.25 (0.13), residues: 1468 sheet: -0.55 (0.23), residues: 500 loop : -0.06 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 485 TYR 0.012 0.001 TYR E 514 PHE 0.013 0.001 PHE D 651 TRP 0.008 0.001 TRP D 685 HIS 0.003 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00424 (23516) covalent geometry : angle 0.68072 (31844) hydrogen bonds : bond 0.03971 ( 1161) hydrogen bonds : angle 4.45189 ( 3363) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 465 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: A 243 MET cc_start: 0.8390 (ttp) cc_final: 0.7774 (ttt) REVERT: A 293 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8664 (p) REVERT: A 346 LEU cc_start: 0.8106 (mt) cc_final: 0.7897 (mt) REVERT: A 353 GLN cc_start: 0.7435 (mm-40) cc_final: 0.6795 (tp40) REVERT: A 365 LYS cc_start: 0.7452 (mmtm) cc_final: 0.7064 (mmmm) REVERT: A 448 GLN cc_start: 0.8311 (pt0) cc_final: 0.7957 (pt0) REVERT: A 615 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.7381 (mpt) REVERT: D 226 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8108 (m-30) REVERT: D 243 MET cc_start: 0.8459 (ttp) cc_final: 0.8141 (ttt) REVERT: D 285 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7244 (tm130) REVERT: D 293 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8631 (p) REVERT: D 316 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8387 (mmt) REVERT: D 349 MET cc_start: 0.6950 (mmm) cc_final: 0.6463 (mmm) REVERT: D 353 GLN cc_start: 0.7485 (mm-40) cc_final: 0.6840 (mm-40) REVERT: D 365 LYS cc_start: 0.7541 (mmtm) cc_final: 0.7058 (mmmm) REVERT: D 448 GLN cc_start: 0.8269 (pt0) cc_final: 0.7891 (pt0) REVERT: D 476 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7510 (mm-40) REVERT: D 508 VAL cc_start: 0.8601 (t) cc_final: 0.8400 (t) REVERT: D 615 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.7308 (mpt) REVERT: E 60 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7035 (mt-10) REVERT: E 226 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: E 243 MET cc_start: 0.8354 (ttp) cc_final: 0.8035 (ttt) REVERT: E 285 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7227 (tm130) REVERT: E 293 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8659 (p) REVERT: E 318 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7730 (ttm) REVERT: E 322 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6693 (mpp) REVERT: E 346 LEU cc_start: 0.8115 (mt) cc_final: 0.7913 (mt) REVERT: E 349 MET cc_start: 0.6919 (mmm) cc_final: 0.6349 (mmt) REVERT: E 353 GLN cc_start: 0.7449 (mm-40) cc_final: 0.6799 (mm110) REVERT: E 365 LYS cc_start: 0.7412 (mmtm) cc_final: 0.7023 (mmmt) REVERT: E 448 GLN cc_start: 0.8205 (pt0) cc_final: 0.7851 (pt0) REVERT: E 516 GLU cc_start: 0.7259 (mm-30) cc_final: 0.7028 (mp0) REVERT: E 615 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.7390 (mpt) REVERT: F 226 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: F 243 MET cc_start: 0.8339 (ttp) cc_final: 0.7765 (ttt) REVERT: F 285 GLN cc_start: 0.7689 (tm-30) cc_final: 0.7329 (tm130) REVERT: F 293 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8665 (p) REVERT: F 316 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8437 (mmt) REVERT: F 318 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7721 (ttm) REVERT: F 322 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6749 (mpp) REVERT: F 349 MET cc_start: 0.6930 (mmm) cc_final: 0.6362 (mmm) REVERT: F 353 GLN cc_start: 0.7423 (mm-40) cc_final: 0.6795 (mm110) REVERT: F 448 GLN cc_start: 0.8232 (pt0) cc_final: 0.7864 (pt0) REVERT: F 615 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.7359 (mpt) outliers start: 74 outliers final: 35 residues processed: 507 average time/residue: 0.6979 time to fit residues: 427.8027 Evaluate side-chains 512 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 458 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 322 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 499 GLU Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 285 GLN Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 169 PHE Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 318 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 615 MET Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 60 optimal weight: 1.9990 chunk 258 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 237 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 ASN D 383 ASN D 656 ASN E 75 ASN E 656 ASN F 656 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.150335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.120447 restraints weight = 74282.078| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.65 r_work: 0.3148 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23516 Z= 0.176 Angle : 0.682 11.666 31844 Z= 0.344 Chirality : 0.107 1.532 3560 Planarity : 0.004 0.053 4064 Dihedral : 9.409 172.628 3546 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.05 % Allowed : 19.40 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.71 (0.16), residues: 2968 helix: 1.30 (0.13), residues: 1468 sheet: -0.55 (0.23), residues: 500 loop : -0.05 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 513 TYR 0.010 0.001 TYR E 514 PHE 0.013 0.001 PHE D 651 TRP 0.007 0.001 TRP F 685 HIS 0.003 0.001 HIS F 436 Details of bonding type rmsd covalent geometry : bond 0.00386 (23516) covalent geometry : angle 0.68182 (31844) hydrogen bonds : bond 0.03937 ( 1161) hydrogen bonds : angle 4.42918 ( 3363) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 459 time to evaluate : 0.723 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: A 60 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7038 (mt-10) REVERT: A 226 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: A 243 MET cc_start: 0.8395 (ttp) cc_final: 0.7790 (ttt) REVERT: A 293 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8660 (p) REVERT: A 346 LEU cc_start: 0.8124 (mt) cc_final: 0.7920 (mt) REVERT: A 353 GLN cc_start: 0.7441 (mm-40) cc_final: 0.6802 (tp40) REVERT: A 365 LYS cc_start: 0.7454 (mmtm) cc_final: 0.7071 (mmmm) REVERT: A 448 GLN cc_start: 0.8295 (pt0) cc_final: 0.7933 (pt0) REVERT: A 615 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.7375 (mpt) REVERT: D 60 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7031 (mt-10) REVERT: D 226 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: D 243 MET cc_start: 0.8426 (ttp) cc_final: 0.8109 (ttt) REVERT: D 285 GLN cc_start: 0.7588 (tm-30) cc_final: 0.7235 (tm130) REVERT: D 293 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8628 (p) REVERT: D 316 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8380 (mmt) REVERT: D 349 MET cc_start: 0.6938 (mmm) cc_final: 0.6400 (mmm) REVERT: D 353 GLN cc_start: 0.7458 (mm-40) cc_final: 0.6814 (mm110) REVERT: D 365 LYS cc_start: 0.7533 (mmtm) cc_final: 0.7055 (mmmm) REVERT: D 448 GLN cc_start: 0.8242 (pt0) cc_final: 0.7885 (pt0) REVERT: D 476 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7497 (mm-40) REVERT: D 485 ARG cc_start: 0.7043 (ttm-80) cc_final: 0.6713 (ttm110) REVERT: D 486 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7573 (mp) REVERT: D 508 VAL cc_start: 0.8600 (t) cc_final: 0.8397 (t) REVERT: D 615 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.7291 (mpt) REVERT: E 60 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7017 (mt-10) REVERT: E 226 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8034 (m-30) REVERT: E 243 MET cc_start: 0.8307 (ttp) cc_final: 0.7992 (ttt) REVERT: E 285 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7218 (tm130) REVERT: E 293 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8653 (p) REVERT: E 318 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7737 (ttm) REVERT: E 322 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.6700 (mpp) REVERT: E 349 MET cc_start: 0.6927 (mmm) cc_final: 0.6357 (mmt) REVERT: E 353 GLN cc_start: 0.7446 (mm-40) cc_final: 0.6792 (mm110) REVERT: E 365 LYS cc_start: 0.7416 (mmtm) cc_final: 0.7033 (mmmt) REVERT: E 448 GLN cc_start: 0.8227 (pt0) cc_final: 0.7896 (pt0) REVERT: E 615 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.7390 (mpt) REVERT: F 60 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7024 (mt-10) REVERT: F 226 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: F 243 MET cc_start: 0.8339 (ttp) cc_final: 0.7776 (ttt) REVERT: F 285 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7268 (tm130) REVERT: F 293 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8657 (p) REVERT: F 316 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8429 (mmt) REVERT: F 322 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.6732 (mpp) REVERT: F 349 MET cc_start: 0.6924 (mmm) cc_final: 0.6339 (mmm) REVERT: F 353 GLN cc_start: 0.7424 (mm-40) cc_final: 0.6790 (mm110) REVERT: F 448 GLN cc_start: 0.8225 (pt0) cc_final: 0.7859 (pt0) REVERT: F 486 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7522 (mp) REVERT: F 615 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.7362 (mpt) outliers start: 73 outliers final: 39 residues processed: 501 average time/residue: 0.6691 time to fit residues: 405.2081 Evaluate side-chains 515 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 456 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 499 GLU Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 285 GLN Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 169 PHE Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 615 MET Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 166 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 210 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 178 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 ASN D 453 HIS E 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.150135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.120083 restraints weight = 74863.078| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.67 r_work: 0.3157 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23516 Z= 0.176 Angle : 0.682 11.666 31844 Z= 0.344 Chirality : 0.107 1.532 3560 Planarity : 0.004 0.053 4064 Dihedral : 9.409 172.628 3546 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.51 % Allowed : 20.15 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.71 (0.16), residues: 2968 helix: 1.30 (0.13), residues: 1468 sheet: -0.55 (0.23), residues: 500 loop : -0.05 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 513 TYR 0.010 0.001 TYR E 514 PHE 0.013 0.001 PHE D 651 TRP 0.007 0.001 TRP F 685 HIS 0.003 0.001 HIS F 436 Details of bonding type rmsd covalent geometry : bond 0.00386 (23516) covalent geometry : angle 0.68182 (31844) hydrogen bonds : bond 0.03937 ( 1161) hydrogen bonds : angle 4.42918 ( 3363) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5936 Ramachandran restraints generated. 2968 Oldfield, 0 Emsley, 2968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 456 time to evaluate : 0.741 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: A 60 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7052 (mt-10) REVERT: A 226 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8023 (m-30) REVERT: A 243 MET cc_start: 0.8385 (ttp) cc_final: 0.7775 (ttt) REVERT: A 293 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8668 (p) REVERT: A 346 LEU cc_start: 0.8126 (mt) cc_final: 0.7920 (mt) REVERT: A 353 GLN cc_start: 0.7413 (mm-40) cc_final: 0.6768 (tp40) REVERT: A 365 LYS cc_start: 0.7430 (mmtm) cc_final: 0.7046 (mmmm) REVERT: A 448 GLN cc_start: 0.8286 (pt0) cc_final: 0.7918 (pt0) REVERT: A 615 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.7369 (mpt) REVERT: D 60 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7084 (mt-10) REVERT: D 226 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8112 (m-30) REVERT: D 243 MET cc_start: 0.8411 (ttp) cc_final: 0.8093 (ttt) REVERT: D 285 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7246 (tm130) REVERT: D 293 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8634 (p) REVERT: D 316 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8377 (mmt) REVERT: D 349 MET cc_start: 0.6938 (mmm) cc_final: 0.6399 (mmm) REVERT: D 353 GLN cc_start: 0.7436 (mm-40) cc_final: 0.6790 (mm110) REVERT: D 365 LYS cc_start: 0.7527 (mmtm) cc_final: 0.7048 (mmmm) REVERT: D 448 GLN cc_start: 0.8244 (pt0) cc_final: 0.7885 (pt0) REVERT: D 476 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7496 (mm-40) REVERT: D 485 ARG cc_start: 0.7035 (ttm-80) cc_final: 0.6703 (ttm110) REVERT: D 486 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7541 (mp) REVERT: D 508 VAL cc_start: 0.8589 (t) cc_final: 0.8387 (t) REVERT: D 615 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.7291 (mpt) REVERT: E 60 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7024 (mt-10) REVERT: E 226 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: E 243 MET cc_start: 0.8293 (ttp) cc_final: 0.7977 (ttt) REVERT: E 285 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7228 (tm130) REVERT: E 293 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8658 (p) REVERT: E 318 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7735 (ttm) REVERT: E 322 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.6673 (mpp) REVERT: E 349 MET cc_start: 0.6924 (mmm) cc_final: 0.6346 (mmt) REVERT: E 353 GLN cc_start: 0.7438 (mm-40) cc_final: 0.6778 (mm110) REVERT: E 365 LYS cc_start: 0.7400 (mmtm) cc_final: 0.7015 (mmmt) REVERT: E 448 GLN cc_start: 0.8226 (pt0) cc_final: 0.7887 (pt0) REVERT: E 615 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.7372 (mpt) REVERT: F 226 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: F 243 MET cc_start: 0.8328 (ttp) cc_final: 0.7762 (ttt) REVERT: F 285 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7294 (tm130) REVERT: F 293 VAL cc_start: 0.8871 (OUTLIER) cc_final: 0.8663 (p) REVERT: F 316 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8420 (mmt) REVERT: F 322 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.6723 (mpp) REVERT: F 349 MET cc_start: 0.6938 (mmm) cc_final: 0.6351 (mmm) REVERT: F 353 GLN cc_start: 0.7411 (mm-40) cc_final: 0.6772 (mm110) REVERT: F 448 GLN cc_start: 0.8220 (pt0) cc_final: 0.7851 (pt0) REVERT: F 486 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7487 (mp) REVERT: F 615 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.7350 (mpt) outliers start: 60 outliers final: 39 residues processed: 490 average time/residue: 0.6912 time to fit residues: 408.1549 Evaluate side-chains 515 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 456 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 169 PHE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 499 GLU Chi-restraints excluded: chain D residue 516 GLU Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 169 PHE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 285 GLN Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 318 MET Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 615 MET Chi-restraints excluded: chain E residue 632 ASP Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain F residue 169 PHE Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 615 MET Chi-restraints excluded: chain F residue 632 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 279 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 280 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 383 ASN D 453 HIS E 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.150139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.120223 restraints weight = 74811.978| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.66 r_work: 0.3159 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23516 Z= 0.176 Angle : 0.682 11.666 31844 Z= 0.344 Chirality : 0.107 1.532 3560 Planarity : 0.004 0.053 4064 Dihedral : 9.409 172.628 3546 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.51 % Allowed : 20.15 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.71 (0.16), residues: 2968 helix: 1.30 (0.13), residues: 1468 sheet: -0.55 (0.23), residues: 500 loop : -0.05 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 513 TYR 0.010 0.001 TYR E 514 PHE 0.013 0.001 PHE D 651 TRP 0.007 0.001 TRP F 685 HIS 0.003 0.001 HIS F 436 Details of bonding type rmsd covalent geometry : bond 0.00386 (23516) covalent geometry : angle 0.68182 (31844) hydrogen bonds : bond 0.03937 ( 1161) hydrogen bonds : angle 4.42918 ( 3363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11944.87 seconds wall clock time: 202 minutes 14.56 seconds (12134.56 seconds total)