Starting phenix.real_space_refine on Sat Aug 23 13:46:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dtf_27696/08_2025/8dtf_27696.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dtf_27696/08_2025/8dtf_27696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dtf_27696/08_2025/8dtf_27696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dtf_27696/08_2025/8dtf_27696.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dtf_27696/08_2025/8dtf_27696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dtf_27696/08_2025/8dtf_27696.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 7907 2.51 5 N 2071 2.21 5 O 2340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s 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: 12414 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6203 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 767} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 6211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6211 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 767} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 3.35, per 1000 atoms: 0.27 Number of scatterers: 12414 At special positions: 0 Unit cell: (164.56, 106.48, 97.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2340 8.00 N 2071 7.00 C 7907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 672.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3032 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 4 sheets defined 72.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 58 through 73 removed outlier: 3.535A pdb=" N LYS A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 92 through 107 Processing helix chain 'A' and resid 110 through 124 removed outlier: 3.684A pdb=" N GLU A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 141 removed outlier: 3.579A pdb=" N ALA A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 165 Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 185 through 199 removed outlier: 3.640A pdb=" N TYR A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.511A pdb=" N TYR A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 250 removed outlier: 4.016A pdb=" N ALA A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 275 Processing helix chain 'A' and resid 276 through 291 removed outlier: 3.529A pdb=" N TYR A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 309 Processing helix chain 'A' and resid 310 through 325 Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 378 through 393 Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 412 through 427 Processing helix chain 'A' and resid 430 through 445 removed outlier: 3.693A pdb=" N TYR A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 Processing helix chain 'A' and resid 497 through 507 removed outlier: 5.067A pdb=" N ALA A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Proline residue: A 504 - end of helix Processing helix chain 'A' and resid 525 through 539 removed outlier: 3.611A pdb=" N LYS A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 560 Processing helix chain 'A' and resid 576 through 582 Processing helix chain 'A' and resid 647 through 653 removed outlier: 3.984A pdb=" N SER A 651 " --> pdb=" O THR A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 667 through 681 Processing helix chain 'A' and resid 691 through 694 Processing helix chain 'A' and resid 695 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 724 through 731 Processing helix chain 'A' and resid 732 through 735 removed outlier: 3.528A pdb=" N MET A 735 " --> pdb=" O TYR A 732 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 732 through 735' Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 767 through 781 removed outlier: 5.008A pdb=" N GLY A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 774 " --> pdb=" O HIS A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 789 through 803 removed outlier: 3.585A pdb=" N ASP A 803 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 821 removed outlier: 4.697A pdb=" N ARG A 815 " --> pdb=" O ARG A 811 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP A 816 " --> pdb=" O MET A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 824 No H-bonds generated for 'chain 'A' and resid 822 through 824' Processing helix chain 'A' and resid 825 through 846 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 58 through 73 removed outlier: 3.536A pdb=" N LYS B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 90 Processing helix chain 'B' and resid 92 through 107 Processing helix chain 'B' and resid 110 through 124 removed outlier: 3.684A pdb=" N GLU B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 141 removed outlier: 3.580A pdb=" N ALA B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 165 Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 185 through 199 removed outlier: 3.640A pdb=" N TYR B 189 " --> pdb=" O TYR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 219 through 233 removed outlier: 3.510A pdb=" N TYR B 223 " --> pdb=" O TYR B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 250 removed outlier: 4.016A pdb=" N ALA B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 275 Processing helix chain 'B' and resid 276 through 291 removed outlier: 3.529A pdb=" N TYR B 290 " --> pdb=" O LYS B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 309 Processing helix chain 'B' and resid 310 through 325 Processing helix chain 'B' and resid 328 through 342 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 362 through 377 Processing helix chain 'B' and resid 378 through 393 Processing helix chain 'B' and resid 396 through 410 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 430 through 445 removed outlier: 3.693A pdb=" N TYR B 443 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 466 Processing helix chain 'B' and resid 497 through 507 removed outlier: 5.067A pdb=" N ALA B 503 " --> pdb=" O TYR B 499 " (cutoff:3.500A) Proline residue: B 504 - end of helix Processing helix chain 'B' and resid 525 through 539 removed outlier: 3.611A pdb=" N LYS B 538 " --> pdb=" O LYS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 560 Processing helix chain 'B' and resid 576 through 582 Processing helix chain 'B' and resid 647 through 653 removed outlier: 3.983A pdb=" N SER B 651 " --> pdb=" O THR B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 Processing helix chain 'B' and resid 667 through 681 Processing helix chain 'B' and resid 691 through 694 Processing helix chain 'B' and resid 695 through 709 Processing helix chain 'B' and resid 712 through 714 No H-bonds generated for 'chain 'B' and resid 712 through 714' Processing helix chain 'B' and resid 724 through 731 Processing helix chain 'B' and resid 732 through 735 removed outlier: 3.528A pdb=" N MET B 735 " --> pdb=" O TYR B 732 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 732 through 735' Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 767 through 781 removed outlier: 5.010A pdb=" N GLY B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 774 " --> pdb=" O HIS B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 784 No H-bonds generated for 'chain 'B' and resid 782 through 784' Processing helix chain 'B' and resid 789 through 803 removed outlier: 3.585A pdb=" N ASP B 803 " --> pdb=" O ASP B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 821 removed outlier: 4.697A pdb=" N ARG B 815 " --> pdb=" O ARG B 811 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP B 816 " --> pdb=" O MET B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 824 No H-bonds generated for 'chain 'B' and resid 822 through 824' Processing helix chain 'B' and resid 825 through 846 Processing sheet with id=AA1, first strand: chain 'A' and resid 541 through 544 removed outlier: 8.168A pdb=" N VAL A 541 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 515 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LYS A 543 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL A 517 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 483 " --> pdb=" O LYS A 514 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL A 516 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 485 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N TYR A 518 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR A 487 " --> pdb=" O TYR A 518 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN A 588 " --> pdb=" O TYR A 605 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE A 607 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR A 590 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N ASP A 609 " --> pdb=" O THR A 590 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG A 606 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU A 628 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N THR A 608 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 716 through 719 removed outlier: 8.654A pdb=" N ASP A 717 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU A 686 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU A 719 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 688 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER A 738 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N MET A 763 " --> pdb=" O SER A 738 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ALA A 787 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A 762 " --> pdb=" O ALA A 787 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 541 through 544 removed outlier: 8.167A pdb=" N VAL B 541 " --> pdb=" O TYR B 513 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL B 515 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LYS B 543 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL B 517 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE B 483 " --> pdb=" O LYS B 514 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL B 516 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE B 485 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N TYR B 518 " --> pdb=" O ILE B 485 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR B 487 " --> pdb=" O TYR B 518 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR B 484 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL B 566 " --> pdb=" O THR B 484 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY B 486 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLN B 588 " --> pdb=" O TYR B 605 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE B 607 " --> pdb=" O GLN B 588 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR B 590 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N ASP B 609 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG B 606 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU B 628 " --> pdb=" O ARG B 606 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR B 608 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 716 through 719 removed outlier: 8.652A pdb=" N ASP B 717 " --> pdb=" O SER B 684 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 686 " --> pdb=" O ASP B 717 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU B 719 " --> pdb=" O LEU B 686 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 688 " --> pdb=" O LEU B 719 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER B 738 " --> pdb=" O VAL B 761 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N MET B 763 " --> pdb=" O SER B 738 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA B 787 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR B 762 " --> pdb=" O ALA B 787 " (cutoff:3.500A) 813 hydrogen bonds defined for protein. 2412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4041 1.34 - 1.46: 1950 1.46 - 1.58: 6565 1.58 - 1.70: 0 1.70 - 1.82: 142 Bond restraints: 12698 Sorted by residual: bond pdb=" CG LEU B 628 " pdb=" CD1 LEU B 628 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.81e+00 bond pdb=" CG LEU A 628 " pdb=" CD1 LEU A 628 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.81e+00 bond pdb=" CB ILE A 607 " pdb=" CG2 ILE A 607 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.12e+00 bond pdb=" CB ILE B 607 " pdb=" CG2 ILE B 607 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.12e+00 bond pdb=" CE LYS B 174 " pdb=" NZ LYS B 174 " ideal model delta sigma weight residual 1.489 1.453 0.036 3.00e-02 1.11e+03 1.47e+00 ... (remaining 12693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 16640 1.68 - 3.36: 547 3.36 - 5.04: 69 5.04 - 6.73: 25 6.73 - 8.41: 4 Bond angle restraints: 17285 Sorted by residual: angle pdb=" C THR B 590 " pdb=" N TRP B 591 " pdb=" CA TRP B 591 " ideal model delta sigma weight residual 121.54 115.33 6.21 1.91e+00 2.74e-01 1.06e+01 angle pdb=" C THR A 590 " pdb=" N TRP A 591 " pdb=" CA TRP A 591 " ideal model delta sigma weight residual 121.54 115.35 6.19 1.91e+00 2.74e-01 1.05e+01 angle pdb=" CA GLU A 170 " pdb=" CB GLU A 170 " pdb=" CG GLU A 170 " ideal model delta sigma weight residual 114.10 120.12 -6.02 2.00e+00 2.50e-01 9.07e+00 angle pdb=" CA GLU B 170 " pdb=" CB GLU B 170 " pdb=" CG GLU B 170 " ideal model delta sigma weight residual 114.10 120.06 -5.96 2.00e+00 2.50e-01 8.89e+00 angle pdb=" N ILE A 592 " pdb=" CA ILE A 592 " pdb=" C ILE A 592 " ideal model delta sigma weight residual 109.34 115.51 -6.17 2.08e+00 2.31e-01 8.80e+00 ... (remaining 17280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 7054 17.10 - 34.21: 421 34.21 - 51.31: 90 51.31 - 68.42: 14 68.42 - 85.52: 6 Dihedral angle restraints: 7585 sinusoidal: 2853 harmonic: 4732 Sorted by residual: dihedral pdb=" CA ALA B 745 " pdb=" C ALA B 745 " pdb=" N GLY B 746 " pdb=" CA GLY B 746 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ALA A 745 " pdb=" C ALA A 745 " pdb=" N GLY A 746 " pdb=" CA GLY A 746 " ideal model delta harmonic sigma weight residual 180.00 161.60 18.40 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA THR A 656 " pdb=" C THR A 656 " pdb=" N PHE A 657 " pdb=" CA PHE A 657 " ideal model delta harmonic sigma weight residual 180.00 163.54 16.46 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 7582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1451 0.043 - 0.087: 355 0.087 - 0.130: 113 0.130 - 0.174: 19 0.174 - 0.217: 6 Chirality restraints: 1944 Sorted by residual: chirality pdb=" CA GLU B 170 " pdb=" N GLU B 170 " pdb=" C GLU B 170 " pdb=" CB GLU B 170 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA GLU A 170 " pdb=" N GLU A 170 " pdb=" C GLU A 170 " pdb=" CB GLU A 170 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA PHE B 463 " pdb=" N PHE B 463 " pdb=" C PHE B 463 " pdb=" CB PHE B 463 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.93e-01 ... (remaining 1941 not shown) Planarity restraints: 2231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 463 " 0.028 2.00e-02 2.50e+03 2.08e-02 7.58e+00 pdb=" CG PHE B 463 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 463 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE B 463 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 463 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 463 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 463 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 463 " -0.028 2.00e-02 2.50e+03 2.07e-02 7.52e+00 pdb=" CG PHE A 463 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 463 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 463 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 463 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 463 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 463 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 393 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO A 394 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " 0.031 5.00e-02 4.00e+02 ... (remaining 2228 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2549 2.78 - 3.31: 13295 3.31 - 3.84: 21903 3.84 - 4.37: 25730 4.37 - 4.90: 42378 Nonbonded interactions: 105855 Sorted by model distance: nonbonded pdb=" O LYS A 58 " pdb=" OD1 ASP A 61 " model vdw 2.250 3.040 nonbonded pdb=" O LYS B 58 " pdb=" OD1 ASP B 61 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR A 484 " pdb=" O LYS A 561 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR B 484 " pdb=" O LYS B 561 " model vdw 2.266 3.040 nonbonded pdb=" OD1 ASN B 442 " pdb=" OH TYR B 594 " model vdw 2.322 3.040 ... (remaining 105850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 44 through 511 or (resid 512 and (name N or name CA or nam \ e C or name O or name CB )) or resid 513 through 558 or (resid 559 and (name N o \ r name CA or name C or name O or name CB )) or resid 560 through 846)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.490 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.003 0.055 12698 Z= 0.150 Angle : 0.722 8.406 17285 Z= 0.401 Chirality : 0.044 0.217 1944 Planarity : 0.006 0.056 2231 Dihedral : 11.936 85.520 4553 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.35 (0.20), residues: 1602 helix: 0.78 (0.14), residues: 1100 sheet: 0.72 (0.54), residues: 102 loop : -1.27 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG B 701 TYR 0.038 0.004 TYR B 284 PHE 0.046 0.003 PHE B 463 TRP 0.026 0.003 TRP A 459 HIS 0.004 0.001 HIS B 508 Details of bonding type rmsd covalent geometry : bond 0.00320 (12698) covalent geometry : angle 0.72212 (17285) hydrogen bonds : bond 0.11006 ( 813) hydrogen bonds : angle 5.32008 ( 2412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8145 (mp) cc_final: 0.7880 (tt) REVERT: B 452 LEU cc_start: 0.8446 (tp) cc_final: 0.8239 (tp) REVERT: B 466 LEU cc_start: 0.8127 (mp) cc_final: 0.7877 (tt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.0852 time to fit residues: 22.7213 Evaluate side-chains 122 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.0980 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 167 ASN A 619 GLN B 80 HIS B 167 ASN B 619 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.126046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.084666 restraints weight = 28441.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.086189 restraints weight = 17028.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.086390 restraints weight = 11393.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.086528 restraints weight = 10507.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.086643 restraints weight = 10023.332| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12698 Z= 0.223 Angle : 0.630 6.973 17285 Z= 0.327 Chirality : 0.044 0.192 1944 Planarity : 0.005 0.052 2231 Dihedral : 3.934 16.519 1756 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.61 % Allowed : 5.97 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.91 (0.21), residues: 1602 helix: 1.89 (0.15), residues: 1106 sheet: 0.50 (0.52), residues: 104 loop : -0.21 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 481 TYR 0.023 0.002 TYR A 284 PHE 0.025 0.002 PHE A 253 TRP 0.014 0.002 TRP B 459 HIS 0.004 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00510 (12698) covalent geometry : angle 0.62971 (17285) hydrogen bonds : bond 0.04381 ( 813) hydrogen bonds : angle 4.42389 ( 2412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 732 TYR cc_start: 0.7747 (m-80) cc_final: 0.7512 (m-80) REVERT: B 732 TYR cc_start: 0.7718 (m-80) cc_final: 0.7481 (m-80) outliers start: 21 outliers final: 11 residues processed: 140 average time/residue: 0.0781 time to fit residues: 17.9271 Evaluate side-chains 125 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 85 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 157 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.126879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.092766 restraints weight = 28783.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090548 restraints weight = 19609.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.090874 restraints weight = 19377.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.091382 restraints weight = 14045.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.091593 restraints weight = 13123.013| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12698 Z= 0.139 Angle : 0.549 11.614 17285 Z= 0.274 Chirality : 0.040 0.134 1944 Planarity : 0.004 0.045 2231 Dihedral : 3.862 16.193 1756 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.84 % Allowed : 8.19 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 2.31 (0.22), residues: 1602 helix: 2.27 (0.16), residues: 1110 sheet: 0.18 (0.53), residues: 108 loop : -0.22 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 685 TYR 0.016 0.001 TYR A 284 PHE 0.018 0.002 PHE B 829 TRP 0.006 0.001 TRP B 841 HIS 0.003 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00313 (12698) covalent geometry : angle 0.54925 (17285) hydrogen bonds : bond 0.03556 ( 813) hydrogen bonds : angle 4.00750 ( 2412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7400 (m100) cc_final: 0.7112 (m100) REVERT: A 580 MET cc_start: 0.8955 (tpt) cc_final: 0.8665 (tpp) REVERT: A 654 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.6409 (t80) REVERT: A 732 TYR cc_start: 0.7524 (m-80) cc_final: 0.7248 (m-80) REVERT: B 238 MET cc_start: 0.6114 (tpp) cc_final: 0.5910 (tpp) REVERT: B 461 TRP cc_start: 0.7404 (m100) cc_final: 0.7104 (m100) REVERT: B 580 MET cc_start: 0.8928 (tpt) cc_final: 0.8633 (tpp) REVERT: B 654 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.6356 (t80) REVERT: B 732 TYR cc_start: 0.7504 (m-80) cc_final: 0.7187 (m-80) outliers start: 24 outliers final: 12 residues processed: 148 average time/residue: 0.1027 time to fit residues: 23.3631 Evaluate side-chains 131 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 1 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.124965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.081700 restraints weight = 28528.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.084158 restraints weight = 15141.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085793 restraints weight = 10171.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.086663 restraints weight = 7948.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.087217 restraints weight = 6906.931| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12698 Z= 0.225 Angle : 0.592 9.391 17285 Z= 0.301 Chirality : 0.042 0.238 1944 Planarity : 0.004 0.046 2231 Dihedral : 3.981 16.549 1756 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.99 % Allowed : 10.03 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 2.20 (0.21), residues: 1602 helix: 2.24 (0.15), residues: 1108 sheet: 0.24 (0.55), residues: 108 loop : -0.50 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 481 TYR 0.013 0.001 TYR A 284 PHE 0.013 0.002 PHE B 829 TRP 0.010 0.001 TRP A 542 HIS 0.023 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00518 (12698) covalent geometry : angle 0.59231 (17285) hydrogen bonds : bond 0.03913 ( 813) hydrogen bonds : angle 4.11539 ( 2412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 HIS cc_start: 0.9150 (m90) cc_final: 0.8935 (m90) REVERT: A 461 TRP cc_start: 0.7267 (m100) cc_final: 0.6925 (m100) REVERT: A 546 TYR cc_start: 0.7915 (t80) cc_final: 0.7642 (t80) REVERT: A 580 MET cc_start: 0.9014 (tpt) cc_final: 0.8779 (tpp) REVERT: A 633 LEU cc_start: 0.9017 (mt) cc_final: 0.8727 (mt) REVERT: A 654 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.6144 (t80) REVERT: B 116 HIS cc_start: 0.9120 (m90) cc_final: 0.8879 (m90) REVERT: B 461 TRP cc_start: 0.7258 (m100) cc_final: 0.6923 (m100) REVERT: B 546 TYR cc_start: 0.7899 (t80) cc_final: 0.7649 (t80) REVERT: B 580 MET cc_start: 0.9001 (tpt) cc_final: 0.8758 (tpp) REVERT: B 633 LEU cc_start: 0.9035 (mt) cc_final: 0.8759 (mt) REVERT: B 654 PHE cc_start: 0.6554 (OUTLIER) cc_final: 0.6128 (t80) outliers start: 26 outliers final: 16 residues processed: 140 average time/residue: 0.0726 time to fit residues: 16.3695 Evaluate side-chains 126 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 73 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 chunk 104 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 HIS ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.127326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.087402 restraints weight = 28585.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.088450 restraints weight = 15945.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.088918 restraints weight = 10683.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.088994 restraints weight = 10393.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089263 restraints weight = 9677.126| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12698 Z= 0.114 Angle : 0.526 8.888 17285 Z= 0.260 Chirality : 0.040 0.179 1944 Planarity : 0.004 0.042 2231 Dihedral : 3.922 18.456 1756 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.91 % Allowed : 10.57 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 2.48 (0.22), residues: 1602 helix: 2.46 (0.16), residues: 1108 sheet: 0.19 (0.55), residues: 108 loop : -0.37 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.021 0.001 TYR A 134 PHE 0.012 0.001 PHE B 829 TRP 0.016 0.001 TRP B 542 HIS 0.011 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00259 (12698) covalent geometry : angle 0.52572 (17285) hydrogen bonds : bond 0.03124 ( 813) hydrogen bonds : angle 3.76342 ( 2412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7374 (m100) cc_final: 0.7052 (m100) REVERT: A 580 MET cc_start: 0.9020 (tpt) cc_final: 0.8747 (tpp) REVERT: A 633 LEU cc_start: 0.8967 (mt) cc_final: 0.8694 (mt) REVERT: A 654 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.6272 (t80) REVERT: A 732 TYR cc_start: 0.7616 (m-80) cc_final: 0.7246 (m-80) REVERT: A 800 LEU cc_start: 0.8803 (tp) cc_final: 0.8447 (tt) REVERT: B 461 TRP cc_start: 0.7373 (m100) cc_final: 0.7051 (m100) REVERT: B 580 MET cc_start: 0.9000 (tpt) cc_final: 0.8728 (tpp) REVERT: B 633 LEU cc_start: 0.9021 (mt) cc_final: 0.8748 (mt) REVERT: B 654 PHE cc_start: 0.6863 (OUTLIER) cc_final: 0.6287 (t80) REVERT: B 732 TYR cc_start: 0.7640 (m-80) cc_final: 0.7267 (m-80) REVERT: B 800 LEU cc_start: 0.8795 (tp) cc_final: 0.8430 (tt) outliers start: 25 outliers final: 18 residues processed: 138 average time/residue: 0.0718 time to fit residues: 15.8261 Evaluate side-chains 128 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 20 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 151 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN A 442 ASN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.127172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.084337 restraints weight = 28416.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.086876 restraints weight = 14975.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.088568 restraints weight = 9982.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.089458 restraints weight = 7812.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.090167 restraints weight = 6755.515| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12698 Z= 0.110 Angle : 0.517 11.200 17285 Z= 0.254 Chirality : 0.039 0.151 1944 Planarity : 0.004 0.042 2231 Dihedral : 3.824 16.253 1756 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.99 % Allowed : 11.18 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 2.50 (0.22), residues: 1602 helix: 2.47 (0.16), residues: 1110 sheet: 0.25 (0.55), residues: 108 loop : -0.37 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.020 0.001 TYR A 546 PHE 0.010 0.001 PHE B 829 TRP 0.013 0.001 TRP A 542 HIS 0.003 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00247 (12698) covalent geometry : angle 0.51749 (17285) hydrogen bonds : bond 0.03046 ( 813) hydrogen bonds : angle 3.69978 ( 2412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7242 (m100) cc_final: 0.6886 (m100) REVERT: A 580 MET cc_start: 0.9011 (tpt) cc_final: 0.8788 (tpp) REVERT: A 633 LEU cc_start: 0.9014 (mt) cc_final: 0.8734 (mt) REVERT: A 654 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.6142 (t80) REVERT: B 134 TYR cc_start: 0.7905 (m-80) cc_final: 0.7207 (m-80) REVERT: B 461 TRP cc_start: 0.7227 (m100) cc_final: 0.6882 (m100) REVERT: B 569 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8606 (p) REVERT: B 580 MET cc_start: 0.8969 (tpt) cc_final: 0.8736 (tpp) REVERT: B 633 LEU cc_start: 0.9030 (mt) cc_final: 0.8766 (mt) REVERT: B 654 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.6100 (t80) outliers start: 26 outliers final: 20 residues processed: 130 average time/residue: 0.0845 time to fit residues: 17.5222 Evaluate side-chains 131 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 153 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN A 571 HIS A 768 HIS B 435 GLN B 442 ASN B 571 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.123068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.082845 restraints weight = 28332.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.082525 restraints weight = 16955.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.082857 restraints weight = 12343.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.083545 restraints weight = 12219.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.083345 restraints weight = 10624.935| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 12698 Z= 0.278 Angle : 0.633 8.582 17285 Z= 0.319 Chirality : 0.042 0.153 1944 Planarity : 0.005 0.047 2231 Dihedral : 4.054 17.215 1756 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.37 % Allowed : 11.33 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 2.04 (0.21), residues: 1602 helix: 2.17 (0.15), residues: 1106 sheet: 0.07 (0.54), residues: 108 loop : -0.67 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 606 TYR 0.022 0.002 TYR A 134 PHE 0.014 0.002 PHE B 322 TRP 0.012 0.001 TRP B 841 HIS 0.008 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00640 (12698) covalent geometry : angle 0.63328 (17285) hydrogen bonds : bond 0.04182 ( 813) hydrogen bonds : angle 4.11820 ( 2412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 564 ILE cc_start: 0.6717 (mt) cc_final: 0.6510 (mt) REVERT: A 580 MET cc_start: 0.9064 (tpt) cc_final: 0.8862 (tpp) REVERT: A 633 LEU cc_start: 0.9095 (mt) cc_final: 0.8867 (mt) REVERT: A 635 TYR cc_start: 0.8724 (t80) cc_final: 0.8308 (t80) REVERT: A 654 PHE cc_start: 0.6991 (OUTLIER) cc_final: 0.6199 (t80) REVERT: A 800 LEU cc_start: 0.8924 (tp) cc_final: 0.8641 (tt) REVERT: B 580 MET cc_start: 0.9100 (tpt) cc_final: 0.8867 (tpp) REVERT: B 633 LEU cc_start: 0.9121 (mt) cc_final: 0.8903 (mt) REVERT: B 654 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.6163 (t80) REVERT: B 756 MET cc_start: 0.8167 (mmm) cc_final: 0.7842 (mmt) REVERT: B 800 LEU cc_start: 0.8921 (tp) cc_final: 0.8637 (tt) outliers start: 31 outliers final: 24 residues processed: 138 average time/residue: 0.0846 time to fit residues: 18.5212 Evaluate side-chains 132 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 97 PHE Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 32 optimal weight: 0.5980 chunk 126 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 114 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN B 442 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.126206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.087787 restraints weight = 28597.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.088190 restraints weight = 16943.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.087874 restraints weight = 12690.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088014 restraints weight = 13588.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.088290 restraints weight = 11881.806| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12698 Z= 0.111 Angle : 0.534 8.426 17285 Z= 0.268 Chirality : 0.039 0.187 1944 Planarity : 0.004 0.042 2231 Dihedral : 3.961 21.243 1756 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.14 % Allowed : 12.25 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 2.33 (0.22), residues: 1602 helix: 2.41 (0.16), residues: 1112 sheet: 0.13 (0.55), residues: 108 loop : -0.68 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 815 TYR 0.023 0.001 TYR B 546 PHE 0.011 0.001 PHE B 829 TRP 0.016 0.001 TRP B 841 HIS 0.002 0.001 HIS A 770 Details of bonding type rmsd covalent geometry : bond 0.00247 (12698) covalent geometry : angle 0.53375 (17285) hydrogen bonds : bond 0.03112 ( 813) hydrogen bonds : angle 3.76080 ( 2412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7531 (m100) cc_final: 0.7227 (m100) REVERT: A 564 ILE cc_start: 0.6629 (mt) cc_final: 0.6427 (mt) REVERT: A 580 MET cc_start: 0.9036 (tpt) cc_final: 0.8807 (tpp) REVERT: A 633 LEU cc_start: 0.9055 (mt) cc_final: 0.8808 (mt) REVERT: A 635 TYR cc_start: 0.8664 (t80) cc_final: 0.8285 (t80) REVERT: A 654 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6334 (t80) REVERT: A 756 MET cc_start: 0.7869 (mmm) cc_final: 0.7537 (mmt) REVERT: A 800 LEU cc_start: 0.8945 (tp) cc_final: 0.8680 (tt) REVERT: B 461 TRP cc_start: 0.7533 (m100) cc_final: 0.7235 (m100) REVERT: B 580 MET cc_start: 0.9054 (tpt) cc_final: 0.8788 (tpp) REVERT: B 633 LEU cc_start: 0.9092 (mt) cc_final: 0.8852 (mt) REVERT: B 635 TYR cc_start: 0.8661 (t80) cc_final: 0.8311 (t80) REVERT: B 654 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6315 (t80) REVERT: B 800 LEU cc_start: 0.8943 (tp) cc_final: 0.8688 (tt) outliers start: 28 outliers final: 21 residues processed: 132 average time/residue: 0.0785 time to fit residues: 16.5966 Evaluate side-chains 128 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 3 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 22 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN B 442 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.126441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.086918 restraints weight = 28498.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.087570 restraints weight = 15613.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.087574 restraints weight = 12527.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.087998 restraints weight = 10804.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.088090 restraints weight = 10577.127| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12698 Z= 0.115 Angle : 0.534 9.419 17285 Z= 0.267 Chirality : 0.039 0.173 1944 Planarity : 0.004 0.043 2231 Dihedral : 3.848 19.566 1756 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.76 % Allowed : 12.63 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 2.38 (0.22), residues: 1602 helix: 2.45 (0.16), residues: 1114 sheet: 0.15 (0.55), residues: 108 loop : -0.69 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 815 TYR 0.019 0.001 TYR A 134 PHE 0.009 0.001 PHE B 660 TRP 0.019 0.001 TRP B 841 HIS 0.003 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00260 (12698) covalent geometry : angle 0.53409 (17285) hydrogen bonds : bond 0.03028 ( 813) hydrogen bonds : angle 3.70699 ( 2412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7551 (m100) cc_final: 0.7246 (m100) REVERT: A 580 MET cc_start: 0.9054 (tpt) cc_final: 0.8849 (tpp) REVERT: A 633 LEU cc_start: 0.9041 (mt) cc_final: 0.8793 (mt) REVERT: A 635 TYR cc_start: 0.8633 (t80) cc_final: 0.8257 (t80) REVERT: A 654 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.6297 (t80) REVERT: A 800 LEU cc_start: 0.8969 (tp) cc_final: 0.8748 (tt) REVERT: B 134 TYR cc_start: 0.7929 (m-80) cc_final: 0.7339 (m-80) REVERT: B 461 TRP cc_start: 0.7537 (m100) cc_final: 0.7238 (m100) REVERT: B 580 MET cc_start: 0.9078 (tpt) cc_final: 0.8838 (tpp) REVERT: B 633 LEU cc_start: 0.9062 (mt) cc_final: 0.8810 (mt) REVERT: B 654 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6369 (t80) REVERT: B 756 MET cc_start: 0.7848 (mmm) cc_final: 0.7500 (mmt) REVERT: B 800 LEU cc_start: 0.8997 (tp) cc_final: 0.8767 (tt) outliers start: 23 outliers final: 19 residues processed: 127 average time/residue: 0.0808 time to fit residues: 16.2266 Evaluate side-chains 125 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 552 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 140 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 43 optimal weight: 0.0970 chunk 111 optimal weight: 0.0970 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN B 442 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.127564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.085040 restraints weight = 28632.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.087648 restraints weight = 15166.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 77)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089355 restraints weight = 10045.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.090258 restraints weight = 7794.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.090807 restraints weight = 6723.713| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12698 Z= 0.101 Angle : 0.535 10.386 17285 Z= 0.265 Chirality : 0.039 0.165 1944 Planarity : 0.004 0.043 2231 Dihedral : 3.792 19.552 1756 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.61 % Allowed : 12.79 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 2.49 (0.22), residues: 1602 helix: 2.53 (0.16), residues: 1114 sheet: 0.23 (0.56), residues: 108 loop : -0.67 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 462 TYR 0.016 0.001 TYR B 546 PHE 0.007 0.001 PHE B 654 TRP 0.020 0.001 TRP A 841 HIS 0.002 0.000 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00224 (12698) covalent geometry : angle 0.53478 (17285) hydrogen bonds : bond 0.02810 ( 813) hydrogen bonds : angle 3.61673 ( 2412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7217 (m100) cc_final: 0.6883 (m100) REVERT: A 633 LEU cc_start: 0.9006 (mt) cc_final: 0.8781 (mt) REVERT: A 635 TYR cc_start: 0.8638 (t80) cc_final: 0.8247 (t80) REVERT: A 654 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6247 (t80) REVERT: A 756 MET cc_start: 0.7653 (mmm) cc_final: 0.7280 (mmt) REVERT: A 800 LEU cc_start: 0.8825 (tp) cc_final: 0.8620 (tt) REVERT: B 134 TYR cc_start: 0.7902 (m-80) cc_final: 0.7282 (m-80) REVERT: B 461 TRP cc_start: 0.7244 (m100) cc_final: 0.6896 (m100) REVERT: B 633 LEU cc_start: 0.9035 (mt) cc_final: 0.8801 (mt) REVERT: B 635 TYR cc_start: 0.8622 (t80) cc_final: 0.8285 (t80) REVERT: B 654 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.6366 (t80) REVERT: B 756 MET cc_start: 0.7721 (mmm) cc_final: 0.7352 (mmt) REVERT: B 800 LEU cc_start: 0.8805 (tp) cc_final: 0.8599 (tt) outliers start: 21 outliers final: 17 residues processed: 124 average time/residue: 0.0908 time to fit residues: 18.0660 Evaluate side-chains 123 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 823 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 60 optimal weight: 0.0030 chunk 121 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN B 442 ASN ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.126602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083929 restraints weight = 28564.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.086417 restraints weight = 15201.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.088082 restraints weight = 10182.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.088998 restraints weight = 7940.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089462 restraints weight = 6872.592| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12698 Z= 0.120 Angle : 0.542 9.848 17285 Z= 0.269 Chirality : 0.039 0.161 1944 Planarity : 0.004 0.042 2231 Dihedral : 3.774 18.828 1756 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.91 % Allowed : 12.33 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 2.49 (0.22), residues: 1602 helix: 2.55 (0.16), residues: 1114 sheet: 0.15 (0.56), residues: 108 loop : -0.69 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 815 TYR 0.017 0.001 TYR A 134 PHE 0.009 0.001 PHE B 660 TRP 0.018 0.001 TRP B 841 HIS 0.003 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00275 (12698) covalent geometry : angle 0.54238 (17285) hydrogen bonds : bond 0.02996 ( 813) hydrogen bonds : angle 3.66701 ( 2412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2065.57 seconds wall clock time: 36 minutes 30.05 seconds (2190.05 seconds total)