Starting phenix.real_space_refine on Wed Jul 30 14:18:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dtf_27696/07_2025/8dtf_27696.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dtf_27696/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dtf_27696/07_2025/8dtf_27696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dtf_27696/07_2025/8dtf_27696.map" model { file = "/net/cci-nas-00/data/ceres_data/8dtf_27696/07_2025/8dtf_27696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dtf_27696/07_2025/8dtf_27696.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 1} 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: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 8.12, per 1000 atoms: 0.65 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: 2.87 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.47 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: 4.42 Time building geometry restraints manager: 3.42 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: 5.800 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: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.940 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.510 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.026 0.003 TRP A 459 HIS 0.004 0.001 HIS B 508 PHE 0.046 0.003 PHE B 463 TYR 0.038 0.004 TYR B 284 ARG 0.013 0.002 ARG B 701 Details of bonding type rmsd hydrogen bonds : bond 0.11006 ( 813) hydrogen bonds : angle 5.32008 ( 2412) covalent geometry : bond 0.00320 (12698) covalent geometry : angle 0.72212 (17285) *********************** 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 : 1.383 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: 0.2010 time to fit residues: 52.9763 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 : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 0.0970 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.129195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.087912 restraints weight = 28505.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090427 restraints weight = 15474.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.090691 restraints weight = 11158.501| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12698 Z= 0.153 Angle : 0.573 6.638 17285 Z= 0.298 Chirality : 0.042 0.218 1944 Planarity : 0.004 0.046 2231 Dihedral : 3.821 15.845 1756 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.38 % Allowed : 6.28 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.21), residues: 1602 helix: 1.97 (0.15), residues: 1104 sheet: 0.54 (0.53), residues: 104 loop : -0.16 (0.34), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 459 HIS 0.004 0.001 HIS A 293 PHE 0.017 0.002 PHE A 253 TYR 0.021 0.002 TYR A 284 ARG 0.004 0.001 ARG B 676 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 813) hydrogen bonds : angle 4.31323 ( 2412) covalent geometry : bond 0.00341 (12698) covalent geometry : angle 0.57340 (17285) *********************** 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 135 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 732 TYR cc_start: 0.7701 (m-80) cc_final: 0.7474 (m-80) REVERT: B 732 TYR cc_start: 0.7664 (m-80) cc_final: 0.7453 (m-80) REVERT: B 756 MET cc_start: 0.7984 (mmm) cc_final: 0.7682 (mmt) outliers start: 18 outliers final: 13 residues processed: 127 average time/residue: 0.1866 time to fit residues: 38.4004 Evaluate side-chains 126 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 461 TRP Chi-restraints excluded: chain A residue 485 ILE 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 461 TRP Chi-restraints excluded: chain B residue 508 HIS 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 116 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 55 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.128963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.086208 restraints weight = 28641.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.088867 restraints weight = 14759.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.090619 restraints weight = 9753.336| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12698 Z= 0.116 Angle : 0.529 11.111 17285 Z= 0.267 Chirality : 0.040 0.139 1944 Planarity : 0.004 0.042 2231 Dihedral : 3.786 15.594 1756 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.45 % Allowed : 7.35 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.22), residues: 1602 helix: 2.32 (0.16), residues: 1108 sheet: 0.59 (0.54), residues: 104 loop : -0.08 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 459 HIS 0.004 0.001 HIS A 293 PHE 0.009 0.001 PHE B 660 TYR 0.017 0.001 TYR A 284 ARG 0.003 0.000 ARG B 815 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 813) hydrogen bonds : angle 3.94881 ( 2412) covalent geometry : bond 0.00253 (12698) covalent geometry : angle 0.52948 (17285) *********************** 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 152 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7114 (m100) cc_final: 0.6812 (m100) REVERT: B 461 TRP cc_start: 0.7158 (m100) cc_final: 0.6831 (m100) REVERT: B 732 TYR cc_start: 0.7508 (m-80) cc_final: 0.7181 (m-80) outliers start: 19 outliers final: 10 residues processed: 144 average time/residue: 0.3080 time to fit residues: 69.1852 Evaluate side-chains 125 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 485 ILE 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 405 VAL Chi-restraints excluded: chain B residue 508 HIS 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 4 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 126 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.128642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.086561 restraints weight = 28370.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089020 restraints weight = 14983.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.090627 restraints weight = 9980.392| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12698 Z= 0.127 Angle : 0.532 12.297 17285 Z= 0.264 Chirality : 0.040 0.240 1944 Planarity : 0.004 0.042 2231 Dihedral : 3.768 15.124 1756 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.38 % Allowed : 8.73 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.22), residues: 1602 helix: 2.47 (0.16), residues: 1108 sheet: 0.45 (0.55), residues: 108 loop : -0.16 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 841 HIS 0.003 0.001 HIS B 495 PHE 0.017 0.001 PHE B 829 TYR 0.013 0.001 TYR A 284 ARG 0.010 0.001 ARG B 676 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 813) hydrogen bonds : angle 3.79464 ( 2412) covalent geometry : bond 0.00286 (12698) covalent geometry : angle 0.53226 (17285) *********************** 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 150 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.7756 (m-80) cc_final: 0.7197 (m-80) REVERT: A 461 TRP cc_start: 0.7212 (m100) cc_final: 0.6901 (m100) REVERT: B 134 TYR cc_start: 0.7702 (m-80) cc_final: 0.7153 (m-80) REVERT: B 461 TRP cc_start: 0.7253 (m100) cc_final: 0.6922 (m100) REVERT: B 732 TYR cc_start: 0.7636 (m-80) cc_final: 0.7416 (m-80) outliers start: 18 outliers final: 11 residues processed: 145 average time/residue: 0.2417 time to fit residues: 54.9182 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 : 1.658 ------------------------------------------------------------------------------- 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 552 LYS Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 678 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 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 37 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.128342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.086171 restraints weight = 28365.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.088799 restraints weight = 14727.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.090544 restraints weight = 9702.433| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2580 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= 0.124 Angle : 0.533 10.193 17285 Z= 0.262 Chirality : 0.040 0.234 1944 Planarity : 0.004 0.041 2231 Dihedral : 3.800 15.908 1756 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.38 % Allowed : 10.80 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.22), residues: 1602 helix: 2.54 (0.16), residues: 1108 sheet: 0.45 (0.55), residues: 108 loop : -0.19 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 542 HIS 0.004 0.001 HIS A 495 PHE 0.011 0.001 PHE B 829 TYR 0.017 0.001 TYR A 732 ARG 0.005 0.000 ARG A 676 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 813) hydrogen bonds : angle 3.72054 ( 2412) covalent geometry : bond 0.00282 (12698) covalent geometry : angle 0.53336 (17285) *********************** 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 136 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 HIS cc_start: 0.9103 (m90) cc_final: 0.8895 (m90) REVERT: A 461 TRP cc_start: 0.7215 (m100) cc_final: 0.6894 (m100) REVERT: A 633 LEU cc_start: 0.8921 (mt) cc_final: 0.8554 (mt) REVERT: A 800 LEU cc_start: 0.8695 (tp) cc_final: 0.8344 (tt) REVERT: B 461 TRP cc_start: 0.7282 (m100) cc_final: 0.6948 (m100) REVERT: B 633 LEU cc_start: 0.8927 (mt) cc_final: 0.8579 (mt) REVERT: B 732 TYR cc_start: 0.7637 (m-80) cc_final: 0.7284 (m-80) REVERT: B 800 LEU cc_start: 0.8708 (tp) cc_final: 0.8356 (tt) outliers start: 18 outliers final: 13 residues processed: 131 average time/residue: 0.1966 time to fit residues: 41.0885 Evaluate side-chains 119 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 556 MET 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 508 HIS 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 75 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 B 442 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.126675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.083783 restraints weight = 28669.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.086334 restraints weight = 14988.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.087884 restraints weight = 9931.951| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12698 Z= 0.157 Angle : 0.550 9.607 17285 Z= 0.272 Chirality : 0.040 0.184 1944 Planarity : 0.004 0.043 2231 Dihedral : 3.811 16.062 1756 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.84 % Allowed : 11.03 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.22), residues: 1602 helix: 2.51 (0.16), residues: 1108 sheet: 0.38 (0.56), residues: 108 loop : -0.25 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 841 HIS 0.006 0.001 HIS B 116 PHE 0.012 0.001 PHE B 654 TYR 0.020 0.001 TYR B 134 ARG 0.005 0.000 ARG A 685 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 813) hydrogen bonds : angle 3.79644 ( 2412) covalent geometry : bond 0.00360 (12698) covalent geometry : angle 0.54956 (17285) *********************** 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 139 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 HIS cc_start: 0.9145 (m90) cc_final: 0.8919 (m90) REVERT: A 461 TRP cc_start: 0.7316 (m100) cc_final: 0.6981 (m100) REVERT: A 633 LEU cc_start: 0.9006 (mt) cc_final: 0.8712 (mt) REVERT: A 800 LEU cc_start: 0.8871 (tp) cc_final: 0.8571 (tt) REVERT: B 461 TRP cc_start: 0.7302 (m100) cc_final: 0.6983 (m100) REVERT: B 633 LEU cc_start: 0.9049 (mt) cc_final: 0.8752 (mt) REVERT: B 800 LEU cc_start: 0.8874 (tp) cc_final: 0.8574 (tt) outliers start: 24 outliers final: 19 residues processed: 134 average time/residue: 0.2007 time to fit residues: 42.5474 Evaluate side-chains 125 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 508 HIS 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 644 VAL 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 644 VAL 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 26 optimal weight: 0.5980 chunk 53 optimal weight: 0.0570 chunk 131 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.1304 ------------------------------------------------------------------------------- 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 B 442 ASN B 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.126081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.083148 restraints weight = 28458.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085678 restraints weight = 14900.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.087365 restraints weight = 9937.285| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12698 Z= 0.156 Angle : 0.550 8.953 17285 Z= 0.271 Chirality : 0.040 0.198 1944 Planarity : 0.004 0.043 2231 Dihedral : 3.825 16.393 1756 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.22 % Allowed : 11.26 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.22), residues: 1602 helix: 2.53 (0.16), residues: 1108 sheet: 0.37 (0.56), residues: 108 loop : -0.38 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 542 HIS 0.004 0.001 HIS B 495 PHE 0.011 0.001 PHE B 829 TYR 0.016 0.001 TYR A 546 ARG 0.003 0.000 ARG A 676 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 813) hydrogen bonds : angle 3.75581 ( 2412) covalent geometry : bond 0.00359 (12698) covalent geometry : angle 0.55039 (17285) *********************** 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 142 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 HIS cc_start: 0.9147 (m90) cc_final: 0.8925 (m90) REVERT: A 461 TRP cc_start: 0.7268 (m100) cc_final: 0.6960 (m100) REVERT: A 546 TYR cc_start: 0.7660 (t80) cc_final: 0.7412 (t80) REVERT: A 633 LEU cc_start: 0.9035 (mt) cc_final: 0.8761 (mt) REVERT: B 461 TRP cc_start: 0.7327 (m100) cc_final: 0.7002 (m100) REVERT: B 633 LEU cc_start: 0.9059 (mt) cc_final: 0.8781 (mt) outliers start: 29 outliers final: 22 residues processed: 134 average time/residue: 0.1969 time to fit residues: 41.5666 Evaluate side-chains 129 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 508 HIS Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 644 VAL 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 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 644 VAL 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 37 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.126713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.084120 restraints weight = 28808.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.086691 restraints weight = 15146.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.088388 restraints weight = 10016.795| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3230 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= 0.127 Angle : 0.535 9.675 17285 Z= 0.262 Chirality : 0.039 0.176 1944 Planarity : 0.004 0.042 2231 Dihedral : 3.784 16.379 1756 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.37 % Allowed : 11.41 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.22), residues: 1602 helix: 2.56 (0.16), residues: 1112 sheet: 0.30 (0.56), residues: 108 loop : -0.51 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 542 HIS 0.004 0.001 HIS A 467 PHE 0.010 0.001 PHE B 829 TYR 0.021 0.001 TYR B 134 ARG 0.002 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 813) hydrogen bonds : angle 3.68666 ( 2412) covalent geometry : bond 0.00289 (12698) covalent geometry : angle 0.53494 (17285) *********************** 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 146 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 HIS cc_start: 0.9090 (m90) cc_final: 0.8889 (m-70) REVERT: A 461 TRP cc_start: 0.7282 (m100) cc_final: 0.6988 (m100) REVERT: A 633 LEU cc_start: 0.8993 (mt) cc_final: 0.8723 (mt) REVERT: A 635 TYR cc_start: 0.8637 (t80) cc_final: 0.8196 (t80) REVERT: A 654 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.6499 (t80) REVERT: A 800 LEU cc_start: 0.8737 (tp) cc_final: 0.8458 (tt) REVERT: B 461 TRP cc_start: 0.7309 (m100) cc_final: 0.7028 (m100) REVERT: B 633 LEU cc_start: 0.9030 (mt) cc_final: 0.8763 (mt) REVERT: B 654 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.6431 (t80) REVERT: B 800 LEU cc_start: 0.8764 (tp) cc_final: 0.8480 (tt) outliers start: 31 outliers final: 23 residues processed: 137 average time/residue: 0.1940 time to fit residues: 42.1902 Evaluate side-chains 133 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 508 HIS Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 556 MET 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 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 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 117 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 chunk 54 optimal weight: 0.0020 chunk 47 optimal weight: 3.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.126705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.084200 restraints weight = 28615.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.086732 restraints weight = 15087.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.088399 restraints weight = 10005.831| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3315 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= 0.117 Angle : 0.534 8.822 17285 Z= 0.263 Chirality : 0.039 0.175 1944 Planarity : 0.004 0.041 2231 Dihedral : 3.765 16.168 1756 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.99 % Allowed : 11.64 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.22), residues: 1602 helix: 2.57 (0.16), residues: 1112 sheet: 0.23 (0.56), residues: 108 loop : -0.54 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 841 HIS 0.002 0.001 HIS B 768 PHE 0.009 0.001 PHE B 829 TYR 0.009 0.001 TYR A 732 ARG 0.003 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.03020 ( 813) hydrogen bonds : angle 3.67731 ( 2412) covalent geometry : bond 0.00268 (12698) covalent geometry : angle 0.53368 (17285) *********************** 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 138 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 HIS cc_start: 0.9081 (m90) cc_final: 0.8878 (m-70) REVERT: A 461 TRP cc_start: 0.7273 (m100) cc_final: 0.6977 (m100) REVERT: A 633 LEU cc_start: 0.8993 (mt) cc_final: 0.8716 (mt) REVERT: A 635 TYR cc_start: 0.8628 (t80) cc_final: 0.8198 (t80) REVERT: A 654 PHE cc_start: 0.7013 (OUTLIER) cc_final: 0.6525 (t80) REVERT: A 800 LEU cc_start: 0.8811 (tp) cc_final: 0.8564 (tt) REVERT: B 461 TRP cc_start: 0.7313 (m100) cc_final: 0.7038 (m100) REVERT: B 633 LEU cc_start: 0.9018 (mt) cc_final: 0.8747 (mt) REVERT: B 654 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.6494 (t80) REVERT: B 800 LEU cc_start: 0.8850 (tp) cc_final: 0.8597 (tt) outliers start: 26 outliers final: 22 residues processed: 133 average time/residue: 0.2035 time to fit residues: 42.7850 Evaluate side-chains 132 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 508 HIS Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 556 MET 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 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 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 155 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 158 optimal weight: 10.0000 chunk 105 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 55 optimal weight: 0.1980 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 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 = 0.3982 r_free = 0.3982 target = 0.127198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.084864 restraints weight = 28642.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087423 restraints weight = 15092.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089014 restraints weight = 10009.946| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12698 Z= 0.110 Angle : 0.542 10.147 17285 Z= 0.264 Chirality : 0.039 0.168 1944 Planarity : 0.004 0.042 2231 Dihedral : 3.739 16.014 1756 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.84 % Allowed : 11.94 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.22), residues: 1602 helix: 2.60 (0.16), residues: 1110 sheet: 0.24 (0.56), residues: 108 loop : -0.47 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 841 HIS 0.002 0.000 HIS B 768 PHE 0.008 0.001 PHE B 829 TYR 0.017 0.001 TYR A 134 ARG 0.003 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.02909 ( 813) hydrogen bonds : angle 3.62822 ( 2412) covalent geometry : bond 0.00250 (12698) covalent geometry : angle 0.54156 (17285) ********************** 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 136 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 HIS cc_start: 0.9130 (m90) cc_final: 0.8912 (m-70) REVERT: A 461 TRP cc_start: 0.7296 (m100) cc_final: 0.6959 (m100) REVERT: A 633 LEU cc_start: 0.8977 (mt) cc_final: 0.8697 (mt) REVERT: A 635 TYR cc_start: 0.8604 (t80) cc_final: 0.8185 (t80) REVERT: A 654 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.6461 (t80) REVERT: A 755 TYR cc_start: 0.8182 (t80) cc_final: 0.7900 (t80) REVERT: A 800 LEU cc_start: 0.8872 (tp) cc_final: 0.8641 (tt) REVERT: B 461 TRP cc_start: 0.7301 (m100) cc_final: 0.7015 (m100) REVERT: B 633 LEU cc_start: 0.9002 (mt) cc_final: 0.8726 (mt) REVERT: B 635 TYR cc_start: 0.8616 (t80) cc_final: 0.8208 (t80) REVERT: B 654 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6482 (t80) REVERT: B 800 LEU cc_start: 0.8871 (tp) cc_final: 0.8636 (tt) outliers start: 24 outliers final: 19 residues processed: 133 average time/residue: 0.2043 time to fit residues: 42.8589 Evaluate side-chains 126 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 508 HIS 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 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 485 ILE Chi-restraints excluded: chain B residue 508 HIS Chi-restraints excluded: chain B residue 569 THR 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 123 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 40 optimal weight: 0.0270 chunk 144 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.127899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.085863 restraints weight = 28671.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.088458 restraints weight = 15050.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.090147 restraints weight = 9954.881| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12698 Z= 0.100 Angle : 0.533 9.875 17285 Z= 0.259 Chirality : 0.039 0.163 1944 Planarity : 0.004 0.042 2231 Dihedral : 3.697 15.583 1756 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.61 % Allowed : 12.25 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.22), residues: 1602 helix: 2.65 (0.16), residues: 1110 sheet: 0.25 (0.57), residues: 108 loop : -0.48 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 841 HIS 0.002 0.000 HIS B 768 PHE 0.009 0.001 PHE A 660 TYR 0.014 0.001 TYR A 546 ARG 0.003 0.000 ARG B 558 Details of bonding type rmsd hydrogen bonds : bond 0.02806 ( 813) hydrogen bonds : angle 3.57681 ( 2412) covalent geometry : bond 0.00225 (12698) covalent geometry : angle 0.53340 (17285) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4616.15 seconds wall clock time: 82 minutes 32.98 seconds (4952.98 seconds total)