Starting phenix.real_space_refine on Sat Jan 18 15:31:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dtf_27696/01_2025/8dtf_27696.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dtf_27696/01_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_27696/01_2025/8dtf_27696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dtf_27696/01_2025/8dtf_27696.map" model { file = "/net/cci-nas-00/data/ceres_data/8dtf_27696/01_2025/8dtf_27696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dtf_27696/01_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 8.60, per 1000 atoms: 0.69 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: 2.98 Conformation dependent library (CDL) restraints added in 1.6 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: 1.29 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: 4.36 Time building geometry restraints manager: 3.41 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: 7.910 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.300 Process input model: 30.950 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.200 ------------------------------------------------------------------------------- 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= 0.209 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 *********************** 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 : 1.385 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: 0.2066 time to fit residues: 54.3832 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 : 1.291 ------------------------------------------------------------------------------- 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 = 0.087918 restraints weight = 28505.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090417 restraints weight = 15471.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.090694 restraints weight = 11151.474| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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= 0.221 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 *********************** 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 : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 732 TYR cc_start: 0.7697 (m-80) cc_final: 0.7469 (m-80) REVERT: B 732 TYR cc_start: 0.7659 (m-80) cc_final: 0.7447 (m-80) REVERT: B 756 MET cc_start: 0.7985 (mmm) cc_final: 0.7683 (mmt) outliers start: 18 outliers final: 13 residues processed: 127 average time/residue: 0.2020 time to fit residues: 41.0320 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 : 1.469 ------------------------------------------------------------------------------- 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: 0.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 55 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.128845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.086104 restraints weight = 28640.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.088736 restraints weight = 14812.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.090492 restraints weight = 9739.830| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12698 Z= 0.165 Angle : 0.527 10.918 17285 Z= 0.266 Chirality : 0.040 0.142 1944 Planarity : 0.004 0.042 2231 Dihedral : 3.784 15.538 1756 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.70 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: 2.48 (0.22), residues: 1602 helix: 2.34 (0.16), residues: 1108 sheet: 0.60 (0.54), residues: 104 loop : -0.07 (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 0.012 0.001 PHE B 660 TYR 0.017 0.001 TYR A 284 ARG 0.003 0.000 ARG B 815 *********************** 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 151 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7116 (m100) cc_final: 0.6813 (m100) REVERT: B 461 TRP cc_start: 0.7159 (m100) cc_final: 0.6833 (m100) REVERT: B 569 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8717 (p) outliers start: 19 outliers final: 9 residues processed: 143 average time/residue: 0.2303 time to fit residues: 50.0367 Evaluate side-chains 126 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 569 THR 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: 0.8980 chunk 95 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.128134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.085684 restraints weight = 28317.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.088246 restraints weight = 14948.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.089901 restraints weight = 9960.276| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12698 Z= 0.205 Angle : 0.534 11.875 17285 Z= 0.266 Chirality : 0.040 0.229 1944 Planarity : 0.004 0.041 2231 Dihedral : 3.768 15.246 1756 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.53 % Allowed : 8.96 % Favored : 89.51 % 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: 0.46 (0.55), residues: 108 loop : -0.17 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 841 HIS 0.003 0.001 HIS B 495 PHE 0.016 0.001 PHE B 829 TYR 0.012 0.001 TYR B 284 ARG 0.008 0.000 ARG A 676 *********************** 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 154 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.7733 (m-80) cc_final: 0.7194 (m-80) REVERT: A 461 TRP cc_start: 0.7231 (m100) cc_final: 0.6899 (m100) REVERT: B 134 TYR cc_start: 0.7724 (m-80) cc_final: 0.7175 (m-80) REVERT: B 461 TRP cc_start: 0.7257 (m100) cc_final: 0.6920 (m100) outliers start: 20 outliers final: 12 residues processed: 149 average time/residue: 0.2398 time to fit residues: 55.7549 Evaluate side-chains 127 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 152 optimal weight: 0.1980 chunk 118 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.128188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.089166 restraints weight = 28338.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.089823 restraints weight = 16121.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.090104 restraints weight = 11224.168| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2584 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= 0.185 Angle : 0.538 10.305 17285 Z= 0.264 Chirality : 0.040 0.228 1944 Planarity : 0.004 0.044 2231 Dihedral : 3.810 15.083 1756 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.38 % Allowed : 10.95 % Favored : 87.67 % 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: 2.61 (0.22), residues: 1602 helix: 2.50 (0.16), residues: 1108 sheet: 0.47 (0.56), residues: 108 loop : -0.21 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 542 HIS 0.017 0.001 HIS A 508 PHE 0.013 0.001 PHE B 829 TYR 0.013 0.001 TYR B 732 ARG 0.009 0.000 ARG B 676 *********************** 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 133 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7339 (m100) cc_final: 0.7046 (m100) REVERT: A 800 LEU cc_start: 0.8791 (tp) cc_final: 0.8410 (tt) REVERT: B 461 TRP cc_start: 0.7403 (m100) cc_final: 0.7094 (m100) REVERT: B 633 LEU cc_start: 0.8939 (mt) cc_final: 0.8561 (mt) REVERT: B 800 LEU cc_start: 0.8803 (tp) cc_final: 0.8429 (tt) outliers start: 18 outliers final: 14 residues processed: 128 average time/residue: 0.2067 time to fit residues: 41.6887 Evaluate side-chains 117 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.126976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.084193 restraints weight = 28684.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.086781 restraints weight = 15005.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.088509 restraints weight = 9924.284| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2776 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= 0.222 Angle : 0.541 9.410 17285 Z= 0.267 Chirality : 0.040 0.186 1944 Planarity : 0.004 0.044 2231 Dihedral : 3.820 15.954 1756 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.91 % Allowed : 11.10 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.49 (0.16), residues: 1108 sheet: 0.38 (0.56), residues: 108 loop : -0.26 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 841 HIS 0.012 0.001 HIS A 508 PHE 0.012 0.001 PHE B 829 TYR 0.020 0.001 TYR B 134 ARG 0.008 0.001 ARG B 676 *********************** 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 137 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7271 (m100) cc_final: 0.6948 (m100) REVERT: B 461 TRP cc_start: 0.7273 (m100) cc_final: 0.6956 (m100) REVERT: B 569 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8701 (p) REVERT: B 633 LEU cc_start: 0.9018 (mt) cc_final: 0.8724 (mt) REVERT: B 635 TYR cc_start: 0.8656 (t80) cc_final: 0.8231 (t80) outliers start: 25 outliers final: 21 residues processed: 133 average time/residue: 0.2045 time to fit residues: 42.8304 Evaluate side-chains 127 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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 602 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 569 THR Chi-restraints excluded: chain B residue 602 THR 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: 0.7980 chunk 53 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 155 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 HIS B 435 GLN B 442 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.126345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.083261 restraints weight = 28479.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.085766 restraints weight = 14956.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087303 restraints weight = 9970.879| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2966 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= 0.234 Angle : 0.549 8.759 17285 Z= 0.271 Chirality : 0.040 0.199 1944 Planarity : 0.004 0.043 2231 Dihedral : 3.811 16.304 1756 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.07 % Allowed : 11.26 % Favored : 86.68 % 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: 2.55 (0.22), residues: 1602 helix: 2.51 (0.16), residues: 1106 sheet: 0.37 (0.56), residues: 108 loop : -0.34 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 841 HIS 0.011 0.001 HIS A 508 PHE 0.012 0.001 PHE B 829 TYR 0.019 0.001 TYR A 546 ARG 0.004 0.000 ARG B 676 *********************** 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 139 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7296 (m100) cc_final: 0.6974 (m100) REVERT: B 461 TRP cc_start: 0.7257 (m100) cc_final: 0.6937 (m100) REVERT: B 633 LEU cc_start: 0.9051 (mt) cc_final: 0.8772 (mt) REVERT: B 635 TYR cc_start: 0.8649 (t80) cc_final: 0.8229 (t80) outliers start: 27 outliers final: 23 residues processed: 132 average time/residue: 0.2212 time to fit residues: 45.9273 Evaluate side-chains 129 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 494 THR 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 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: 0.7980 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 141 optimal weight: 0.5980 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 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 HIS 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 = 0.126601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.085990 restraints weight = 28708.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.087124 restraints weight = 16163.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.087987 restraints weight = 11679.021| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3088 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= 0.190 Angle : 0.533 8.403 17285 Z= 0.263 Chirality : 0.039 0.219 1944 Planarity : 0.004 0.041 2231 Dihedral : 3.803 16.244 1756 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.91 % Allowed : 11.56 % 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: 2.56 (0.22), residues: 1602 helix: 2.53 (0.16), residues: 1106 sheet: 0.33 (0.56), residues: 108 loop : -0.40 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 542 HIS 0.007 0.001 HIS A 508 PHE 0.011 0.001 PHE B 829 TYR 0.020 0.001 TYR B 134 ARG 0.004 0.000 ARG B 676 *********************** 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 137 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 TRP cc_start: 0.7384 (m100) cc_final: 0.7095 (m100) REVERT: A 635 TYR cc_start: 0.8616 (t80) cc_final: 0.8226 (t80) REVERT: A 654 PHE cc_start: 0.6879 (OUTLIER) cc_final: 0.6395 (t80) REVERT: B 461 TRP cc_start: 0.7418 (m100) cc_final: 0.7125 (m100) REVERT: B 569 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8737 (p) REVERT: B 633 LEU cc_start: 0.9038 (mt) cc_final: 0.8750 (mt) REVERT: B 635 TYR cc_start: 0.8638 (t80) cc_final: 0.8231 (t80) REVERT: B 654 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.6317 (t80) outliers start: 25 outliers final: 19 residues processed: 130 average time/residue: 0.2078 time to fit residues: 42.4989 Evaluate side-chains 127 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.339 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.1389 > 50: distance: 77 - 154: 13.509 distance: 80 - 167: 9.454 distance: 91 - 170: 29.847 distance: 118 - 121: 14.030 distance: 121 - 122: 8.746 distance: 122 - 123: 8.053 distance: 122 - 125: 11.938 distance: 123 - 124: 4.119 distance: 123 - 132: 14.029 distance: 125 - 126: 10.905 distance: 126 - 127: 11.826 distance: 127 - 128: 7.842 distance: 128 - 129: 14.452 distance: 129 - 130: 11.671 distance: 129 - 131: 13.953 distance: 132 - 133: 10.563 distance: 132 - 138: 18.637 distance: 133 - 134: 23.011 distance: 133 - 136: 11.612 distance: 134 - 135: 18.500 distance: 134 - 139: 22.633 distance: 136 - 137: 27.646 distance: 137 - 138: 14.508 distance: 139 - 140: 10.069 distance: 140 - 141: 35.115 distance: 140 - 143: 28.973 distance: 141 - 142: 18.563 distance: 141 - 144: 9.491 distance: 144 - 145: 7.401 distance: 144 - 150: 8.697 distance: 145 - 146: 10.994 distance: 145 - 148: 24.300 distance: 146 - 147: 26.742 distance: 146 - 151: 8.378 distance: 148 - 149: 12.277 distance: 149 - 150: 26.309 distance: 151 - 152: 23.620 distance: 152 - 153: 3.322 distance: 152 - 155: 11.312 distance: 153 - 154: 7.710 distance: 155 - 156: 19.211 distance: 155 - 157: 33.670 distance: 158 - 159: 13.424 distance: 159 - 160: 19.860 distance: 159 - 162: 12.043 distance: 160 - 161: 12.513 distance: 160 - 167: 21.206 distance: 162 - 163: 8.452 distance: 163 - 164: 31.105 distance: 164 - 165: 16.071 distance: 164 - 166: 18.027 distance: 167 - 168: 4.620 distance: 168 - 169: 6.309 distance: 168 - 171: 23.816 distance: 169 - 170: 25.238 distance: 169 - 174: 7.713 distance: 171 - 172: 10.120 distance: 171 - 173: 33.753 distance: 174 - 175: 4.213 distance: 175 - 176: 4.672 distance: 175 - 178: 15.515 distance: 176 - 177: 12.720 distance: 176 - 181: 6.211 distance: 178 - 179: 4.101 distance: 178 - 180: 16.836 distance: 181 - 182: 16.784 distance: 182 - 183: 19.447 distance: 182 - 185: 7.557 distance: 183 - 184: 19.926 distance: 183 - 195: 15.043 distance: 185 - 186: 15.617 distance: 186 - 187: 9.082 distance: 186 - 188: 11.806 distance: 187 - 189: 5.500 distance: 188 - 190: 10.396 distance: 188 - 191: 3.914 distance: 189 - 190: 8.464 distance: 190 - 192: 8.361 distance: 191 - 193: 8.008 distance: 192 - 194: 7.151 distance: 193 - 194: 13.586 distance: 195 - 196: 23.459 distance: 196 - 197: 31.342 distance: 196 - 199: 15.723 distance: 197 - 198: 29.129 distance: 197 - 203: 30.147 distance: 199 - 200: 30.220 distance: 199 - 201: 33.457 distance: 200 - 202: 18.333