Starting phenix.real_space_refine on Sat Aug 23 17:14:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bgw_16041/08_2025/8bgw_16041.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bgw_16041/08_2025/8bgw_16041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bgw_16041/08_2025/8bgw_16041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bgw_16041/08_2025/8bgw_16041.map" model { file = "/net/cci-nas-00/data/ceres_data/8bgw_16041/08_2025/8bgw_16041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bgw_16041/08_2025/8bgw_16041.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 6 7.16 5 P 1 5.49 5 S 48 5.16 5 C 8356 2.51 5 N 1999 2.21 5 O 2515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12927 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5921 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 750, 5902 Classifications: {'peptide': 750} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 713} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 750, 5902 Classifications: {'peptide': 750} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 713} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 6070 Chain: "B" Number of atoms: 5920 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 750, 5901 Classifications: {'peptide': 750} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 713} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 750, 5901 Classifications: {'peptide': 750} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 713} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 6069 Chain: "A" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 320 Unusual residues: {' CA': 1, ' FE': 1, '10M': 1, 'HEM': 2, 'LOP': 7, 'UQ1': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'LOP:plan-1': 4, 'LOP:plan-3': 5, 'LOP:plan-2': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 317 Unusual residues: {' CA': 1, ' FE': 1, '10M': 1, 'HEM': 2, 'LOP': 6, 'UQ1': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LOP:plan-2': 2, 'LOP:plan-1': 3, 'LOP:plan-3': 2} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 230 Classifications: {'water': 230} Link IDs: {None: 229} Chain: "B" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 219 Classifications: {'water': 219} Link IDs: {None: 218} Time building chain proxies: 4.37, per 1000 atoms: 0.34 Number of scatterers: 12927 At special positions: 0 Unit cell: (71.89, 111.93, 101.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 6 26.01 Ca 2 19.99 S 48 16.00 P 1 15.00 O 2515 8.00 N 1999 7.00 C 8356 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 838.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2714 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 6 sheets defined 79.6% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 4 through 32 Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 112 through 129 Processing helix chain 'A' and resid 142 through 160 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 182 through 202 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 226 through 255 Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 307 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 323 through 355 Proline residue: A 352 - end of helix Processing helix chain 'A' and resid 362 through 390 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 412 through 440 removed outlier: 3.568A pdb=" N GLY A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 445 through 462 removed outlier: 4.109A pdb=" N TYR A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 removed outlier: 4.053A pdb=" N TYR A 468 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 487 Processing helix chain 'A' and resid 491 through 508 Processing helix chain 'A' and resid 513 through 532 removed outlier: 3.765A pdb=" N GLY A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 539 Processing helix chain 'A' and resid 545 through 565 removed outlier: 3.525A pdb=" N MET A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Proline residue: A 562 - end of helix removed outlier: 3.593A pdb=" N VAL A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 576 removed outlier: 4.127A pdb=" N GLU A 569 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 586 through 603 Processing helix chain 'A' and resid 605 through 611 removed outlier: 3.503A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 removed outlier: 3.790A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 654 removed outlier: 4.272A pdb=" N PHE A 640 " --> pdb=" O GLY A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 682 Processing helix chain 'A' and resid 682 through 697 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 704 through 709 Processing helix chain 'A' and resid 710 through 719 Processing helix chain 'A' and resid 719 through 744 removed outlier: 4.312A pdb=" N GLY A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 32 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 112 through 129 Processing helix chain 'B' and resid 142 through 160 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 182 through 202 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 226 through 255 Processing helix chain 'B' and resid 268 through 272 Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 282 through 307 Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 323 through 355 Proline residue: B 352 - end of helix Processing helix chain 'B' and resid 362 through 390 Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 412 through 440 removed outlier: 3.568A pdb=" N GLY B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Proline residue: B 436 - end of helix Processing helix chain 'B' and resid 445 through 462 removed outlier: 4.110A pdb=" N TYR B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 removed outlier: 4.053A pdb=" N TYR B 468 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 487 Processing helix chain 'B' and resid 491 through 508 Processing helix chain 'B' and resid 513 through 532 removed outlier: 3.762A pdb=" N GLY B 530 " --> pdb=" O LEU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 539 Processing helix chain 'B' and resid 545 through 565 removed outlier: 3.525A pdb=" N MET B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Proline residue: B 562 - end of helix removed outlier: 3.593A pdb=" N VAL B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 576 removed outlier: 4.130A pdb=" N GLU B 569 " --> pdb=" O VAL B 565 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 605 through 611 removed outlier: 3.503A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 621 removed outlier: 3.791A pdb=" N TYR B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 654 removed outlier: 4.271A pdb=" N PHE B 640 " --> pdb=" O GLY B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 682 Processing helix chain 'B' and resid 682 through 697 Processing helix chain 'B' and resid 698 through 703 Processing helix chain 'B' and resid 704 through 709 Processing helix chain 'B' and resid 710 through 719 Processing helix chain 'B' and resid 719 through 744 removed outlier: 4.309A pdb=" N GLY B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 5.747A pdb=" N ARG A 47 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER A 42 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU A 39 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU A 141 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA A 41 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'A' and resid 312 through 313 removed outlier: 3.786A pdb=" N ILE A 316 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 50 removed outlier: 5.747A pdb=" N ARG B 47 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N SER B 42 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLU B 39 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU B 141 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA B 41 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'B' and resid 312 through 313 removed outlier: 3.787A pdb=" N ILE B 316 " --> pdb=" O PHE B 313 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2468 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 3967 1.36 - 1.55: 8794 1.55 - 1.73: 11 1.73 - 1.92: 96 1.92 - 2.10: 12 Bond restraints: 12880 Sorted by residual: bond pdb=" C12 LOP B 812 " pdb=" C13 LOP B 812 " ideal model delta sigma weight residual 1.530 1.307 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C11 LOP B 810 " pdb=" C12 LOP B 810 " ideal model delta sigma weight residual 1.523 1.309 0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C10 LOP A 812 " pdb=" C11 LOP A 812 " ideal model delta sigma weight residual 1.524 1.316 0.208 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C32 LOP B 811 " pdb=" C33 LOP B 811 " ideal model delta sigma weight residual 1.523 1.320 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C13 LOP A 807 " pdb=" C14 LOP A 807 " ideal model delta sigma weight residual 1.497 1.301 0.196 2.00e-02 2.50e+03 9.63e+01 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 15290 3.04 - 6.09: 2081 6.09 - 9.13: 120 9.13 - 12.18: 6 12.18 - 15.22: 20 Bond angle restraints: 17517 Sorted by residual: angle pdb=" CA ASP A 82 " pdb=" CB ASP A 82 " pdb=" CG ASP A 82 " ideal model delta sigma weight residual 112.60 104.60 8.00 1.00e+00 1.00e+00 6.40e+01 angle pdb=" CA ASP B 82 " pdb=" CB ASP B 82 " pdb=" CG ASP B 82 " ideal model delta sigma weight residual 112.60 104.69 7.91 1.00e+00 1.00e+00 6.26e+01 angle pdb=" CA PHE B 635 " pdb=" CB PHE B 635 " pdb=" CG PHE B 635 " ideal model delta sigma weight residual 113.80 106.77 7.03 1.00e+00 1.00e+00 4.95e+01 angle pdb=" CA PHE A 635 " pdb=" CB PHE A 635 " pdb=" CG PHE A 635 " ideal model delta sigma weight residual 113.80 106.78 7.02 1.00e+00 1.00e+00 4.93e+01 angle pdb=" CA PHE A 598 " pdb=" CB PHE A 598 " pdb=" CG PHE A 598 " ideal model delta sigma weight residual 113.80 107.56 6.24 1.00e+00 1.00e+00 3.89e+01 ... (remaining 17512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.36: 6784 27.36 - 54.72: 431 54.72 - 82.08: 81 82.08 - 109.44: 23 109.44 - 136.80: 6 Dihedral angle restraints: 7325 sinusoidal: 3049 harmonic: 4276 Sorted by residual: dihedral pdb=" CA PRO B 81 " pdb=" C PRO B 81 " pdb=" N ASP B 82 " pdb=" CA ASP B 82 " ideal model delta harmonic sigma weight residual 180.00 151.34 28.66 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA PRO A 81 " pdb=" C PRO A 81 " pdb=" N ASP A 82 " pdb=" CA ASP A 82 " ideal model delta harmonic sigma weight residual 180.00 151.35 28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ILE A 679 " pdb=" C ILE A 679 " pdb=" N PHE A 680 " pdb=" CA PHE A 680 " ideal model delta harmonic sigma weight residual -180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 7322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 863 0.059 - 0.117: 621 0.117 - 0.176: 257 0.176 - 0.235: 61 0.235 - 0.293: 20 Chirality restraints: 1822 Sorted by residual: chirality pdb=" CA ILE B 620 " pdb=" N ILE B 620 " pdb=" C ILE B 620 " pdb=" CB ILE B 620 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ILE A 620 " pdb=" N ILE A 620 " pdb=" C ILE A 620 " pdb=" CB ILE A 620 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA VAL B 628 " pdb=" N VAL B 628 " pdb=" C VAL B 628 " pdb=" CB VAL B 628 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1819 not shown) Planarity restraints: 2145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ1 B 806 " 0.044 2.00e-02 2.50e+03 4.66e-01 6.51e+03 pdb=" C2 UQ1 B 806 " 0.270 2.00e-02 2.50e+03 pdb=" C3 UQ1 B 806 " -0.235 2.00e-02 2.50e+03 pdb=" C4 UQ1 B 806 " 0.044 2.00e-02 2.50e+03 pdb=" C5 UQ1 B 806 " 0.177 2.00e-02 2.50e+03 pdb=" C6 UQ1 B 806 " -0.114 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 806 " -0.647 2.00e-02 2.50e+03 pdb=" CM5 UQ1 B 806 " 0.558 2.00e-02 2.50e+03 pdb=" O1 UQ1 B 806 " -0.091 2.00e-02 2.50e+03 pdb=" O2 UQ1 B 806 " 0.846 2.00e-02 2.50e+03 pdb=" O3 UQ1 B 806 " -0.977 2.00e-02 2.50e+03 pdb=" O4 UQ1 B 806 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ1 A 806 " 0.121 2.00e-02 2.50e+03 2.51e-01 1.90e+03 pdb=" C2 UQ1 A 806 " -0.032 2.00e-02 2.50e+03 pdb=" C3 UQ1 A 806 " -0.089 2.00e-02 2.50e+03 pdb=" C4 UQ1 A 806 " 0.188 2.00e-02 2.50e+03 pdb=" C5 UQ1 A 806 " -0.021 2.00e-02 2.50e+03 pdb=" C6 UQ1 A 806 " -0.039 2.00e-02 2.50e+03 pdb=" C7 UQ1 A 806 " -0.249 2.00e-02 2.50e+03 pdb=" CM5 UQ1 A 806 " -0.240 2.00e-02 2.50e+03 pdb=" O1 UQ1 A 806 " 0.362 2.00e-02 2.50e+03 pdb=" O2 UQ1 A 806 " -0.115 2.00e-02 2.50e+03 pdb=" O3 UQ1 A 806 " -0.406 2.00e-02 2.50e+03 pdb=" O4 UQ1 A 806 " 0.519 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ1 B 806 " 0.178 2.00e-02 2.50e+03 2.58e-01 8.33e+02 pdb=" C11 UQ1 B 806 " 0.043 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 806 " 0.303 2.00e-02 2.50e+03 pdb=" C8 UQ1 B 806 " -0.449 2.00e-02 2.50e+03 pdb=" C9 UQ1 B 806 " -0.076 2.00e-02 2.50e+03 ... (remaining 2142 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 252 2.52 - 3.11: 11424 3.11 - 3.71: 25603 3.71 - 4.30: 37678 4.30 - 4.90: 59751 Nonbonded interactions: 134708 Sorted by model distance: nonbonded pdb=" NE2 HIS B 629 " pdb="FE HEM B 803 " model vdw 1.923 3.080 nonbonded pdb=" NE2 HIS A 629 " pdb="FE HEM A 802 " model vdw 1.924 3.080 nonbonded pdb=" NE2 HIS B 631 " pdb="FE HEM B 802 " model vdw 1.945 3.080 nonbonded pdb=" NE2 HIS A 631 " pdb="FE HEM A 801 " model vdw 1.945 3.080 nonbonded pdb=" OD2 ASP B 86 " pdb=" OH TYR B 156 " model vdw 2.038 3.040 ... (remaining 134703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 301 or resid 303 through 717 or resid 719 throug \ h 749 or (resid 750 and (name N or name CA or name C or name O )) or resid 802 o \ r resid 806 or (resid 807 and (name C10 or name C11 or name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C24 or name C25 or name C26 or name C27 or name \ C28 or name C29 or name C30 or name C31 or name C32 or name C6 or name C7 or nam \ e C8 or name C9 or name O6 )) or (resid 808 and (name C10 or name C11 or name C1 \ 2 or name C13 or name C14 or name C15 or name C24 or name C25 or name C26 or nam \ e C27 or name C28 or name C29 or name C30 or name C31 or name C32 or name C33 or \ name C34 or name C35 or name C4 or name C5 or name C6 or name C7 or name C8 or \ name C9 or name O5 or name O6 or name O7 or name O8 )) or resid 809 or (resid 81 \ 0 and (name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or n \ ame C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C30 \ or name C31 or name C32 or name C33 or name C34 or name C6 or name C7 or name C8 \ or name C9 )) or resid 812)) selection = (chain 'B' and (resid 1 through 301 or resid 303 through 717 or resid 719 throug \ h 750 or resid 802 or resid 806 or (resid 807 and (name C10 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or n \ ame C19 or name C20 or name C21 or name C22 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C30 or name C31 or name C32 or name \ C6 or name C7 or name C8 or name C9 or name O6 )) or resid 808 through 809 or (r \ esid 810 and (name C10 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or na \ me C30 or name C31 or name C32 or name C33 or name C34 or name C6 or name C7 or \ name C8 or name C9 )) or (resid 812 and (name C10 or name C11 or name C12 or nam \ e C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ 0 or name C31 or name C32 or name C33 or name C34 or name C6 or name C7 or name \ C8 or name C9 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.010 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.510 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:8.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 : 0.016 0.259 12884 Z= 0.987 Angle : 2.058 15.221 17517 Z= 1.446 Chirality : 0.090 0.293 1822 Planarity : 0.021 0.466 2145 Dihedral : 19.296 136.796 4611 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.08 % Favored : 93.38 % Rotamer: Outliers : 3.84 % Allowed : 8.45 % Favored : 87.71 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.60 (0.18), residues: 1500 helix: -2.44 (0.12), residues: 1052 sheet: None (None), residues: 0 loop : -1.66 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.003 ARG B 328 TYR 0.073 0.012 TYR B 324 PHE 0.065 0.009 PHE B 635 TRP 0.085 0.015 TRP B 215 HIS 0.027 0.009 HIS B 89 Details of bonding type rmsd covalent geometry : bond 0.01579 (12880) covalent geometry : angle 2.05844 (17517) hydrogen bonds : bond 0.17548 ( 860) hydrogen bonds : angle 9.11744 ( 2468) Misc. bond : bond 0.24097 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 0.452 Fit side-chains REVERT: A 184 ASN cc_start: 0.7826 (m-40) cc_final: 0.7025 (t0) REVERT: A 187 ARG cc_start: 0.7725 (ttp-110) cc_final: 0.7499 (ttp-110) REVERT: A 228 GLU cc_start: 0.6307 (mm-30) cc_final: 0.5920 (mt-10) REVERT: A 273 PHE cc_start: 0.7934 (m-80) cc_final: 0.7603 (m-80) REVERT: A 280 ARG cc_start: 0.7529 (mtm-85) cc_final: 0.7295 (mtt90) REVERT: A 353 LEU cc_start: 0.8500 (tt) cc_final: 0.8290 (tp) REVERT: A 430 MET cc_start: 0.8730 (mmm) cc_final: 0.8277 (mmm) REVERT: A 494 GLU cc_start: 0.6697 (tp30) cc_final: 0.6497 (tp30) REVERT: A 513 ARG cc_start: 0.7377 (ttt90) cc_final: 0.6295 (ttt180) REVERT: A 515 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6973 (tpt) REVERT: A 571 TRP cc_start: 0.7553 (t60) cc_final: 0.7101 (t-100) REVERT: A 575 ARG cc_start: 0.6342 (mtp85) cc_final: 0.5917 (ttm110) REVERT: A 673 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.6798 (mt) REVERT: A 734 MET cc_start: 0.8304 (tpp) cc_final: 0.7967 (tpp) REVERT: B 5 ARG cc_start: 0.6045 (ttm110) cc_final: 0.5842 (ttm-80) REVERT: B 31 ARG cc_start: 0.6947 (mtm-85) cc_final: 0.6704 (mtm110) REVERT: B 38 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6611 (mm-30) REVERT: B 184 ASN cc_start: 0.7820 (m-40) cc_final: 0.6933 (t0) REVERT: B 228 GLU cc_start: 0.6319 (mm-30) cc_final: 0.5945 (mt-10) REVERT: B 273 PHE cc_start: 0.7915 (m-80) cc_final: 0.7595 (m-80) REVERT: B 353 LEU cc_start: 0.8492 (tt) cc_final: 0.8285 (tp) REVERT: B 430 MET cc_start: 0.8719 (mmm) cc_final: 0.8255 (mmm) REVERT: B 513 ARG cc_start: 0.7379 (ttt90) cc_final: 0.6301 (ttt180) REVERT: B 515 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6943 (tpt) REVERT: B 546 THR cc_start: 0.7952 (t) cc_final: 0.7693 (m) REVERT: B 571 TRP cc_start: 0.7653 (t60) cc_final: 0.7120 (t-100) REVERT: B 572 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7048 (mt-10) REVERT: B 575 ARG cc_start: 0.6460 (mtp85) cc_final: 0.5924 (ttm110) REVERT: B 584 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7077 (pt0) REVERT: B 673 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.6796 (mt) REVERT: B 708 MET cc_start: 0.8792 (mmm) cc_final: 0.8583 (mmt) REVERT: B 734 MET cc_start: 0.8304 (tpp) cc_final: 0.7968 (tpp) outliers start: 45 outliers final: 15 residues processed: 191 average time/residue: 0.6575 time to fit residues: 135.1130 Evaluate side-chains 156 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 729 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 224 HIS A 612 ASN A 621 GLN A 710 GLN B 612 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.137807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115870 restraints weight = 16862.188| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.26 r_work: 0.3276 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.439 12884 Z= 0.204 Angle : 0.811 17.115 17517 Z= 0.382 Chirality : 0.044 0.186 1822 Planarity : 0.005 0.036 2145 Dihedral : 15.255 88.609 2115 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.62 % Allowed : 11.26 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.21), residues: 1500 helix: 0.23 (0.15), residues: 1052 sheet: None (None), residues: 0 loop : -0.46 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 703 TYR 0.024 0.003 TYR B 78 PHE 0.028 0.002 PHE B 194 TRP 0.034 0.003 TRP A 338 HIS 0.008 0.002 HIS A 629 Details of bonding type rmsd covalent geometry : bond 0.00439 (12880) covalent geometry : angle 0.81069 (17517) hydrogen bonds : bond 0.05976 ( 860) hydrogen bonds : angle 5.94487 ( 2468) Misc. bond : bond 0.34615 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.493 Fit side-chains REVERT: A 184 ASN cc_start: 0.8154 (m-40) cc_final: 0.7936 (t0) REVERT: A 187 ARG cc_start: 0.8184 (ttp-110) cc_final: 0.7975 (ttp-110) REVERT: A 273 PHE cc_start: 0.8365 (m-80) cc_final: 0.7940 (m-80) REVERT: A 368 ASP cc_start: 0.8152 (m-30) cc_final: 0.7886 (m-30) REVERT: A 430 MET cc_start: 0.8744 (mmm) cc_final: 0.8480 (mmm) REVERT: A 460 LEU cc_start: 0.7036 (mt) cc_final: 0.6820 (mp) REVERT: A 468 TYR cc_start: 0.8890 (p90) cc_final: 0.8573 (p90) REVERT: A 514 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6526 (tpt170) REVERT: A 515 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7004 (tpt) REVERT: A 673 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7358 (mt) REVERT: B 184 ASN cc_start: 0.8183 (m-40) cc_final: 0.7959 (t0) REVERT: B 273 PHE cc_start: 0.8344 (m-80) cc_final: 0.7869 (m-80) REVERT: B 368 ASP cc_start: 0.8169 (m-30) cc_final: 0.7966 (m-30) REVERT: B 430 MET cc_start: 0.8773 (mmm) cc_final: 0.8475 (mmm) REVERT: B 460 LEU cc_start: 0.7060 (mt) cc_final: 0.6846 (mp) REVERT: B 468 TYR cc_start: 0.8884 (p90) cc_final: 0.8519 (p90) REVERT: B 514 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6121 (ttp-110) REVERT: B 515 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.6911 (tpt) REVERT: B 572 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7357 (mt-10) REVERT: B 673 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7374 (mt) REVERT: B 708 MET cc_start: 0.8843 (mmm) cc_final: 0.8563 (mmt) outliers start: 19 outliers final: 4 residues processed: 166 average time/residue: 0.5791 time to fit residues: 103.9181 Evaluate side-chains 145 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 chunk 86 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 121 optimal weight: 0.2980 chunk 105 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 320 GLN A 612 ASN B 32 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 151 GLN B 710 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.136689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.111610 restraints weight = 28928.213| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.69 r_work: 0.3214 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.517 12884 Z= 0.228 Angle : 0.797 17.374 17517 Z= 0.365 Chirality : 0.044 0.193 1822 Planarity : 0.005 0.040 2145 Dihedral : 13.453 83.474 2091 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.62 % Allowed : 11.95 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.21), residues: 1500 helix: 0.85 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.37 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 703 TYR 0.021 0.003 TYR B 78 PHE 0.026 0.002 PHE B 635 TRP 0.027 0.003 TRP A 338 HIS 0.009 0.002 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00495 (12880) covalent geometry : angle 0.79654 (17517) hydrogen bonds : bond 0.05748 ( 860) hydrogen bonds : angle 5.81152 ( 2468) Misc. bond : bond 0.39144 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.438 Fit side-chains REVERT: A 184 ASN cc_start: 0.8296 (m-40) cc_final: 0.7967 (t0) REVERT: A 187 ARG cc_start: 0.8280 (ttp-110) cc_final: 0.8070 (ttp-110) REVERT: A 358 ARG cc_start: 0.7824 (ptt90) cc_final: 0.7619 (ptt-90) REVERT: A 430 MET cc_start: 0.8844 (mmm) cc_final: 0.8518 (mmm) REVERT: A 460 LEU cc_start: 0.7162 (mt) cc_final: 0.6927 (mp) REVERT: A 468 TYR cc_start: 0.8912 (p90) cc_final: 0.8596 (p90) REVERT: A 477 MET cc_start: 0.8571 (tmm) cc_final: 0.8242 (tmm) REVERT: A 514 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6501 (tpt170) REVERT: A 515 MET cc_start: 0.7426 (tmm) cc_final: 0.7114 (tpt) REVERT: A 673 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7611 (mt) REVERT: B 184 ASN cc_start: 0.8298 (m-40) cc_final: 0.8012 (t0) REVERT: B 430 MET cc_start: 0.8855 (mmm) cc_final: 0.8541 (mmm) REVERT: B 460 LEU cc_start: 0.7150 (mt) cc_final: 0.6940 (mp) REVERT: B 468 TYR cc_start: 0.8915 (p90) cc_final: 0.8591 (p90) REVERT: B 477 MET cc_start: 0.8557 (tmm) cc_final: 0.8317 (tmm) REVERT: B 514 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6469 (tpt170) REVERT: B 515 MET cc_start: 0.7367 (tmm) cc_final: 0.7092 (tpt) REVERT: B 572 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7540 (mt-10) REVERT: B 673 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7619 (mt) REVERT: B 699 MET cc_start: 0.8667 (tpp) cc_final: 0.8457 (tpp) outliers start: 19 outliers final: 2 residues processed: 151 average time/residue: 0.5913 time to fit residues: 96.2517 Evaluate side-chains 134 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 76 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** 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 = 0.3653 r_free = 0.3653 target = 0.136431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111322 restraints weight = 28779.279| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.69 r_work: 0.3208 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.527 12884 Z= 0.237 Angle : 0.795 17.923 17517 Z= 0.361 Chirality : 0.044 0.180 1822 Planarity : 0.005 0.040 2145 Dihedral : 12.566 83.448 2085 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 1.79 % Allowed : 12.29 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.21), residues: 1500 helix: 0.94 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.25 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 328 TYR 0.019 0.002 TYR B 78 PHE 0.026 0.002 PHE A 635 TRP 0.023 0.002 TRP A 338 HIS 0.009 0.002 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00516 (12880) covalent geometry : angle 0.79522 (17517) hydrogen bonds : bond 0.05714 ( 860) hydrogen bonds : angle 5.81689 ( 2468) Misc. bond : bond 0.39871 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.320 Fit side-chains REVERT: A 184 ASN cc_start: 0.8315 (m-40) cc_final: 0.7951 (t0) REVERT: A 187 ARG cc_start: 0.8320 (ttp-110) cc_final: 0.8031 (ttp80) REVERT: A 358 ARG cc_start: 0.7842 (ptt90) cc_final: 0.7628 (ptt-90) REVERT: A 430 MET cc_start: 0.8871 (mmm) cc_final: 0.8652 (mmm) REVERT: A 460 LEU cc_start: 0.7150 (mt) cc_final: 0.6921 (mp) REVERT: A 468 TYR cc_start: 0.8924 (p90) cc_final: 0.8596 (p90) REVERT: A 477 MET cc_start: 0.8577 (tmm) cc_final: 0.8257 (tmm) REVERT: A 514 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6302 (tpt170) REVERT: A 515 MET cc_start: 0.7433 (tmm) cc_final: 0.7128 (tpt) REVERT: A 673 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7522 (mt) REVERT: B 184 ASN cc_start: 0.8322 (m-40) cc_final: 0.8005 (t0) REVERT: B 430 MET cc_start: 0.8880 (mmm) cc_final: 0.8541 (mmm) REVERT: B 460 LEU cc_start: 0.7169 (mt) cc_final: 0.6944 (mp) REVERT: B 468 TYR cc_start: 0.8913 (p90) cc_final: 0.8571 (p90) REVERT: B 477 MET cc_start: 0.8604 (tmm) cc_final: 0.8291 (tmm) REVERT: B 514 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6372 (tpt170) REVERT: B 515 MET cc_start: 0.7398 (tmm) cc_final: 0.7100 (tpt) REVERT: B 572 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7513 (mt-10) REVERT: B 673 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7544 (mt) REVERT: B 699 MET cc_start: 0.8679 (tpp) cc_final: 0.8457 (tpp) outliers start: 21 outliers final: 5 residues processed: 148 average time/residue: 0.5822 time to fit residues: 93.3652 Evaluate side-chains 140 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 113 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.0570 chunk 51 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS ** B 75 HIS ** 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 = 0.3666 r_free = 0.3666 target = 0.137470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.112886 restraints weight = 25190.183| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.58 r_work: 0.3231 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.515 12884 Z= 0.229 Angle : 0.780 17.751 17517 Z= 0.354 Chirality : 0.043 0.176 1822 Planarity : 0.005 0.041 2145 Dihedral : 12.296 84.563 2085 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.54 % Allowed : 12.71 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.21), residues: 1500 helix: 0.98 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.17 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 703 TYR 0.017 0.002 TYR B 78 PHE 0.023 0.002 PHE A 635 TRP 0.023 0.002 TRP A 338 HIS 0.009 0.002 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00498 (12880) covalent geometry : angle 0.78019 (17517) hydrogen bonds : bond 0.05560 ( 860) hydrogen bonds : angle 5.78812 ( 2468) Misc. bond : bond 0.38754 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.368 Fit side-chains REVERT: A 184 ASN cc_start: 0.8312 (m-40) cc_final: 0.7950 (t0) REVERT: A 187 ARG cc_start: 0.8284 (ttp-110) cc_final: 0.8022 (ttp80) REVERT: A 358 ARG cc_start: 0.7821 (ptt90) cc_final: 0.7575 (ptt-90) REVERT: A 368 ASP cc_start: 0.8017 (m-30) cc_final: 0.7776 (m-30) REVERT: A 430 MET cc_start: 0.8857 (mmm) cc_final: 0.8626 (mmm) REVERT: A 460 LEU cc_start: 0.7194 (mt) cc_final: 0.6954 (mp) REVERT: A 468 TYR cc_start: 0.8887 (p90) cc_final: 0.8564 (p90) REVERT: A 477 MET cc_start: 0.8560 (tmm) cc_final: 0.8237 (tmm) REVERT: A 490 GLU cc_start: 0.6540 (tt0) cc_final: 0.5954 (mt-10) REVERT: A 514 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6332 (tpt170) REVERT: A 515 MET cc_start: 0.7363 (tmm) cc_final: 0.7027 (tpt) REVERT: A 673 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7511 (mt) REVERT: B 184 ASN cc_start: 0.8294 (m-40) cc_final: 0.8026 (t0) REVERT: B 187 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7710 (ttp-110) REVERT: B 430 MET cc_start: 0.8851 (mmm) cc_final: 0.8643 (mmm) REVERT: B 460 LEU cc_start: 0.7172 (mt) cc_final: 0.6944 (mp) REVERT: B 468 TYR cc_start: 0.8895 (p90) cc_final: 0.8610 (p90) REVERT: B 477 MET cc_start: 0.8539 (tmm) cc_final: 0.8218 (tmm) REVERT: B 490 GLU cc_start: 0.6502 (tt0) cc_final: 0.6277 (tt0) REVERT: B 513 ARG cc_start: 0.7421 (ttt90) cc_final: 0.6711 (ttt90) REVERT: B 514 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6316 (tpt170) REVERT: B 515 MET cc_start: 0.7316 (tmm) cc_final: 0.7028 (tpt) REVERT: B 572 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7502 (mt-10) REVERT: B 673 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7506 (mt) REVERT: B 699 MET cc_start: 0.8659 (tpp) cc_final: 0.8448 (tpp) outliers start: 18 outliers final: 6 residues processed: 146 average time/residue: 0.6313 time to fit residues: 99.8207 Evaluate side-chains 143 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 70 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 133 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 140 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS ** B 75 HIS ** 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 = 0.3686 r_free = 0.3686 target = 0.138902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114989 restraints weight = 27785.325| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.72 r_work: 0.3225 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.484 12884 Z= 0.210 Angle : 0.760 18.760 17517 Z= 0.344 Chirality : 0.043 0.159 1822 Planarity : 0.005 0.042 2145 Dihedral : 12.006 83.926 2085 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.45 % Allowed : 13.05 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.22), residues: 1500 helix: 1.05 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.04 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 575 TYR 0.016 0.002 TYR B 78 PHE 0.021 0.002 PHE A 635 TRP 0.022 0.002 TRP A 338 HIS 0.008 0.002 HIS A 629 Details of bonding type rmsd covalent geometry : bond 0.00456 (12880) covalent geometry : angle 0.75998 (17517) hydrogen bonds : bond 0.05356 ( 860) hydrogen bonds : angle 5.71910 ( 2468) Misc. bond : bond 0.36013 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.408 Fit side-chains REVERT: A 184 ASN cc_start: 0.8316 (m-40) cc_final: 0.7963 (t0) REVERT: A 187 ARG cc_start: 0.8338 (ttp-110) cc_final: 0.8084 (ttp80) REVERT: A 358 ARG cc_start: 0.7848 (ptt90) cc_final: 0.7602 (ptt-90) REVERT: A 430 MET cc_start: 0.8841 (mmm) cc_final: 0.8512 (mmm) REVERT: A 468 TYR cc_start: 0.8862 (p90) cc_final: 0.8564 (p90) REVERT: A 477 MET cc_start: 0.8538 (tmm) cc_final: 0.8257 (tmm) REVERT: A 490 GLU cc_start: 0.6411 (tt0) cc_final: 0.6040 (mt-10) REVERT: A 513 ARG cc_start: 0.7393 (ttt90) cc_final: 0.6644 (ttt90) REVERT: A 514 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.6292 (tpt170) REVERT: A 515 MET cc_start: 0.7351 (tmm) cc_final: 0.7129 (tpp) REVERT: A 673 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7492 (mt) REVERT: B 184 ASN cc_start: 0.8302 (m-40) cc_final: 0.8014 (t0) REVERT: B 430 MET cc_start: 0.8831 (mmm) cc_final: 0.8514 (mmm) REVERT: B 468 TYR cc_start: 0.8872 (p90) cc_final: 0.8595 (p90) REVERT: B 477 MET cc_start: 0.8545 (tmm) cc_final: 0.8247 (tmm) REVERT: B 514 ARG cc_start: 0.6740 (OUTLIER) cc_final: 0.6207 (tpt170) REVERT: B 515 MET cc_start: 0.7373 (tmm) cc_final: 0.7061 (tpt) REVERT: B 572 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7388 (mt-10) REVERT: B 673 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7490 (mt) outliers start: 17 outliers final: 6 residues processed: 136 average time/residue: 0.6672 time to fit residues: 97.8873 Evaluate side-chains 136 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 90 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111067 restraints weight = 26758.844| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.62 r_work: 0.3206 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.518 12884 Z= 0.256 Angle : 0.806 18.985 17517 Z= 0.363 Chirality : 0.044 0.170 1822 Planarity : 0.005 0.042 2145 Dihedral : 12.126 84.543 2085 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.37 % Allowed : 12.97 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.21), residues: 1500 helix: 0.93 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : 0.03 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 328 TYR 0.017 0.002 TYR B 324 PHE 0.025 0.002 PHE A 635 TRP 0.020 0.002 TRP A 338 HIS 0.008 0.002 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00559 (12880) covalent geometry : angle 0.80588 (17517) hydrogen bonds : bond 0.05801 ( 860) hydrogen bonds : angle 5.87005 ( 2468) Misc. bond : bond 0.38999 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.428 Fit side-chains REVERT: A 184 ASN cc_start: 0.8315 (m-40) cc_final: 0.7982 (t0) REVERT: A 187 ARG cc_start: 0.8307 (ttp-110) cc_final: 0.8099 (ttp80) REVERT: A 358 ARG cc_start: 0.7765 (ptt90) cc_final: 0.7513 (ptt-90) REVERT: A 430 MET cc_start: 0.8898 (mmm) cc_final: 0.8631 (mmm) REVERT: A 468 TYR cc_start: 0.8899 (p90) cc_final: 0.8635 (p90) REVERT: A 477 MET cc_start: 0.8528 (tmm) cc_final: 0.8216 (tmm) REVERT: A 490 GLU cc_start: 0.6493 (tt0) cc_final: 0.6052 (mt-10) REVERT: A 494 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6942 (tp30) REVERT: A 514 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6202 (tpt170) REVERT: A 515 MET cc_start: 0.7313 (tmm) cc_final: 0.7094 (tpp) REVERT: A 673 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7547 (mt) REVERT: B 184 ASN cc_start: 0.8270 (m-40) cc_final: 0.8024 (t0) REVERT: B 430 MET cc_start: 0.8895 (mmm) cc_final: 0.8634 (mmm) REVERT: B 468 TYR cc_start: 0.8891 (p90) cc_final: 0.8647 (p90) REVERT: B 477 MET cc_start: 0.8529 (tmm) cc_final: 0.8222 (tmm) REVERT: B 490 GLU cc_start: 0.6541 (tt0) cc_final: 0.5924 (mt-10) REVERT: B 514 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6219 (tpt170) REVERT: B 515 MET cc_start: 0.7395 (tmm) cc_final: 0.7061 (tpt) REVERT: B 572 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7514 (mt-10) REVERT: B 673 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7511 (mt) outliers start: 16 outliers final: 5 residues processed: 140 average time/residue: 0.6058 time to fit residues: 92.1448 Evaluate side-chains 142 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 139 optimal weight: 0.5980 chunk 31 optimal weight: 0.0570 chunk 94 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 125 optimal weight: 0.1980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS B 32 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117318 restraints weight = 31665.991| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.81 r_work: 0.3231 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.452 12884 Z= 0.194 Angle : 0.751 18.302 17517 Z= 0.342 Chirality : 0.042 0.151 1822 Planarity : 0.005 0.043 2145 Dihedral : 11.621 84.315 2085 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.37 % Allowed : 13.23 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.22), residues: 1500 helix: 1.05 (0.15), residues: 1050 sheet: None (None), residues: 0 loop : 0.17 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 280 TYR 0.016 0.002 TYR B 78 PHE 0.019 0.002 PHE B 635 TRP 0.023 0.002 TRP A 338 HIS 0.007 0.002 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00421 (12880) covalent geometry : angle 0.75080 (17517) hydrogen bonds : bond 0.05180 ( 860) hydrogen bonds : angle 5.68578 ( 2468) Misc. bond : bond 0.33690 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.466 Fit side-chains REVERT: A 1 MET cc_start: 0.6315 (ttm) cc_final: 0.6017 (ttm) REVERT: A 28 GLU cc_start: 0.7187 (tt0) cc_final: 0.6786 (tt0) REVERT: A 184 ASN cc_start: 0.8335 (m-40) cc_final: 0.7939 (t0) REVERT: A 187 ARG cc_start: 0.8344 (ttp-110) cc_final: 0.8093 (ttp80) REVERT: A 358 ARG cc_start: 0.7834 (ptt90) cc_final: 0.7588 (ptt-90) REVERT: A 430 MET cc_start: 0.8827 (mmm) cc_final: 0.8500 (mmm) REVERT: A 468 TYR cc_start: 0.8862 (p90) cc_final: 0.8571 (p90) REVERT: A 477 MET cc_start: 0.8539 (tmm) cc_final: 0.8286 (tmm) REVERT: A 513 ARG cc_start: 0.7432 (ttt180) cc_final: 0.6673 (ttt90) REVERT: A 514 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.6311 (tpt170) REVERT: A 673 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7478 (mt) REVERT: B 28 GLU cc_start: 0.7207 (tt0) cc_final: 0.6877 (tt0) REVERT: B 31 ARG cc_start: 0.7239 (mtm-85) cc_final: 0.6980 (mtm110) REVERT: B 184 ASN cc_start: 0.8298 (m-40) cc_final: 0.8000 (t0) REVERT: B 430 MET cc_start: 0.8821 (mmm) cc_final: 0.8514 (mmm) REVERT: B 468 TYR cc_start: 0.8862 (p90) cc_final: 0.8593 (p90) REVERT: B 477 MET cc_start: 0.8538 (tmm) cc_final: 0.8300 (tmm) REVERT: B 490 GLU cc_start: 0.6583 (tt0) cc_final: 0.6106 (mt-10) REVERT: B 513 ARG cc_start: 0.7356 (ttt180) cc_final: 0.6608 (ttt90) REVERT: B 514 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6286 (tpt170) REVERT: B 515 MET cc_start: 0.7429 (tmm) cc_final: 0.7228 (tpp) REVERT: B 572 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7381 (mt-10) REVERT: B 673 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7480 (mt) outliers start: 16 outliers final: 5 residues processed: 135 average time/residue: 0.6249 time to fit residues: 91.8338 Evaluate side-chains 134 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 42 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 16 optimal weight: 0.0370 chunk 102 optimal weight: 0.0770 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 113 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** 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 = 0.3709 r_free = 0.3709 target = 0.140608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116900 restraints weight = 21068.061| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.44 r_work: 0.3291 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.448 12884 Z= 0.190 Angle : 0.739 18.257 17517 Z= 0.337 Chirality : 0.042 0.149 1822 Planarity : 0.005 0.043 2145 Dihedral : 11.393 83.965 2085 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.02 % Allowed : 13.91 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.22), residues: 1500 helix: 1.10 (0.15), residues: 1050 sheet: None (None), residues: 0 loop : 0.14 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 280 TYR 0.016 0.002 TYR B 78 PHE 0.018 0.002 PHE B 635 TRP 0.023 0.002 TRP A 338 HIS 0.007 0.002 HIS A 629 Details of bonding type rmsd covalent geometry : bond 0.00413 (12880) covalent geometry : angle 0.73884 (17517) hydrogen bonds : bond 0.05097 ( 860) hydrogen bonds : angle 5.62976 ( 2468) Misc. bond : bond 0.33809 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.372 Fit side-chains REVERT: A 1 MET cc_start: 0.6306 (ttm) cc_final: 0.6022 (ttm) REVERT: A 28 GLU cc_start: 0.7095 (tt0) cc_final: 0.6734 (tt0) REVERT: A 184 ASN cc_start: 0.8253 (m-40) cc_final: 0.7931 (t0) REVERT: A 187 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.8022 (ttp80) REVERT: A 358 ARG cc_start: 0.7796 (ptt90) cc_final: 0.7565 (ptt-90) REVERT: A 430 MET cc_start: 0.8773 (mmm) cc_final: 0.8465 (mmm) REVERT: A 468 TYR cc_start: 0.8780 (p90) cc_final: 0.8513 (p90) REVERT: A 477 MET cc_start: 0.8500 (tmm) cc_final: 0.8202 (tmm) REVERT: A 513 ARG cc_start: 0.7348 (ttt180) cc_final: 0.6624 (ttt90) REVERT: A 514 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6334 (tpt170) REVERT: A 673 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7452 (mt) REVERT: A 699 MET cc_start: 0.8522 (tpp) cc_final: 0.8221 (tpt) REVERT: B 28 GLU cc_start: 0.7163 (tt0) cc_final: 0.6840 (tt0) REVERT: B 31 ARG cc_start: 0.7260 (mtm-85) cc_final: 0.7019 (mtm110) REVERT: B 430 MET cc_start: 0.8761 (mmm) cc_final: 0.8485 (mmm) REVERT: B 468 TYR cc_start: 0.8808 (p90) cc_final: 0.8560 (p90) REVERT: B 477 MET cc_start: 0.8489 (tmm) cc_final: 0.8210 (tmm) REVERT: B 490 GLU cc_start: 0.6456 (tt0) cc_final: 0.6127 (mt-10) REVERT: B 513 ARG cc_start: 0.7350 (ttt180) cc_final: 0.6628 (ttt90) REVERT: B 514 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.6272 (tpt170) REVERT: B 572 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7298 (mt-10) REVERT: B 673 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7446 (mt) REVERT: B 699 MET cc_start: 0.8480 (tpp) cc_final: 0.8182 (tpt) outliers start: 12 outliers final: 7 residues processed: 134 average time/residue: 0.6018 time to fit residues: 87.5054 Evaluate side-chains 134 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 116 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 62 optimal weight: 0.0870 chunk 60 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 87 optimal weight: 0.0770 chunk 74 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.116238 restraints weight = 29270.158| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.76 r_work: 0.3246 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.461 12884 Z= 0.194 Angle : 0.745 18.278 17517 Z= 0.338 Chirality : 0.042 0.151 1822 Planarity : 0.005 0.043 2145 Dihedral : 11.288 83.409 2085 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.19 % Allowed : 13.91 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.22), residues: 1500 helix: 1.09 (0.15), residues: 1050 sheet: None (None), residues: 0 loop : 0.13 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 280 TYR 0.016 0.002 TYR B 78 PHE 0.019 0.002 PHE B 635 TRP 0.022 0.002 TRP A 338 HIS 0.007 0.002 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00422 (12880) covalent geometry : angle 0.74451 (17517) hydrogen bonds : bond 0.05140 ( 860) hydrogen bonds : angle 5.63209 ( 2468) Misc. bond : bond 0.34819 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.386 Fit side-chains REVERT: A 1 MET cc_start: 0.6312 (ttm) cc_final: 0.6025 (ttm) REVERT: A 28 GLU cc_start: 0.7098 (tt0) cc_final: 0.6732 (tt0) REVERT: A 184 ASN cc_start: 0.8303 (m-40) cc_final: 0.7935 (t0) REVERT: A 187 ARG cc_start: 0.8348 (ttp-110) cc_final: 0.8102 (ttp80) REVERT: A 358 ARG cc_start: 0.7819 (ptt90) cc_final: 0.7595 (ptt-90) REVERT: A 430 MET cc_start: 0.8814 (mmm) cc_final: 0.8512 (mmm) REVERT: A 468 TYR cc_start: 0.8816 (p90) cc_final: 0.8558 (p90) REVERT: A 477 MET cc_start: 0.8537 (tmm) cc_final: 0.8239 (tmm) REVERT: A 513 ARG cc_start: 0.7376 (ttt180) cc_final: 0.6636 (ttt90) REVERT: A 514 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.6309 (tpt170) REVERT: A 673 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7452 (mt) REVERT: A 699 MET cc_start: 0.8582 (tpp) cc_final: 0.8280 (tpt) REVERT: B 28 GLU cc_start: 0.7160 (tt0) cc_final: 0.6847 (tt0) REVERT: B 31 ARG cc_start: 0.7273 (mtm-85) cc_final: 0.7026 (mtm110) REVERT: B 187 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7731 (ttp-110) REVERT: B 430 MET cc_start: 0.8808 (mmm) cc_final: 0.8531 (mmm) REVERT: B 468 TYR cc_start: 0.8840 (p90) cc_final: 0.8599 (p90) REVERT: B 477 MET cc_start: 0.8540 (tmm) cc_final: 0.8254 (tmm) REVERT: B 490 GLU cc_start: 0.6410 (tt0) cc_final: 0.6118 (mt-10) REVERT: B 513 ARG cc_start: 0.7376 (ttt180) cc_final: 0.6636 (ttt90) REVERT: B 514 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.6263 (tpt170) REVERT: B 572 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7267 (mt-10) REVERT: B 673 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7483 (mt) REVERT: B 699 MET cc_start: 0.8516 (tpp) cc_final: 0.8212 (tpt) outliers start: 14 outliers final: 8 residues processed: 129 average time/residue: 0.6247 time to fit residues: 87.1047 Evaluate side-chains 133 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 127 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 141 optimal weight: 0.6980 chunk 33 optimal weight: 0.0670 chunk 66 optimal weight: 0.4980 chunk 78 optimal weight: 0.0870 chunk 111 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.140718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116647 restraints weight = 22381.407| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.49 r_work: 0.3286 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.456 12884 Z= 0.193 Angle : 0.743 18.451 17517 Z= 0.338 Chirality : 0.042 0.151 1822 Planarity : 0.005 0.043 2145 Dihedral : 11.125 83.302 2085 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.11 % Allowed : 14.08 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.22), residues: 1500 helix: 1.10 (0.15), residues: 1050 sheet: None (None), residues: 0 loop : 0.14 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 280 TYR 0.016 0.002 TYR B 78 PHE 0.018 0.002 PHE B 635 TRP 0.022 0.002 TRP A 338 HIS 0.006 0.001 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00420 (12880) covalent geometry : angle 0.74275 (17517) hydrogen bonds : bond 0.05117 ( 860) hydrogen bonds : angle 5.62174 ( 2468) Misc. bond : bond 0.34442 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5077.97 seconds wall clock time: 87 minutes 11.87 seconds (5231.87 seconds total)