Starting phenix.real_space_refine on Thu Jul 31 15:04:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bgw_16041/07_2025/8bgw_16041.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bgw_16041/07_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_16041/07_2025/8bgw_16041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bgw_16041/07_2025/8bgw_16041.map" model { file = "/net/cci-nas-00/data/ceres_data/8bgw_16041/07_2025/8bgw_16041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bgw_16041/07_2025/8bgw_16041.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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-1': 3, 'LOP:plan-3': 2, 'LOP:plan-2': 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: 15.68, per 1000 atoms: 1.21 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: 4.34 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 1.66 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: 4.69 Time building geometry restraints manager: 4.86 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: 3.020 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: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 44.590 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:14.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.085 0.015 TRP B 215 HIS 0.027 0.009 HIS B 89 PHE 0.065 0.009 PHE B 635 TYR 0.073 0.012 TYR B 324 ARG 0.054 0.003 ARG B 328 Details of bonding type rmsd hydrogen bonds : bond 0.17548 ( 860) hydrogen bonds : angle 9.11744 ( 2468) covalent geometry : bond 0.01579 (12880) covalent geometry : angle 2.05844 (17517) 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 : 1.342 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 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: 1.5516 time to fit residues: 320.0566 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 : 1.464 ------------------------------------------------------------------------------- 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 126 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 38 optimal weight: 0.1980 chunk 76 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 224 HIS A 612 ASN A 621 GLN B 612 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.134963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.110682 restraints weight = 25304.273| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.56 r_work: 0.3200 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.526 12884 Z= 0.246 Angle : 0.854 18.598 17517 Z= 0.396 Chirality : 0.046 0.189 1822 Planarity : 0.005 0.036 2145 Dihedral : 15.583 91.582 2115 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.62 % Allowed : 11.01 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1500 helix: 0.19 (0.15), residues: 1046 sheet: None (None), residues: 0 loop : -0.53 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 338 HIS 0.009 0.002 HIS B 629 PHE 0.029 0.003 PHE B 194 TYR 0.024 0.003 TYR B 78 ARG 0.005 0.001 ARG B 703 Details of bonding type rmsd hydrogen bonds : bond 0.06285 ( 860) hydrogen bonds : angle 6.03014 ( 2468) covalent geometry : bond 0.00530 (12880) covalent geometry : angle 0.85447 (17517) Misc. bond : bond 0.40772 ( 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 167 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.526 Fit side-chains REVERT: A 184 ASN cc_start: 0.8240 (m-40) cc_final: 0.7951 (t0) REVERT: A 187 ARG cc_start: 0.8291 (ttp-110) cc_final: 0.8070 (ttp-110) REVERT: A 358 ARG cc_start: 0.7238 (ppt170) cc_final: 0.6917 (ptt-90) REVERT: A 368 ASP cc_start: 0.8206 (m-30) cc_final: 0.7951 (m-30) REVERT: A 430 MET cc_start: 0.8852 (mmm) cc_final: 0.8530 (mmm) REVERT: A 468 TYR cc_start: 0.8953 (p90) cc_final: 0.8606 (p90) REVERT: A 477 MET cc_start: 0.8526 (tmm) cc_final: 0.8293 (tmm) REVERT: A 514 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6329 (ttp-110) REVERT: A 515 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7036 (tpt) REVERT: A 673 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7534 (mt) REVERT: A 699 MET cc_start: 0.8704 (tpp) cc_final: 0.8485 (tpp) REVERT: B 184 ASN cc_start: 0.8258 (m-40) cc_final: 0.7996 (t0) REVERT: B 430 MET cc_start: 0.8875 (mmm) cc_final: 0.8674 (mmm) REVERT: B 468 TYR cc_start: 0.8933 (p90) cc_final: 0.8603 (p90) REVERT: B 477 MET cc_start: 0.8525 (tmm) cc_final: 0.8304 (tmm) REVERT: B 514 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6261 (ttp-110) REVERT: B 515 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6967 (tpt) REVERT: B 571 TRP cc_start: 0.7900 (t60) cc_final: 0.7695 (t-100) REVERT: B 572 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7508 (mt-10) REVERT: B 584 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7511 (pt0) REVERT: B 673 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7544 (mt) REVERT: B 699 MET cc_start: 0.8700 (tpp) cc_final: 0.8482 (tpp) REVERT: B 708 MET cc_start: 0.8850 (mmm) cc_final: 0.8576 (mmt) outliers start: 19 outliers final: 4 residues processed: 158 average time/residue: 1.5137 time to fit residues: 259.2182 Evaluate side-chains 140 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 140 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 136 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 73 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 0.2980 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 224 HIS A 320 GLN A 612 ASN A 710 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 151 GLN B 320 GLN B 710 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111904 restraints weight = 29826.818| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.71 r_work: 0.3217 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.499 12884 Z= 0.219 Angle : 0.785 17.302 17517 Z= 0.360 Chirality : 0.044 0.185 1822 Planarity : 0.005 0.040 2145 Dihedral : 13.516 83.471 2091 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.37 % Allowed : 11.86 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1500 helix: 0.89 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.38 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 338 HIS 0.009 0.002 HIS B 629 PHE 0.025 0.002 PHE A 635 TYR 0.021 0.002 TYR A 78 ARG 0.005 0.001 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.05660 ( 860) hydrogen bonds : angle 5.78454 ( 2468) covalent geometry : bond 0.00476 (12880) covalent geometry : angle 0.78516 (17517) Misc. bond : bond 0.37927 ( 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 166 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 1.322 Fit side-chains REVERT: A 184 ASN cc_start: 0.8304 (m-40) cc_final: 0.7975 (t0) REVERT: A 187 ARG cc_start: 0.8270 (ttp-110) cc_final: 0.8048 (ttp-110) REVERT: A 358 ARG cc_start: 0.7240 (ppt170) cc_final: 0.6919 (ptt-90) REVERT: A 430 MET cc_start: 0.8843 (mmm) cc_final: 0.8518 (mmm) REVERT: A 460 LEU cc_start: 0.7138 (mt) cc_final: 0.6917 (mp) REVERT: A 468 TYR cc_start: 0.8923 (p90) cc_final: 0.8591 (p90) REVERT: A 514 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6512 (tpt170) REVERT: A 515 MET cc_start: 0.7492 (tmm) cc_final: 0.7159 (tpt) REVERT: A 673 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7546 (mt) REVERT: B 184 ASN cc_start: 0.8289 (m-40) cc_final: 0.8001 (t0) REVERT: B 430 MET cc_start: 0.8857 (mmm) cc_final: 0.8554 (mmm) REVERT: B 460 LEU cc_start: 0.7126 (mt) cc_final: 0.6900 (mp) REVERT: B 468 TYR cc_start: 0.8904 (p90) cc_final: 0.8552 (p90) REVERT: B 514 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6473 (tpt170) REVERT: B 515 MET cc_start: 0.7380 (tmm) cc_final: 0.7102 (tpt) REVERT: B 572 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7525 (mt-10) REVERT: B 584 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7467 (pt0) REVERT: B 673 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7574 (mt) outliers start: 16 outliers final: 2 residues processed: 157 average time/residue: 1.4265 time to fit residues: 242.8714 Evaluate side-chains 138 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 94 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 121 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 99 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 32 GLN ** 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 = 0.3658 r_free = 0.3658 target = 0.136835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112599 restraints weight = 24421.544| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.55 r_work: 0.3231 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.69 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 = 0.43 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.514 12884 Z= 0.226 Angle : 0.784 17.820 17517 Z= 0.356 Chirality : 0.043 0.170 1822 Planarity : 0.005 0.041 2145 Dihedral : 12.606 83.669 2085 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.88 % Allowed : 11.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.21), residues: 1500 helix: 0.95 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.25 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 338 HIS 0.008 0.002 HIS A 629 PHE 0.024 0.002 PHE A 635 TYR 0.019 0.002 TYR B 78 ARG 0.005 0.001 ARG B 280 Details of bonding type rmsd hydrogen bonds : bond 0.05613 ( 860) hydrogen bonds : angle 5.78002 ( 2468) covalent geometry : bond 0.00491 (12880) covalent geometry : angle 0.78399 (17517) Misc. bond : bond 0.38790 ( 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: 22 poor density : 138 time to evaluate : 1.627 Fit side-chains REVERT: A 184 ASN cc_start: 0.8297 (m-40) cc_final: 0.7977 (t0) REVERT: A 187 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.8070 (ttp-110) REVERT: A 358 ARG cc_start: 0.7237 (ppt170) cc_final: 0.6959 (ptt-90) REVERT: A 430 MET cc_start: 0.8850 (mmm) cc_final: 0.8512 (mmm) REVERT: A 460 LEU cc_start: 0.7140 (mt) cc_final: 0.6906 (mp) REVERT: A 468 TYR cc_start: 0.8904 (p90) cc_final: 0.8587 (p90) REVERT: A 477 MET cc_start: 0.8576 (tmm) cc_final: 0.8374 (tmm) REVERT: A 514 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.6314 (tpt170) REVERT: A 515 MET cc_start: 0.7435 (tmm) cc_final: 0.7098 (tpt) REVERT: A 673 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7512 (mt) REVERT: B 184 ASN cc_start: 0.8297 (m-40) cc_final: 0.8017 (t0) REVERT: B 430 MET cc_start: 0.8868 (mmm) cc_final: 0.8547 (mmm) REVERT: B 460 LEU cc_start: 0.7110 (mt) cc_final: 0.6881 (mp) REVERT: B 468 TYR cc_start: 0.8895 (p90) cc_final: 0.8602 (p90) REVERT: B 514 ARG cc_start: 0.6872 (OUTLIER) cc_final: 0.6361 (tpt170) REVERT: B 515 MET cc_start: 0.7350 (tmm) cc_final: 0.7050 (tpt) REVERT: B 572 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7452 (mt-10) REVERT: B 673 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7528 (mt) outliers start: 22 outliers final: 8 residues processed: 148 average time/residue: 1.5206 time to fit residues: 244.3178 Evaluate side-chains 144 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 440 THR Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 728 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 440 THR 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 44 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 710 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.135821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.111352 restraints weight = 24042.378| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.53 r_work: 0.3210 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2530 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= 0.255 Angle : 0.811 18.704 17517 Z= 0.367 Chirality : 0.045 0.188 1822 Planarity : 0.005 0.041 2145 Dihedral : 12.428 84.556 2085 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.88 % Allowed : 12.29 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1500 helix: 0.89 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.12 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 338 HIS 0.009 0.002 HIS A 629 PHE 0.026 0.002 PHE A 635 TYR 0.016 0.002 TYR B 324 ARG 0.005 0.001 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.05835 ( 860) hydrogen bonds : angle 5.88031 ( 2468) covalent geometry : bond 0.00556 (12880) covalent geometry : angle 0.81108 (17517) Misc. bond : bond 0.40009 ( 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 161 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.413 Fit side-chains REVERT: A 184 ASN cc_start: 0.8311 (m-40) cc_final: 0.7949 (t0) REVERT: A 187 ARG cc_start: 0.8259 (ttp-110) cc_final: 0.7994 (ttp80) REVERT: A 358 ARG cc_start: 0.7227 (ppt170) cc_final: 0.6944 (ptt-90) REVERT: A 368 ASP cc_start: 0.8057 (m-30) cc_final: 0.7807 (m-30) REVERT: A 430 MET cc_start: 0.8902 (mmm) cc_final: 0.8626 (mmm) REVERT: A 460 LEU cc_start: 0.7299 (mt) cc_final: 0.7061 (mp) REVERT: A 468 TYR cc_start: 0.8905 (p90) cc_final: 0.8625 (p90) REVERT: A 477 MET cc_start: 0.8562 (tmm) cc_final: 0.8304 (tmm) REVERT: A 490 GLU cc_start: 0.6589 (tt0) cc_final: 0.5765 (mt-10) REVERT: A 514 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6332 (tpt170) REVERT: A 515 MET cc_start: 0.7372 (tmm) cc_final: 0.7154 (tpp) REVERT: A 673 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7569 (mt) REVERT: A 699 MET cc_start: 0.8602 (tpp) cc_final: 0.8382 (tpp) REVERT: B 184 ASN cc_start: 0.8325 (m-40) cc_final: 0.8029 (t0) REVERT: B 430 MET cc_start: 0.8903 (mmm) cc_final: 0.8653 (mmm) REVERT: B 460 LEU cc_start: 0.7276 (mt) cc_final: 0.7037 (mp) REVERT: B 468 TYR cc_start: 0.8920 (p90) cc_final: 0.8608 (p90) REVERT: B 514 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6317 (tpt170) REVERT: B 515 MET cc_start: 0.7328 (tmm) cc_final: 0.7048 (tpt) REVERT: B 572 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7492 (mt-10) REVERT: B 673 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7573 (mt) outliers start: 22 outliers final: 9 residues processed: 149 average time/residue: 1.5251 time to fit residues: 245.8789 Evaluate side-chains 149 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 440 THR Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 728 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 440 THR 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 17 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 32 GLN ** 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 = 0.136533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.111176 restraints weight = 29984.088| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.80 r_work: 0.3187 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.517 12884 Z= 0.248 Angle : 0.806 19.362 17517 Z= 0.363 Chirality : 0.044 0.173 1822 Planarity : 0.005 0.041 2145 Dihedral : 12.244 84.466 2085 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.62 % Allowed : 12.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.21), residues: 1500 helix: 0.90 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.03 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 338 HIS 0.009 0.002 HIS B 629 PHE 0.023 0.002 PHE A 635 TYR 0.017 0.002 TYR B 30 ARG 0.005 0.001 ARG B 328 Details of bonding type rmsd hydrogen bonds : bond 0.05706 ( 860) hydrogen bonds : angle 5.86319 ( 2468) covalent geometry : bond 0.00541 (12880) covalent geometry : angle 0.80561 (17517) Misc. bond : bond 0.38892 ( 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 151 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.426 Fit side-chains REVERT: A 184 ASN cc_start: 0.8370 (m-40) cc_final: 0.7946 (t0) REVERT: A 187 ARG cc_start: 0.8311 (ttp-110) cc_final: 0.8020 (ttp80) REVERT: A 358 ARG cc_start: 0.7267 (ppt170) cc_final: 0.6926 (ptt-90) REVERT: A 368 ASP cc_start: 0.8050 (m-30) cc_final: 0.7826 (m-30) REVERT: A 430 MET cc_start: 0.8915 (mmm) cc_final: 0.8646 (mmm) REVERT: A 460 LEU cc_start: 0.7306 (mt) cc_final: 0.7061 (mp) REVERT: A 468 TYR cc_start: 0.8926 (p90) cc_final: 0.8643 (p90) REVERT: A 477 MET cc_start: 0.8623 (tmm) cc_final: 0.8375 (tmm) REVERT: A 490 GLU cc_start: 0.6518 (tt0) cc_final: 0.5979 (mt-10) REVERT: A 513 ARG cc_start: 0.7531 (ttt90) cc_final: 0.6797 (ttt90) REVERT: A 514 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6279 (tpt170) REVERT: A 515 MET cc_start: 0.7403 (tmm) cc_final: 0.7186 (tpp) REVERT: A 673 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7580 (mt) REVERT: B 184 ASN cc_start: 0.8359 (m-40) cc_final: 0.8035 (t0) REVERT: B 430 MET cc_start: 0.8905 (mmm) cc_final: 0.8661 (mmm) REVERT: B 460 LEU cc_start: 0.7279 (mt) cc_final: 0.7036 (mp) REVERT: B 468 TYR cc_start: 0.8933 (p90) cc_final: 0.8652 (p90) REVERT: B 490 GLU cc_start: 0.6541 (tt0) cc_final: 0.5933 (mt-10) REVERT: B 513 ARG cc_start: 0.7519 (ttt90) cc_final: 0.6780 (ttt90) REVERT: B 514 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.6243 (tpt170) REVERT: B 515 MET cc_start: 0.7385 (tmm) cc_final: 0.7048 (tpt) REVERT: B 572 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7512 (mt-10) REVERT: B 673 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7531 (mt) outliers start: 19 outliers final: 9 residues processed: 141 average time/residue: 1.5107 time to fit residues: 231.6662 Evaluate side-chains 141 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 440 THR Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain B residue 1 MET 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 440 THR 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 48 optimal weight: 0.4980 chunk 143 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 41 optimal weight: 0.0970 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 113 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.139997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115373 restraints weight = 24613.285| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.56 r_work: 0.3266 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.449 12884 Z= 0.196 Angle : 0.753 18.341 17517 Z= 0.341 Chirality : 0.042 0.153 1822 Planarity : 0.005 0.041 2145 Dihedral : 11.754 84.356 2085 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.45 % Allowed : 12.97 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1500 helix: 1.03 (0.15), residues: 1052 sheet: None (None), residues: 0 loop : 0.08 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 338 HIS 0.007 0.002 HIS A 629 PHE 0.019 0.002 PHE A 635 TYR 0.017 0.002 TYR B 78 ARG 0.004 0.001 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.05208 ( 860) hydrogen bonds : angle 5.68544 ( 2468) covalent geometry : bond 0.00427 (12880) covalent geometry : angle 0.75252 (17517) Misc. bond : bond 0.33432 ( 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 151 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.358 Fit side-chains REVERT: A 1 MET cc_start: 0.6340 (ttm) cc_final: 0.6058 (ttm) REVERT: A 184 ASN cc_start: 0.8265 (m-40) cc_final: 0.7949 (t0) REVERT: A 187 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.8022 (ttp80) REVERT: A 358 ARG cc_start: 0.7214 (ppt170) cc_final: 0.6892 (ptt-90) REVERT: A 368 ASP cc_start: 0.7988 (m-30) cc_final: 0.7750 (m-30) REVERT: A 430 MET cc_start: 0.8797 (mmm) cc_final: 0.8467 (mmm) REVERT: A 468 TYR cc_start: 0.8826 (p90) cc_final: 0.8529 (p90) REVERT: A 477 MET cc_start: 0.8552 (tmm) cc_final: 0.8339 (tmm) REVERT: A 514 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.6333 (tpt170) REVERT: A 673 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7468 (mt) REVERT: A 699 MET cc_start: 0.8576 (tpp) cc_final: 0.8329 (tpp) REVERT: B 31 ARG cc_start: 0.7227 (mtm-85) cc_final: 0.6973 (mtm110) REVERT: B 184 ASN cc_start: 0.8254 (m-40) cc_final: 0.7995 (t0) REVERT: B 430 MET cc_start: 0.8800 (mmm) cc_final: 0.8495 (mmm) REVERT: B 468 TYR cc_start: 0.8855 (p90) cc_final: 0.8557 (p90) REVERT: B 490 GLU cc_start: 0.6530 (tt0) cc_final: 0.6021 (mt-10) REVERT: B 514 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.6246 (tpt170) REVERT: B 515 MET cc_start: 0.7187 (tmm) cc_final: 0.6956 (tpp) REVERT: B 572 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7381 (mt-10) REVERT: B 673 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7478 (mt) outliers start: 17 outliers final: 6 residues processed: 139 average time/residue: 1.5086 time to fit residues: 227.2732 Evaluate side-chains 137 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 1 MET 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 43 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** 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 = 0.3647 r_free = 0.3647 target = 0.135762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.112366 restraints weight = 33371.827| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.91 r_work: 0.3165 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.526 12884 Z= 0.275 Angle : 0.823 19.118 17517 Z= 0.373 Chirality : 0.045 0.177 1822 Planarity : 0.005 0.041 2145 Dihedral : 12.104 84.683 2085 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.54 % Allowed : 13.14 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1500 helix: 0.87 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : 0.05 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 338 HIS 0.008 0.002 HIS A 629 PHE 0.026 0.002 PHE A 635 TYR 0.018 0.002 TYR B 324 ARG 0.006 0.001 ARG B 328 Details of bonding type rmsd hydrogen bonds : bond 0.05924 ( 860) hydrogen bonds : angle 5.91224 ( 2468) covalent geometry : bond 0.00604 (12880) covalent geometry : angle 0.82347 (17517) Misc. bond : bond 0.39888 ( 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 148 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.287 Fit side-chains REVERT: A 1 MET cc_start: 0.6394 (ttm) cc_final: 0.6072 (ttm) REVERT: A 133 ASP cc_start: 0.7093 (t0) cc_final: 0.6861 (t0) REVERT: A 184 ASN cc_start: 0.8344 (m-40) cc_final: 0.8024 (t0) REVERT: A 187 ARG cc_start: 0.8347 (ttp-110) cc_final: 0.8072 (ttp-110) REVERT: A 358 ARG cc_start: 0.7288 (ppt170) cc_final: 0.6893 (ptt-90) REVERT: A 368 ASP cc_start: 0.8111 (m-30) cc_final: 0.7815 (m-30) REVERT: A 430 MET cc_start: 0.8935 (mmm) cc_final: 0.8643 (mmm) REVERT: A 468 TYR cc_start: 0.8933 (p90) cc_final: 0.8664 (p90) REVERT: A 477 MET cc_start: 0.8596 (tmm) cc_final: 0.8278 (tmm) REVERT: A 513 ARG cc_start: 0.7442 (ttt180) cc_final: 0.6561 (ttt90) REVERT: A 514 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6234 (tpt170) REVERT: A 673 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7532 (mt) REVERT: B 133 ASP cc_start: 0.7077 (t0) cc_final: 0.6855 (t0) REVERT: B 184 ASN cc_start: 0.8308 (m-40) cc_final: 0.8054 (t0) REVERT: B 430 MET cc_start: 0.8933 (mmm) cc_final: 0.8666 (mmm) REVERT: B 468 TYR cc_start: 0.8935 (p90) cc_final: 0.8662 (p90) REVERT: B 490 GLU cc_start: 0.6659 (tt0) cc_final: 0.6103 (mt-10) REVERT: B 514 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.6191 (tpt170) REVERT: B 515 MET cc_start: 0.7388 (tmm) cc_final: 0.7175 (tpp) REVERT: B 572 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7577 (mt-10) REVERT: B 673 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7538 (mt) outliers start: 18 outliers final: 6 residues processed: 139 average time/residue: 1.4289 time to fit residues: 215.5147 Evaluate side-chains 140 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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 440 THR 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 21 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 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** A 710 GLN 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 = 0.3669 r_free = 0.3669 target = 0.137553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112318 restraints weight = 27117.720| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.65 r_work: 0.3223 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 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 = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.508 12884 Z= 0.234 Angle : 0.790 18.665 17517 Z= 0.357 Chirality : 0.043 0.162 1822 Planarity : 0.005 0.042 2145 Dihedral : 11.837 83.871 2085 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.19 % Allowed : 13.57 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.22), residues: 1500 helix: 0.92 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : 0.05 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 338 HIS 0.008 0.002 HIS B 629 PHE 0.021 0.002 PHE A 635 TYR 0.016 0.002 TYR B 30 ARG 0.004 0.001 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.05561 ( 860) hydrogen bonds : angle 5.82719 ( 2468) covalent geometry : bond 0.00509 (12880) covalent geometry : angle 0.78976 (17517) Misc. bond : bond 0.38334 ( 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: 14 poor density : 126 time to evaluate : 1.466 Fit side-chains REVERT: A 1 MET cc_start: 0.6348 (ttm) cc_final: 0.6053 (ttm) REVERT: A 184 ASN cc_start: 0.8306 (m-40) cc_final: 0.7974 (t0) REVERT: A 187 ARG cc_start: 0.8314 (ttp-110) cc_final: 0.8114 (ttp80) REVERT: A 358 ARG cc_start: 0.7253 (ppt170) cc_final: 0.6888 (ptt-90) REVERT: A 368 ASP cc_start: 0.8007 (m-30) cc_final: 0.7749 (m-30) REVERT: A 430 MET cc_start: 0.8858 (mmm) cc_final: 0.8587 (mmm) REVERT: A 468 TYR cc_start: 0.8872 (p90) cc_final: 0.8607 (p90) REVERT: A 477 MET cc_start: 0.8565 (tmm) cc_final: 0.8290 (tmm) REVERT: A 514 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.6220 (tpt170) REVERT: A 673 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7463 (mt) REVERT: A 699 MET cc_start: 0.8627 (tpp) cc_final: 0.8373 (tpp) REVERT: B 184 ASN cc_start: 0.8268 (m-40) cc_final: 0.8037 (t0) REVERT: B 368 ASP cc_start: 0.8096 (m-30) cc_final: 0.7827 (m-30) REVERT: B 430 MET cc_start: 0.8872 (mmm) cc_final: 0.8627 (mmm) REVERT: B 468 TYR cc_start: 0.8868 (p90) cc_final: 0.8606 (p90) REVERT: B 490 GLU cc_start: 0.6478 (tt0) cc_final: 0.6011 (mt-10) REVERT: B 513 ARG cc_start: 0.7376 (ttt180) cc_final: 0.6577 (ttt90) REVERT: B 514 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.6120 (tpt170) REVERT: B 515 MET cc_start: 0.7333 (tmm) cc_final: 0.7127 (tpp) REVERT: B 572 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7427 (mt-10) REVERT: B 673 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7494 (mt) REVERT: B 699 MET cc_start: 0.8546 (tpp) cc_final: 0.8247 (tpt) outliers start: 14 outliers final: 6 residues processed: 132 average time/residue: 1.4741 time to fit residues: 212.0418 Evaluate side-chains 135 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 440 THR 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 35 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 100 optimal weight: 0.2980 chunk 90 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.137530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112746 restraints weight = 25185.681| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.58 r_work: 0.3232 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.511 12884 Z= 0.231 Angle : 0.789 18.721 17517 Z= 0.357 Chirality : 0.043 0.164 1822 Planarity : 0.005 0.042 2145 Dihedral : 11.773 83.985 2085 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.19 % Allowed : 13.65 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1500 helix: 0.92 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : 0.07 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 338 HIS 0.008 0.002 HIS A 629 PHE 0.022 0.002 PHE B 635 TYR 0.016 0.002 TYR B 78 ARG 0.005 0.001 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.05543 ( 860) hydrogen bonds : angle 5.81123 ( 2468) covalent geometry : bond 0.00503 (12880) covalent geometry : angle 0.78887 (17517) Misc. bond : bond 0.38330 ( 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 141 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 1.477 Fit side-chains REVERT: A 1 MET cc_start: 0.6351 (ttm) cc_final: 0.6067 (ttm) REVERT: A 184 ASN cc_start: 0.8298 (m-40) cc_final: 0.7955 (t0) REVERT: A 187 ARG cc_start: 0.8294 (ttp-110) cc_final: 0.8024 (ttp80) REVERT: A 358 ARG cc_start: 0.7263 (ppt170) cc_final: 0.6896 (ptt-90) REVERT: A 368 ASP cc_start: 0.7997 (m-30) cc_final: 0.7750 (m-30) REVERT: A 430 MET cc_start: 0.8850 (mmm) cc_final: 0.8584 (mmm) REVERT: A 468 TYR cc_start: 0.8864 (p90) cc_final: 0.8606 (p90) REVERT: A 477 MET cc_start: 0.8550 (tmm) cc_final: 0.8266 (tmm) REVERT: A 513 ARG cc_start: 0.7367 (ttt180) cc_final: 0.6585 (ttt90) REVERT: A 514 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.6227 (tpt170) REVERT: A 673 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7462 (mt) REVERT: B 184 ASN cc_start: 0.8244 (m-40) cc_final: 0.8019 (t0) REVERT: B 368 ASP cc_start: 0.8064 (m-30) cc_final: 0.7818 (m-30) REVERT: B 430 MET cc_start: 0.8859 (mmm) cc_final: 0.8616 (mmm) REVERT: B 468 TYR cc_start: 0.8876 (p90) cc_final: 0.8618 (p90) REVERT: B 490 GLU cc_start: 0.6463 (tt0) cc_final: 0.6060 (mt-10) REVERT: B 513 ARG cc_start: 0.7334 (ttt180) cc_final: 0.6558 (ttt90) REVERT: B 514 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6122 (tpt170) REVERT: B 572 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7427 (mt-10) REVERT: B 673 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7482 (mt) REVERT: B 699 MET cc_start: 0.8538 (tpp) cc_final: 0.8252 (tpt) outliers start: 14 outliers final: 7 residues processed: 134 average time/residue: 1.5153 time to fit residues: 220.3736 Evaluate side-chains 137 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.477 ------------------------------------------------------------------------------- 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 440 THR 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 440 THR 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 147 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 100 optimal weight: 0.0870 chunk 48 optimal weight: 0.0980 chunk 144 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 73 optimal weight: 0.0970 chunk 85 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 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 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** 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 = 0.3717 r_free = 0.3717 target = 0.141446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116702 restraints weight = 27212.285| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.73 r_work: 0.3266 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.409 12884 Z= 0.182 Angle : 0.738 17.596 17517 Z= 0.338 Chirality : 0.042 0.148 1822 Planarity : 0.005 0.043 2145 Dihedral : 11.288 84.671 2085 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.94 % Allowed : 13.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.22), residues: 1500 helix: 1.04 (0.15), residues: 1052 sheet: None (None), residues: 0 loop : 0.08 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 338 HIS 0.006 0.001 HIS B 629 PHE 0.020 0.002 PHE A 691 TYR 0.017 0.002 TYR B 78 ARG 0.005 0.001 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.05024 ( 860) hydrogen bonds : angle 5.62516 ( 2468) covalent geometry : bond 0.00398 (12880) covalent geometry : angle 0.73776 (17517) Misc. bond : bond 0.31137 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12021.44 seconds wall clock time: 205 minutes 8.67 seconds (12308.67 seconds total)