Starting phenix.real_space_refine on Thu Sep 26 16:26:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgw_16041/09_2024/8bgw_16041.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgw_16041/09_2024/8bgw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgw_16041/09_2024/8bgw_16041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgw_16041/09_2024/8bgw_16041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgw_16041/09_2024/8bgw_16041.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgw_16041/09_2024/8bgw_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-5461/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: 16.30, per 1000 atoms: 1.26 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: 3.76 Conformation dependent library (CDL) restraints added in 2.8 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: 1.43 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: 4.86 Time building geometry restraints manager: 4.17 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: 4.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 43.460 Find NCS groups from input model: 0.640 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:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.300 ------------------------------------------------------------------------------- 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 0.237 12880 Z= 1.031 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 *********************** 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 fitting. rotamer outliers: 45 poor density : 160 time to evaluate : 1.398 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: 1.5157 time to fit residues: 312.5695 Evaluate side-chains 156 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 : 0.005 0.071 12880 Z= 0.352 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 : 14.29 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 *********************** 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 fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 1.299 Fit side-chains REVERT: A 184 ASN cc_start: 0.8095 (m-40) cc_final: 0.7409 (t0) REVERT: A 187 ARG cc_start: 0.7906 (ttp-110) cc_final: 0.7686 (ttp-110) REVERT: A 358 ARG cc_start: 0.6545 (ppt170) cc_final: 0.5940 (ptt-90) REVERT: A 368 ASP cc_start: 0.8076 (m-30) cc_final: 0.7766 (m-30) REVERT: A 430 MET cc_start: 0.8568 (mmm) cc_final: 0.8209 (mmm) REVERT: A 468 TYR cc_start: 0.9033 (p90) cc_final: 0.8680 (p90) REVERT: A 477 MET cc_start: 0.8281 (tmm) cc_final: 0.7890 (tmm) REVERT: A 514 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.5768 (ttp-110) REVERT: A 515 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6826 (tpt) REVERT: A 571 TRP cc_start: 0.7389 (t60) cc_final: 0.7158 (t-100) REVERT: A 673 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.6849 (mt) REVERT: A 734 MET cc_start: 0.8037 (tpp) cc_final: 0.7832 (tpp) REVERT: B 184 ASN cc_start: 0.8094 (m-40) cc_final: 0.7363 (t0) REVERT: B 430 MET cc_start: 0.8565 (mmm) cc_final: 0.8343 (mmm) REVERT: B 468 TYR cc_start: 0.9013 (p90) cc_final: 0.8676 (p90) REVERT: B 477 MET cc_start: 0.8289 (tmm) cc_final: 0.7908 (tmm) REVERT: B 514 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.5777 (ttp-110) REVERT: B 515 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6840 (tpt) REVERT: B 546 THR cc_start: 0.8270 (t) cc_final: 0.8014 (m) REVERT: B 571 TRP cc_start: 0.7510 (t60) cc_final: 0.7204 (t-100) REVERT: B 572 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7181 (mt-10) REVERT: B 584 GLU cc_start: 0.7912 (mm-30) cc_final: 0.6974 (pt0) REVERT: B 673 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.6840 (mt) REVERT: B 721 THR cc_start: 0.8417 (t) cc_final: 0.8115 (m) REVERT: B 734 MET cc_start: 0.8039 (tpp) cc_final: 0.7835 (tpp) outliers start: 19 outliers final: 4 residues processed: 158 average time/residue: 1.4863 time to fit residues: 254.6850 Evaluate side-chains 141 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 75 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 135 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 320 GLN B 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12880 Z= 0.388 Angle : 0.839 18.311 17517 Z= 0.383 Chirality : 0.046 0.201 1822 Planarity : 0.005 0.040 2145 Dihedral : 13.946 84.166 2091 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.62 % Allowed : 11.35 % Favored : 87.03 % 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: 0.50 (0.21), residues: 1500 helix: 0.72 (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 0.027 0.003 TRP A 338 HIS 0.010 0.002 HIS A 629 PHE 0.029 0.002 PHE A 635 TYR 0.022 0.003 TYR B 78 ARG 0.006 0.001 ARG A 328 *********************** 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 156 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.400 Fit side-chains REVERT: A 184 ASN cc_start: 0.8107 (m-40) cc_final: 0.7341 (t0) REVERT: A 187 ARG cc_start: 0.7857 (ttp-110) cc_final: 0.7499 (ttp80) REVERT: A 358 ARG cc_start: 0.6540 (ppt170) cc_final: 0.5943 (ptt-90) REVERT: A 430 MET cc_start: 0.8623 (mmm) cc_final: 0.8351 (mmm) REVERT: A 460 LEU cc_start: 0.7123 (mt) cc_final: 0.6893 (mp) REVERT: A 468 TYR cc_start: 0.9028 (p90) cc_final: 0.8654 (p90) REVERT: A 477 MET cc_start: 0.8232 (tmm) cc_final: 0.7916 (tmm) REVERT: A 514 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.5715 (ttp-110) REVERT: A 515 MET cc_start: 0.7321 (tmm) cc_final: 0.6921 (tpt) REVERT: A 571 TRP cc_start: 0.7379 (t60) cc_final: 0.7144 (t-100) REVERT: A 673 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.6973 (mt) REVERT: B 184 ASN cc_start: 0.8138 (m-40) cc_final: 0.7370 (t0) REVERT: B 430 MET cc_start: 0.8611 (mmm) cc_final: 0.8362 (mmm) REVERT: B 460 LEU cc_start: 0.7123 (mt) cc_final: 0.6877 (mp) REVERT: B 468 TYR cc_start: 0.9008 (p90) cc_final: 0.8687 (p90) REVERT: B 477 MET cc_start: 0.8247 (tmm) cc_final: 0.7935 (tmm) REVERT: B 514 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.5983 (tpt170) REVERT: B 515 MET cc_start: 0.7360 (tmm) cc_final: 0.7108 (tpt) REVERT: B 546 THR cc_start: 0.8221 (t) cc_final: 0.8005 (m) REVERT: B 571 TRP cc_start: 0.7483 (t60) cc_final: 0.7186 (t-100) REVERT: B 572 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7172 (mt-10) REVERT: B 584 GLU cc_start: 0.7844 (mm-30) cc_final: 0.6934 (pt0) REVERT: B 673 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.6947 (mt) outliers start: 19 outliers final: 2 residues processed: 144 average time/residue: 1.4643 time to fit residues: 228.4760 Evaluate side-chains 134 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 134 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN B 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12880 Z= 0.358 Angle : 0.806 18.179 17517 Z= 0.365 Chirality : 0.044 0.181 1822 Planarity : 0.005 0.041 2145 Dihedral : 12.883 84.127 2085 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.13 % Allowed : 11.43 % 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: 0.72 (0.21), residues: 1500 helix: 0.87 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.24 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 338 HIS 0.009 0.002 HIS A 629 PHE 0.025 0.002 PHE B 635 TYR 0.019 0.002 TYR B 78 ARG 0.005 0.001 ARG A 703 *********************** 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 166 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 1.456 Fit side-chains REVERT: A 1 MET cc_start: 0.5746 (ttm) cc_final: 0.5334 (ttm) REVERT: A 184 ASN cc_start: 0.8113 (m-40) cc_final: 0.7340 (t0) REVERT: A 187 ARG cc_start: 0.7889 (ttp-110) cc_final: 0.7543 (ttp80) REVERT: A 358 ARG cc_start: 0.6594 (ppt170) cc_final: 0.6010 (ptt-90) REVERT: A 430 MET cc_start: 0.8600 (mmm) cc_final: 0.8353 (mmm) REVERT: A 460 LEU cc_start: 0.7177 (mt) cc_final: 0.6938 (mp) REVERT: A 468 TYR cc_start: 0.9022 (p90) cc_final: 0.8667 (p90) REVERT: A 477 MET cc_start: 0.8249 (tmm) cc_final: 0.7937 (tmm) REVERT: A 514 ARG cc_start: 0.6372 (OUTLIER) cc_final: 0.5789 (tpt170) REVERT: A 515 MET cc_start: 0.7302 (tmm) cc_final: 0.7057 (tpt) REVERT: A 571 TRP cc_start: 0.7281 (t60) cc_final: 0.7067 (t-100) REVERT: A 673 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.6892 (mt) REVERT: B 184 ASN cc_start: 0.8129 (m-40) cc_final: 0.7355 (t0) REVERT: B 430 MET cc_start: 0.8589 (mmm) cc_final: 0.8352 (mmm) REVERT: B 460 LEU cc_start: 0.7055 (mt) cc_final: 0.6787 (mp) REVERT: B 468 TYR cc_start: 0.9015 (p90) cc_final: 0.8685 (p90) REVERT: B 477 MET cc_start: 0.8272 (tmm) cc_final: 0.7865 (tmm) REVERT: B 514 ARG cc_start: 0.6397 (OUTLIER) cc_final: 0.5486 (ttp-110) REVERT: B 515 MET cc_start: 0.7255 (tmm) cc_final: 0.6880 (tpt) REVERT: B 572 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7156 (mt-10) REVERT: B 584 GLU cc_start: 0.7746 (mm-30) cc_final: 0.6884 (pt0) REVERT: B 673 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.6872 (mt) outliers start: 25 outliers final: 9 residues processed: 153 average time/residue: 1.3809 time to fit residues: 230.7347 Evaluate side-chains 143 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR 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 Chi-restraints excluded: chain B residue 728 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 36 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12880 Z= 0.322 Angle : 0.771 17.703 17517 Z= 0.351 Chirality : 0.043 0.172 1822 Planarity : 0.005 0.041 2145 Dihedral : 12.305 84.043 2085 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.13 % Allowed : 11.95 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.87 (0.21), residues: 1500 helix: 0.96 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.13 (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 B 629 PHE 0.022 0.002 PHE A 635 TYR 0.017 0.002 TYR A 78 ARG 0.004 0.001 ARG A 328 *********************** 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 fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.544 Fit side-chains REVERT: A 1 MET cc_start: 0.5784 (ttm) cc_final: 0.5356 (ttm) REVERT: A 184 ASN cc_start: 0.8135 (m-40) cc_final: 0.7340 (t0) REVERT: A 187 ARG cc_start: 0.7886 (ttp-110) cc_final: 0.7531 (ttp80) REVERT: A 358 ARG cc_start: 0.6578 (ppt170) cc_final: 0.6011 (ptt-90) REVERT: A 430 MET cc_start: 0.8559 (mmm) cc_final: 0.8174 (mmm) REVERT: A 460 LEU cc_start: 0.7028 (mt) cc_final: 0.6763 (mp) REVERT: A 468 TYR cc_start: 0.9006 (p90) cc_final: 0.8661 (p90) REVERT: A 477 MET cc_start: 0.8262 (tmm) cc_final: 0.7864 (tmm) REVERT: A 490 GLU cc_start: 0.6313 (tt0) cc_final: 0.5064 (mt-10) REVERT: A 513 ARG cc_start: 0.7395 (ttt180) cc_final: 0.6335 (ttt180) REVERT: A 514 ARG cc_start: 0.6406 (OUTLIER) cc_final: 0.5851 (tpt170) REVERT: A 515 MET cc_start: 0.7312 (tmm) cc_final: 0.7111 (tpp) REVERT: A 673 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.6819 (mt) REVERT: B 184 ASN cc_start: 0.8114 (m-40) cc_final: 0.7457 (t0) REVERT: B 187 ARG cc_start: 0.7783 (ttp80) cc_final: 0.7255 (ttp-110) REVERT: B 430 MET cc_start: 0.8566 (mmm) cc_final: 0.8344 (mmm) REVERT: B 460 LEU cc_start: 0.7020 (mt) cc_final: 0.6758 (mp) REVERT: B 468 TYR cc_start: 0.9010 (p90) cc_final: 0.8690 (p90) REVERT: B 477 MET cc_start: 0.8277 (tmm) cc_final: 0.7883 (tmm) REVERT: B 513 ARG cc_start: 0.7412 (ttt180) cc_final: 0.6347 (ttt180) REVERT: B 514 ARG cc_start: 0.6372 (OUTLIER) cc_final: 0.5798 (tpt170) REVERT: B 515 MET cc_start: 0.7262 (tmm) cc_final: 0.7020 (tpt) REVERT: B 572 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7118 (mt-10) REVERT: B 584 GLU cc_start: 0.7775 (mm-30) cc_final: 0.6933 (pt0) REVERT: B 673 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.6860 (mt) REVERT: B 699 MET cc_start: 0.8305 (tpp) cc_final: 0.8039 (tpp) outliers start: 25 outliers final: 9 residues processed: 147 average time/residue: 1.4177 time to fit residues: 227.2096 Evaluate side-chains 147 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 440 THR 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 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 48 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 139 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12880 Z= 0.363 Angle : 0.802 18.559 17517 Z= 0.362 Chirality : 0.044 0.169 1822 Planarity : 0.005 0.042 2145 Dihedral : 12.305 84.386 2085 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.79 % Allowed : 12.54 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.90 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : -0.05 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 338 HIS 0.008 0.002 HIS A 629 PHE 0.025 0.002 PHE B 635 TYR 0.016 0.002 TYR B 324 ARG 0.005 0.001 ARG B 328 *********************** 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 fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.520 Fit side-chains REVERT: A 1 MET cc_start: 0.5827 (ttm) cc_final: 0.5267 (ttm) REVERT: A 184 ASN cc_start: 0.8137 (m-40) cc_final: 0.7328 (t0) REVERT: A 187 ARG cc_start: 0.7889 (ttp-110) cc_final: 0.7509 (ttp80) REVERT: A 358 ARG cc_start: 0.6545 (ppt170) cc_final: 0.5971 (ptt-90) REVERT: A 430 MET cc_start: 0.8612 (mmm) cc_final: 0.8325 (mmm) REVERT: A 460 LEU cc_start: 0.7130 (mt) cc_final: 0.6878 (mp) REVERT: A 468 TYR cc_start: 0.9025 (p90) cc_final: 0.8720 (p90) REVERT: A 477 MET cc_start: 0.8248 (tmm) cc_final: 0.7936 (tmm) REVERT: A 490 GLU cc_start: 0.6193 (tt0) cc_final: 0.4888 (mt-10) REVERT: A 513 ARG cc_start: 0.7345 (ttt180) cc_final: 0.6298 (ttt180) REVERT: A 514 ARG cc_start: 0.6390 (OUTLIER) cc_final: 0.5887 (tpt170) REVERT: A 515 MET cc_start: 0.7288 (tmm) cc_final: 0.7087 (tpp) REVERT: A 673 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.6939 (mt) REVERT: B 184 ASN cc_start: 0.8140 (m-40) cc_final: 0.7365 (t0) REVERT: B 368 ASP cc_start: 0.7905 (m-30) cc_final: 0.7683 (m-30) REVERT: B 430 MET cc_start: 0.8604 (mmm) cc_final: 0.8330 (mmm) REVERT: B 460 LEU cc_start: 0.7107 (mt) cc_final: 0.6849 (mp) REVERT: B 468 TYR cc_start: 0.9005 (p90) cc_final: 0.8718 (p90) REVERT: B 477 MET cc_start: 0.8268 (tmm) cc_final: 0.7859 (tmm) REVERT: B 490 GLU cc_start: 0.6442 (tt0) cc_final: 0.5389 (mt-10) REVERT: B 514 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.5833 (tpt170) REVERT: B 515 MET cc_start: 0.7242 (tmm) cc_final: 0.6971 (tpt) REVERT: B 572 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7164 (mt-10) REVERT: B 584 GLU cc_start: 0.7779 (mm-30) cc_final: 0.6942 (pt0) REVERT: B 673 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.6879 (mt) outliers start: 21 outliers final: 8 residues processed: 139 average time/residue: 1.4179 time to fit residues: 214.5357 Evaluate side-chains 140 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 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 16 optimal weight: 0.3980 chunk 82 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 144 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12880 Z= 0.331 Angle : 0.779 18.629 17517 Z= 0.352 Chirality : 0.043 0.164 1822 Planarity : 0.005 0.042 2145 Dihedral : 11.980 84.004 2085 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.45 % Allowed : 13.05 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.93 (0.21), residues: 1500 helix: 0.96 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : 0.02 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 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 A 78 ARG 0.004 0.001 ARG A 575 *********************** 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 143 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.234 Fit side-chains REVERT: A 1 MET cc_start: 0.5800 (ttm) cc_final: 0.5264 (ttm) REVERT: A 184 ASN cc_start: 0.8135 (m-40) cc_final: 0.7332 (t0) REVERT: A 187 ARG cc_start: 0.7885 (ttp-110) cc_final: 0.7511 (ttp80) REVERT: A 358 ARG cc_start: 0.6582 (ppt170) cc_final: 0.6020 (ptt-90) REVERT: A 430 MET cc_start: 0.8573 (mmm) cc_final: 0.8316 (mmm) REVERT: A 468 TYR cc_start: 0.8988 (p90) cc_final: 0.8701 (p90) REVERT: A 477 MET cc_start: 0.8233 (tmm) cc_final: 0.7834 (tmm) REVERT: A 490 GLU cc_start: 0.6143 (tt0) cc_final: 0.4888 (mt-10) REVERT: A 513 ARG cc_start: 0.7375 (ttt180) cc_final: 0.6299 (ttt180) REVERT: A 514 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.5963 (tpt170) REVERT: A 673 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6821 (mt) REVERT: A 699 MET cc_start: 0.8311 (tpp) cc_final: 0.8014 (tpp) REVERT: B 184 ASN cc_start: 0.8130 (m-40) cc_final: 0.7367 (t0) REVERT: B 368 ASP cc_start: 0.7898 (m-30) cc_final: 0.7675 (m-30) REVERT: B 430 MET cc_start: 0.8573 (mmm) cc_final: 0.8332 (mmm) REVERT: B 468 TYR cc_start: 0.8998 (p90) cc_final: 0.8715 (p90) REVERT: B 477 MET cc_start: 0.8287 (tmm) cc_final: 0.7897 (tmm) REVERT: B 490 GLU cc_start: 0.6159 (tt0) cc_final: 0.5176 (mt-10) REVERT: B 514 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.5918 (tpt170) REVERT: B 515 MET cc_start: 0.7274 (tmm) cc_final: 0.6996 (tpt) REVERT: B 572 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7128 (mt-10) REVERT: B 584 GLU cc_start: 0.7785 (mm-30) cc_final: 0.6944 (pt0) REVERT: B 673 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.6816 (mt) REVERT: B 699 MET cc_start: 0.8289 (tpp) cc_final: 0.8001 (tpp) outliers start: 17 outliers final: 8 residues processed: 134 average time/residue: 1.4488 time to fit residues: 210.6854 Evaluate side-chains 140 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 91 optimal weight: 0.0570 chunk 98 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 131 optimal weight: 0.0980 chunk 138 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12880 Z= 0.263 Angle : 0.725 17.180 17517 Z= 0.332 Chirality : 0.041 0.147 1822 Planarity : 0.005 0.042 2145 Dihedral : 11.466 85.116 2085 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.45 % Allowed : 13.48 % 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: 1.16 (0.22), residues: 1500 helix: 1.11 (0.16), residues: 1050 sheet: None (None), residues: 0 loop : 0.16 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 338 HIS 0.006 0.001 HIS B 629 PHE 0.019 0.002 PHE A 691 TYR 0.017 0.002 TYR B 78 ARG 0.004 0.001 ARG B 187 *********************** 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 153 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 1.422 Fit side-chains REVERT: A 1 MET cc_start: 0.5787 (ttm) cc_final: 0.5258 (ttm) REVERT: A 184 ASN cc_start: 0.8111 (m-40) cc_final: 0.7307 (t0) REVERT: A 187 ARG cc_start: 0.7876 (ttp-110) cc_final: 0.7531 (ttp80) REVERT: A 358 ARG cc_start: 0.6541 (ppt170) cc_final: 0.5991 (ptt-90) REVERT: A 430 MET cc_start: 0.8488 (mmm) cc_final: 0.8171 (mmm) REVERT: A 468 TYR cc_start: 0.8926 (p90) cc_final: 0.8637 (p90) REVERT: A 477 MET cc_start: 0.8218 (tmm) cc_final: 0.7982 (tmm) REVERT: A 490 GLU cc_start: 0.6074 (tt0) cc_final: 0.4900 (mt-10) REVERT: A 514 ARG cc_start: 0.6546 (OUTLIER) cc_final: 0.5991 (tpt170) REVERT: A 673 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.6802 (mt) REVERT: A 699 MET cc_start: 0.8270 (tpp) cc_final: 0.7883 (tpt) REVERT: B 184 ASN cc_start: 0.8084 (m-40) cc_final: 0.7342 (t0) REVERT: B 430 MET cc_start: 0.8469 (mmm) cc_final: 0.8175 (mmm) REVERT: B 468 TYR cc_start: 0.8964 (p90) cc_final: 0.8680 (p90) REVERT: B 477 MET cc_start: 0.8186 (tmm) cc_final: 0.7826 (tmm) REVERT: B 490 GLU cc_start: 0.6097 (tt0) cc_final: 0.5451 (mt-10) REVERT: B 514 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.5976 (tpt170) REVERT: B 572 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6990 (mt-10) REVERT: B 584 GLU cc_start: 0.7781 (mm-30) cc_final: 0.6931 (pt0) REVERT: B 673 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.6789 (mt) REVERT: B 699 MET cc_start: 0.8255 (tpp) cc_final: 0.7973 (tpp) REVERT: B 721 THR cc_start: 0.8510 (t) cc_final: 0.7935 (m) outliers start: 17 outliers final: 7 residues processed: 145 average time/residue: 1.4065 time to fit residues: 222.8109 Evaluate side-chains 137 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 710 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 12880 Z= 0.392 Angle : 0.817 18.941 17517 Z= 0.370 Chirality : 0.045 0.172 1822 Planarity : 0.005 0.042 2145 Dihedral : 11.923 84.403 2085 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.28 % Allowed : 13.65 % 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: 0.93 (0.21), residues: 1500 helix: 0.93 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : 0.10 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 372 HIS 0.008 0.002 HIS B 629 PHE 0.025 0.002 PHE A 635 TYR 0.017 0.002 TYR A 324 ARG 0.006 0.001 ARG A 328 *********************** 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 144 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.465 Fit side-chains REVERT: A 1 MET cc_start: 0.5829 (ttm) cc_final: 0.5281 (ttm) REVERT: A 133 ASP cc_start: 0.6956 (t0) cc_final: 0.6606 (t0) REVERT: A 184 ASN cc_start: 0.8137 (m-40) cc_final: 0.7429 (t0) REVERT: A 187 ARG cc_start: 0.7895 (ttp-110) cc_final: 0.7604 (ttp-110) REVERT: A 358 ARG cc_start: 0.6563 (ppt170) cc_final: 0.5981 (ptt-90) REVERT: A 430 MET cc_start: 0.8628 (mmm) cc_final: 0.8326 (mmm) REVERT: A 468 TYR cc_start: 0.8997 (p90) cc_final: 0.8695 (p90) REVERT: A 477 MET cc_start: 0.8264 (tmm) cc_final: 0.7832 (tmm) REVERT: A 490 GLU cc_start: 0.6043 (tt0) cc_final: 0.4831 (mt-10) REVERT: A 514 ARG cc_start: 0.6421 (OUTLIER) cc_final: 0.5810 (tpt170) REVERT: A 673 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.6893 (mt) REVERT: B 133 ASP cc_start: 0.6968 (t0) cc_final: 0.6620 (t0) REVERT: B 184 ASN cc_start: 0.8122 (m-40) cc_final: 0.7352 (t0) REVERT: B 368 ASP cc_start: 0.7718 (m-30) cc_final: 0.7442 (m-30) REVERT: B 430 MET cc_start: 0.8615 (mmm) cc_final: 0.8327 (mmm) REVERT: B 468 TYR cc_start: 0.9006 (p90) cc_final: 0.8721 (p90) REVERT: B 477 MET cc_start: 0.8261 (tmm) cc_final: 0.7946 (tmm) REVERT: B 490 GLU cc_start: 0.6145 (tt0) cc_final: 0.5170 (mt-10) REVERT: B 514 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.5896 (tpt170) REVERT: B 572 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7158 (mt-10) REVERT: B 584 GLU cc_start: 0.7798 (mm-30) cc_final: 0.6891 (pt0) REVERT: B 673 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.6943 (mt) outliers start: 15 outliers final: 6 residues processed: 137 average time/residue: 1.4449 time to fit residues: 214.7019 Evaluate side-chains 137 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR 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 67 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 149 optimal weight: 0.1980 chunk 137 optimal weight: 2.9990 chunk 118 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 72 optimal weight: 0.1980 chunk 94 optimal weight: 0.8980 chunk 126 optimal weight: 0.2980 chunk 36 optimal weight: 0.3980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 710 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12880 Z= 0.267 Angle : 0.737 17.487 17517 Z= 0.337 Chirality : 0.042 0.148 1822 Planarity : 0.005 0.043 2145 Dihedral : 11.314 84.982 2085 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.11 % Allowed : 13.82 % 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: 1.12 (0.22), residues: 1500 helix: 1.07 (0.15), residues: 1050 sheet: None (None), residues: 0 loop : 0.18 (0.33), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 338 HIS 0.006 0.001 HIS B 629 PHE 0.018 0.002 PHE A 691 TYR 0.016 0.002 TYR A 78 ARG 0.007 0.001 ARG B 187 ********************** 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 136 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.425 Fit side-chains REVERT: A 1 MET cc_start: 0.5803 (ttm) cc_final: 0.5355 (ttm) REVERT: A 28 GLU cc_start: 0.6684 (tt0) cc_final: 0.6322 (tt0) REVERT: A 184 ASN cc_start: 0.8110 (m-40) cc_final: 0.7312 (t0) REVERT: A 187 ARG cc_start: 0.7865 (ttp-110) cc_final: 0.7517 (ttp80) REVERT: A 358 ARG cc_start: 0.6604 (ppt170) cc_final: 0.6018 (ptt-90) REVERT: A 430 MET cc_start: 0.8519 (mmm) cc_final: 0.8164 (mmm) REVERT: A 468 TYR cc_start: 0.8935 (p90) cc_final: 0.8643 (p90) REVERT: A 477 MET cc_start: 0.8203 (tmm) cc_final: 0.7851 (tmm) REVERT: A 514 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.5928 (tpt170) REVERT: A 673 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6793 (mt) REVERT: A 699 MET cc_start: 0.8273 (tpp) cc_final: 0.7883 (tpt) REVERT: B 184 ASN cc_start: 0.8118 (m-40) cc_final: 0.7364 (t0) REVERT: B 368 ASP cc_start: 0.7607 (m-30) cc_final: 0.7381 (m-30) REVERT: B 430 MET cc_start: 0.8492 (mmm) cc_final: 0.8156 (mmm) REVERT: B 468 TYR cc_start: 0.8967 (p90) cc_final: 0.8677 (p90) REVERT: B 477 MET cc_start: 0.8191 (tmm) cc_final: 0.7887 (tmm) REVERT: B 490 GLU cc_start: 0.6072 (tt0) cc_final: 0.5433 (mt-10) REVERT: B 513 ARG cc_start: 0.7177 (ttt180) cc_final: 0.6259 (ttt90) REVERT: B 514 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.5932 (tpt170) REVERT: B 572 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7014 (mt-10) REVERT: B 584 GLU cc_start: 0.7823 (mm-30) cc_final: 0.6902 (pt0) REVERT: B 673 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.6782 (mt) REVERT: B 699 MET cc_start: 0.8258 (tpp) cc_final: 0.7850 (tpt) outliers start: 13 outliers final: 5 residues processed: 128 average time/residue: 1.4885 time to fit residues: 206.6616 Evaluate side-chains 132 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 THR 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 109 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.137650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113976 restraints weight = 19892.981| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.39 r_work: 0.3249 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12880 Z= 0.347 Angle : 0.788 18.964 17517 Z= 0.356 Chirality : 0.044 0.164 1822 Planarity : 0.005 0.043 2145 Dihedral : 11.519 84.094 2085 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.94 % Allowed : 14.33 % Favored : 84.73 % 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: 1.02 (0.22), residues: 1500 helix: 1.01 (0.15), residues: 1048 sheet: None (None), residues: 0 loop : 0.13 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 338 HIS 0.007 0.002 HIS A 629 PHE 0.022 0.002 PHE A 635 TYR 0.016 0.002 TYR A 324 ARG 0.006 0.001 ARG B 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4791.97 seconds wall clock time: 84 minutes 53.50 seconds (5093.50 seconds total)