Starting phenix.real_space_refine on Thu Jul 2 13:41:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tnw_41427/07_2026/8tnw_41427.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tnw_41427/07_2026/8tnw_41427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tnw_41427/07_2026/8tnw_41427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tnw_41427/07_2026/8tnw_41427.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tnw_41427/07_2026/8tnw_41427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tnw_41427/07_2026/8tnw_41427.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.330 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: 5 Type Number sf(0) Gaussians S 52 5.16 5 Cl 2 4.86 5 C 5800 2.51 5 N 1468 2.21 5 O 1552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8874 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4436 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 21, 'TRANS': 583} Chain breaks: 3 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 17, 'ASN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 138 Chain: "B" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4436 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 21, 'TRANS': 583} Chain breaks: 3 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 17, 'ASN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 138 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Time building chain proxies: 1.85, per 1000 atoms: 0.21 Number of scatterers: 8874 At special positions: 0 Unit cell: (90.034, 119.77, 94.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 52 16.00 O 1552 8.00 N 1468 7.00 C 5800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 425.3 milliseconds 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 69.8% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 66 through 77 removed outlier: 4.000A pdb=" N VAL A 70 " --> pdb=" O PHE A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.847A pdb=" N TRP A 98 " --> pdb=" O PRO A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 113 removed outlier: 6.110A pdb=" N LEU A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLY A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 133 Proline residue: A 124 - end of helix removed outlier: 3.910A pdb=" N LEU A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 154 removed outlier: 3.936A pdb=" N GLY A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 141 " --> pdb=" O PRO A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 184 Processing helix chain 'A' and resid 214 through 240 Processing helix chain 'A' and resid 241 through 248 removed outlier: 3.565A pdb=" N VAL A 244 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 274 removed outlier: 4.111A pdb=" N LYS A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 296 Processing helix chain 'A' and resid 303 through 316 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 382 through 408 removed outlier: 3.788A pdb=" N ALA A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.658A pdb=" N PHE A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 449 Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.743A pdb=" N VAL A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.838A pdb=" N GLY A 484 " --> pdb=" O LYS A 480 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 508 through 524 Processing helix chain 'A' and resid 526 through 548 Processing helix chain 'A' and resid 591 through 603 Processing helix chain 'A' and resid 605 through 616 removed outlier: 3.603A pdb=" N ILE A 609 " --> pdb=" O ASN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 678 removed outlier: 3.541A pdb=" N ILE A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'A' and resid 711 through 724 removed outlier: 3.545A pdb=" N LYS A 723 " --> pdb=" O ALA A 719 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN A 724 " --> pdb=" O GLU A 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 77 removed outlier: 4.000A pdb=" N VAL B 70 " --> pdb=" O PHE B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'B' and resid 94 through 99 removed outlier: 3.847A pdb=" N TRP B 98 " --> pdb=" O PRO B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 removed outlier: 6.110A pdb=" N LEU B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLY B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 133 Proline residue: B 124 - end of helix removed outlier: 3.910A pdb=" N LEU B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 154 removed outlier: 3.936A pdb=" N GLY B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 141 " --> pdb=" O PRO B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 184 Processing helix chain 'B' and resid 214 through 240 Processing helix chain 'B' and resid 241 through 248 removed outlier: 3.565A pdb=" N VAL B 244 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 274 removed outlier: 4.111A pdb=" N LYS B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 296 Processing helix chain 'B' and resid 303 through 316 Processing helix chain 'B' and resid 335 through 351 Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 382 through 408 removed outlier: 3.788A pdb=" N ALA B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.658A pdb=" N PHE B 431 " --> pdb=" O ILE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 449 Processing helix chain 'B' and resid 454 through 470 removed outlier: 3.743A pdb=" N VAL B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 480 through 496 removed outlier: 3.838A pdb=" N GLY B 484 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA B 494 " --> pdb=" O ASN B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 508 through 524 Processing helix chain 'B' and resid 526 through 548 Processing helix chain 'B' and resid 591 through 603 Processing helix chain 'B' and resid 605 through 616 removed outlier: 3.603A pdb=" N ILE B 609 " --> pdb=" O ASN B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 678 removed outlier: 3.541A pdb=" N ILE B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 697 Processing helix chain 'B' and resid 711 through 724 removed outlier: 3.545A pdb=" N LYS B 723 " --> pdb=" O ALA B 719 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN B 724 " --> pdb=" O GLU B 720 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 563 through 565 removed outlier: 4.179A pdb=" N LYS A 550 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A 580 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N LEU A 556 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 13.408A pdb=" N ILE A 578 " --> pdb=" O LEU A 556 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 579 " --> pdb=" O THR A 648 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE A 583 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N PHE A 709 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 683 " --> pdb=" O PHE A 709 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 163 Processing sheet with id=AA4, first strand: chain 'B' and resid 563 through 565 removed outlier: 4.179A pdb=" N LYS B 550 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE B 580 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N LEU B 556 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 13.408A pdb=" N ILE B 578 " --> pdb=" O LEU B 556 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 579 " --> pdb=" O THR B 648 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE B 583 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N PHE B 709 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU B 683 " --> pdb=" O PHE B 709 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1728 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: 1.60 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1362 1.31 - 1.43: 2390 1.43 - 1.56: 5226 1.56 - 1.69: 2 1.69 - 1.81: 74 Bond restraints: 9054 Sorted by residual: bond pdb=" C LEU A 252 " pdb=" O LEU A 252 " ideal model delta sigma weight residual 1.236 1.184 0.053 1.15e-02 7.56e+03 2.12e+01 bond pdb=" C LEU B 252 " pdb=" O LEU B 252 " ideal model delta sigma weight residual 1.236 1.184 0.053 1.15e-02 7.56e+03 2.12e+01 bond pdb=" CA ALA A 128 " pdb=" CB ALA A 128 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.24e-02 6.50e+03 1.81e+01 bond pdb=" CA ALA B 128 " pdb=" CB ALA B 128 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.24e-02 6.50e+03 1.81e+01 bond pdb=" CA SER A 126 " pdb=" CB SER A 126 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.58e-02 4.01e+03 1.21e+01 ... (remaining 9049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 11919 2.27 - 4.54: 379 4.54 - 6.82: 42 6.82 - 9.09: 0 9.09 - 11.36: 2 Bond angle restraints: 12342 Sorted by residual: angle pdb=" N LEU B 122 " pdb=" CA LEU B 122 " pdb=" C LEU B 122 " ideal model delta sigma weight residual 113.18 107.79 5.39 1.21e+00 6.83e-01 1.99e+01 angle pdb=" N LEU A 122 " pdb=" CA LEU A 122 " pdb=" C LEU A 122 " ideal model delta sigma weight residual 113.18 107.79 5.39 1.21e+00 6.83e-01 1.99e+01 angle pdb=" CA LEU B 252 " pdb=" C LEU B 252 " pdb=" O LEU B 252 " ideal model delta sigma weight residual 120.82 116.30 4.52 1.05e+00 9.07e-01 1.85e+01 angle pdb=" CA LEU A 252 " pdb=" C LEU A 252 " pdb=" O LEU A 252 " ideal model delta sigma weight residual 120.82 116.30 4.52 1.05e+00 9.07e-01 1.85e+01 angle pdb=" N PRO A 124 " pdb=" CA PRO A 124 " pdb=" C PRO A 124 " ideal model delta sigma weight residual 113.57 108.04 5.53 1.31e+00 5.83e-01 1.78e+01 ... (remaining 12337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4659 17.93 - 35.86: 502 35.86 - 53.79: 127 53.79 - 71.72: 30 71.72 - 89.65: 8 Dihedral angle restraints: 5326 sinusoidal: 1812 harmonic: 3514 Sorted by residual: dihedral pdb=" CA THR A 603 " pdb=" C THR A 603 " pdb=" N VAL A 604 " pdb=" CA VAL A 604 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA THR B 603 " pdb=" C THR B 603 " pdb=" N VAL B 604 " pdb=" CA VAL B 604 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA THR B 366 " pdb=" C THR B 366 " pdb=" N GLY B 367 " pdb=" CA GLY B 367 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1301 0.074 - 0.148: 178 0.148 - 0.222: 45 0.222 - 0.296: 0 0.296 - 0.370: 2 Chirality restraints: 1526 Sorted by residual: chirality pdb=" CB VAL B 241 " pdb=" CA VAL B 241 " pdb=" CG1 VAL B 241 " pdb=" CG2 VAL B 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA ILE B 172 " pdb=" N ILE B 172 " pdb=" C ILE B 172 " pdb=" CB ILE B 172 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.30e-01 ... (remaining 1523 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 545 " -0.355 9.50e-02 1.11e+02 1.59e-01 1.55e+01 pdb=" NE ARG B 545 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 545 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 545 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 545 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 545 " 0.281 9.50e-02 1.11e+02 1.26e-01 9.72e+00 pdb=" NE ARG A 545 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 545 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 545 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 545 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 120 " -0.011 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C ILE B 120 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE B 120 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 121 " -0.014 2.00e-02 2.50e+03 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 327 2.72 - 3.26: 9544 3.26 - 3.81: 14787 3.81 - 4.35: 17959 4.35 - 4.90: 29678 Nonbonded interactions: 72295 Sorted by model distance: nonbonded pdb=" O CYS A 78 " pdb=" OG SER A 81 " model vdw 2.170 3.040 nonbonded pdb=" O CYS B 78 " pdb=" OG SER B 81 " model vdw 2.170 3.040 nonbonded pdb=" O LEU A 599 " pdb=" OG1 THR A 603 " model vdw 2.184 3.040 nonbonded pdb=" O LEU B 599 " pdb=" OG1 THR B 603 " model vdw 2.184 3.040 nonbonded pdb=" O GLY A 457 " pdb=" OG1 THR A 460 " model vdw 2.255 3.040 ... (remaining 72290 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.880 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 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 : 0.005 0.074 9054 Z= 0.376 Angle : 0.799 11.360 12342 Z= 0.572 Chirality : 0.056 0.370 1526 Planarity : 0.006 0.159 1516 Dihedral : 16.691 89.650 3054 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.90 % Allowed : 23.83 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.26), residues: 1194 helix: 1.20 (0.19), residues: 788 sheet: 0.70 (0.63), residues: 50 loop : -1.09 (0.38), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 58 TYR 0.014 0.001 TYR A 588 PHE 0.016 0.001 PHE A 394 TRP 0.003 0.001 TRP A 515 HIS 0.002 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.38 ( 9054) covalent geometry : angle 0.79858 / 0.57 (12342) hydrogen bonds : bond 0.14424 / 10.32 ( 594) hydrogen bonds : angle 5.46323 / 3.92 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 205 average time/residue: 0.0686 time to fit residues: 21.5950 Evaluate side-chains 192 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 489 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 0.0070 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 overall best weight: 3.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 GLN A 159 HIS A 268 GLN A 547 GLN A 571 ASN A 605 ASN A 685 GLN B 135 GLN B 159 HIS B 268 GLN B 571 ASN B 605 ASN B 685 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.166187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.124857 restraints weight = 9787.019| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.35 r_work: 0.2944 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9054 Z= 0.165 Angle : 0.556 9.230 12342 Z= 0.287 Chirality : 0.042 0.254 1526 Planarity : 0.003 0.030 1516 Dihedral : 6.701 57.955 1308 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.90 % Allowed : 23.16 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.25), residues: 1194 helix: 1.56 (0.18), residues: 810 sheet: 0.61 (0.60), residues: 54 loop : -1.15 (0.39), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 158 TYR 0.013 0.001 TYR A 588 PHE 0.014 0.001 PHE A 394 TRP 0.005 0.001 TRP A 515 HIS 0.002 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 9054) covalent geometry : angle 0.55574 / 0.29 (12342) hydrogen bonds : bond 0.04326 / 2.98 ( 594) hydrogen bonds : angle 3.86130 / 2.78 ( 1728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.8347 (t80) cc_final: 0.8142 (t80) REVERT: A 716 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7922 (tmm) REVERT: B 102 TYR cc_start: 0.8351 (t80) cc_final: 0.8147 (t80) REVERT: B 716 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7934 (tmm) outliers start: 35 outliers final: 21 residues processed: 213 average time/residue: 0.0800 time to fit residues: 24.8374 Evaluate side-chains 207 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 716 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.165124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.123542 restraints weight = 9803.702| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.36 r_work: 0.2927 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9054 Z= 0.168 Angle : 0.556 8.963 12342 Z= 0.284 Chirality : 0.042 0.275 1526 Planarity : 0.003 0.034 1516 Dihedral : 6.270 59.462 1292 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.12 % Allowed : 23.16 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.25), residues: 1194 helix: 1.57 (0.18), residues: 794 sheet: 0.71 (0.59), residues: 50 loop : -1.30 (0.38), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 499 TYR 0.014 0.001 TYR B 588 PHE 0.016 0.001 PHE B 394 TRP 0.005 0.001 TRP A 515 HIS 0.002 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 9054) covalent geometry : angle 0.55570 / 0.28 (12342) hydrogen bonds : bond 0.04193 / 2.89 ( 594) hydrogen bonds : angle 3.75645 / 2.71 ( 1728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.6213 (tmm) cc_final: 0.5914 (tmm) REVERT: A 716 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7768 (tmm) REVERT: B 88 MET cc_start: 0.6204 (tmm) cc_final: 0.5904 (tmm) REVERT: B 716 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7787 (tmm) outliers start: 37 outliers final: 23 residues processed: 214 average time/residue: 0.0762 time to fit residues: 24.0232 Evaluate side-chains 208 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 716 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 ASN A 547 GLN A 571 ASN B 296 ASN B 571 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.163493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.119886 restraints weight = 9882.426| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.36 r_work: 0.2871 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9054 Z= 0.224 Angle : 0.596 10.243 12342 Z= 0.305 Chirality : 0.043 0.270 1526 Planarity : 0.004 0.038 1516 Dihedral : 6.151 57.137 1288 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.23 % Allowed : 24.39 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.25), residues: 1194 helix: 1.37 (0.18), residues: 800 sheet: 0.58 (0.58), residues: 50 loop : -1.39 (0.37), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 499 TYR 0.018 0.001 TYR B 102 PHE 0.018 0.001 PHE A 394 TRP 0.006 0.001 TRP B 515 HIS 0.003 0.001 HIS A 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 ( 9054) covalent geometry : angle 0.59590 / 0.30 (12342) hydrogen bonds : bond 0.04542 / 3.13 ( 594) hydrogen bonds : angle 3.86697 / 2.78 ( 1728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7762 (mp0) cc_final: 0.7512 (mp0) REVERT: A 88 MET cc_start: 0.6228 (OUTLIER) cc_final: 0.5911 (tmm) REVERT: A 469 LEU cc_start: 0.7589 (mt) cc_final: 0.7305 (mt) REVERT: A 646 LEU cc_start: 0.8814 (tp) cc_final: 0.8592 (tp) REVERT: A 716 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7723 (tmm) REVERT: B 60 GLU cc_start: 0.7770 (mp0) cc_final: 0.7518 (mp0) REVERT: B 88 MET cc_start: 0.6214 (OUTLIER) cc_final: 0.5899 (tmm) REVERT: B 469 LEU cc_start: 0.7580 (mt) cc_final: 0.7299 (mt) REVERT: B 646 LEU cc_start: 0.8812 (tp) cc_final: 0.8596 (tp) REVERT: B 716 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7718 (tmm) outliers start: 38 outliers final: 22 residues processed: 205 average time/residue: 0.0765 time to fit residues: 22.6719 Evaluate side-chains 207 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 716 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 6 optimal weight: 30.0000 chunk 107 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 ASN B 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.164405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.120627 restraints weight = 9874.342| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.33 r_work: 0.2891 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9054 Z= 0.181 Angle : 0.564 10.093 12342 Z= 0.289 Chirality : 0.042 0.302 1526 Planarity : 0.003 0.037 1516 Dihedral : 6.089 56.870 1288 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.01 % Allowed : 23.61 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.25), residues: 1194 helix: 1.39 (0.18), residues: 804 sheet: 0.54 (0.59), residues: 50 loop : -1.38 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 499 TYR 0.012 0.001 TYR A 588 PHE 0.019 0.001 PHE A 394 TRP 0.005 0.001 TRP A 515 HIS 0.002 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 9054) covalent geometry : angle 0.56423 / 0.29 (12342) hydrogen bonds : bond 0.04190 / 2.88 ( 594) hydrogen bonds : angle 3.77612 / 2.71 ( 1728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7962 (mp0) cc_final: 0.7667 (mp0) REVERT: A 88 MET cc_start: 0.6175 (tmm) cc_final: 0.5843 (tmm) REVERT: A 469 LEU cc_start: 0.7641 (mt) cc_final: 0.7402 (mt) REVERT: A 646 LEU cc_start: 0.8844 (tp) cc_final: 0.8641 (tp) REVERT: B 60 GLU cc_start: 0.7992 (mp0) cc_final: 0.7699 (mp0) REVERT: B 88 MET cc_start: 0.6155 (tmm) cc_final: 0.5824 (tmm) REVERT: B 469 LEU cc_start: 0.7632 (mt) cc_final: 0.7390 (mt) outliers start: 36 outliers final: 32 residues processed: 214 average time/residue: 0.0749 time to fit residues: 22.8524 Evaluate side-chains 219 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 570 LYS Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 716 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 25 optimal weight: 30.0000 chunk 11 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 547 GLN A 571 ASN B 547 GLN B 571 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.163679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.122556 restraints weight = 9845.227| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.38 r_work: 0.2915 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9054 Z= 0.154 Angle : 0.546 10.576 12342 Z= 0.279 Chirality : 0.042 0.322 1526 Planarity : 0.003 0.036 1516 Dihedral : 6.040 56.448 1288 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.23 % Allowed : 23.27 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.25), residues: 1194 helix: 1.49 (0.18), residues: 806 sheet: 0.59 (0.60), residues: 50 loop : -1.34 (0.38), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 671 TYR 0.012 0.001 TYR A 588 PHE 0.019 0.001 PHE B 394 TRP 0.004 0.001 TRP A 515 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 9054) covalent geometry : angle 0.54578 / 0.28 (12342) hydrogen bonds : bond 0.03981 / 2.73 ( 594) hydrogen bonds : angle 3.70606 / 2.66 ( 1728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7940 (mp0) cc_final: 0.7599 (mp0) REVERT: A 88 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5812 (tmm) REVERT: A 469 LEU cc_start: 0.7756 (mt) cc_final: 0.7536 (mt) REVERT: B 60 GLU cc_start: 0.7930 (mp0) cc_final: 0.7589 (mp0) REVERT: B 88 MET cc_start: 0.6159 (OUTLIER) cc_final: 0.5816 (tmm) REVERT: B 469 LEU cc_start: 0.7746 (mt) cc_final: 0.7525 (mt) outliers start: 38 outliers final: 34 residues processed: 215 average time/residue: 0.0854 time to fit residues: 25.9855 Evaluate side-chains 223 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 570 LYS Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 716 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 66 optimal weight: 30.0000 chunk 8 optimal weight: 9.9990 chunk 85 optimal weight: 30.0000 chunk 73 optimal weight: 40.0000 chunk 78 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 ASN B 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.161265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.120541 restraints weight = 9936.251| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.44 r_work: 0.2876 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9054 Z= 0.228 Angle : 0.600 10.714 12342 Z= 0.306 Chirality : 0.044 0.333 1526 Planarity : 0.004 0.038 1516 Dihedral : 6.178 56.148 1288 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.68 % Allowed : 23.83 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.25), residues: 1194 helix: 1.31 (0.18), residues: 806 sheet: 0.44 (0.60), residues: 50 loop : -1.40 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 158 TYR 0.011 0.001 TYR A 588 PHE 0.025 0.001 PHE A 394 TRP 0.005 0.001 TRP A 515 HIS 0.003 0.001 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 ( 9054) covalent geometry : angle 0.59954 / 0.31 (12342) hydrogen bonds : bond 0.04487 / 3.08 ( 594) hydrogen bonds : angle 3.87499 / 2.78 ( 1728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7973 (mp0) cc_final: 0.7618 (mp0) REVERT: A 88 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5835 (tmm) REVERT: A 127 ILE cc_start: 0.8570 (mt) cc_final: 0.8245 (mp) REVERT: A 418 MET cc_start: 0.8048 (mmm) cc_final: 0.7831 (mmm) REVERT: A 469 LEU cc_start: 0.7857 (mt) cc_final: 0.7597 (mt) REVERT: A 646 LEU cc_start: 0.8884 (tp) cc_final: 0.8648 (tp) REVERT: B 60 GLU cc_start: 0.7994 (mp0) cc_final: 0.7642 (mp0) REVERT: B 88 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.5822 (tmm) REVERT: B 127 ILE cc_start: 0.8575 (mt) cc_final: 0.8243 (mp) REVERT: B 418 MET cc_start: 0.8035 (mmm) cc_final: 0.7822 (mmm) REVERT: B 469 LEU cc_start: 0.7848 (mt) cc_final: 0.7589 (mt) outliers start: 42 outliers final: 34 residues processed: 208 average time/residue: 0.0788 time to fit residues: 23.7450 Evaluate side-chains 217 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 570 LYS Chi-restraints excluded: chain B residue 573 GLN Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 716 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 6 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 28 optimal weight: 0.0070 chunk 103 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 605 ASN ** 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 = 0.3719 r_free = 0.3719 target = 0.164381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.123161 restraints weight = 9862.584| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.45 r_work: 0.2922 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9054 Z= 0.136 Angle : 0.539 11.489 12342 Z= 0.275 Chirality : 0.041 0.275 1526 Planarity : 0.003 0.039 1516 Dihedral : 6.060 56.403 1288 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.12 % Allowed : 23.72 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1194 helix: 1.45 (0.18), residues: 804 sheet: 0.56 (0.61), residues: 50 loop : -1.39 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 671 TYR 0.011 0.001 TYR B 588 PHE 0.020 0.001 PHE A 394 TRP 0.004 0.001 TRP B 290 HIS 0.002 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 9054) covalent geometry : angle 0.53929 / 0.27 (12342) hydrogen bonds : bond 0.03844 / 2.64 ( 594) hydrogen bonds : angle 3.68623 / 2.65 ( 1728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7966 (mp0) cc_final: 0.7686 (mp0) REVERT: A 88 MET cc_start: 0.6187 (OUTLIER) cc_final: 0.5838 (tmm) REVERT: A 469 LEU cc_start: 0.7855 (mt) cc_final: 0.7614 (mt) REVERT: B 60 GLU cc_start: 0.7961 (mp0) cc_final: 0.7682 (mp0) REVERT: B 88 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5844 (tmm) REVERT: B 469 LEU cc_start: 0.7847 (mt) cc_final: 0.7604 (mt) outliers start: 37 outliers final: 33 residues processed: 212 average time/residue: 0.0694 time to fit residues: 21.0837 Evaluate side-chains 219 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 716 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 100 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 3 optimal weight: 50.0000 chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 547 GLN A 571 ASN B 571 ASN ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.161807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.119823 restraints weight = 9920.789| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.30 r_work: 0.2884 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9054 Z= 0.215 Angle : 0.592 11.342 12342 Z= 0.301 Chirality : 0.044 0.379 1526 Planarity : 0.003 0.041 1516 Dihedral : 6.148 55.928 1288 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.23 % Allowed : 24.28 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.25), residues: 1194 helix: 1.34 (0.18), residues: 806 sheet: 0.10 (0.59), residues: 54 loop : -1.37 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 178 TYR 0.009 0.001 TYR A 588 PHE 0.016 0.001 PHE A 394 TRP 0.005 0.001 TRP A 515 HIS 0.002 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 ( 9054) covalent geometry : angle 0.59248 / 0.30 (12342) hydrogen bonds : bond 0.04317 / 2.97 ( 594) hydrogen bonds : angle 3.81197 / 2.74 ( 1728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 0.308 Fit side-chains REVERT: A 60 GLU cc_start: 0.8093 (mp0) cc_final: 0.7721 (mp0) REVERT: A 88 MET cc_start: 0.6187 (OUTLIER) cc_final: 0.5853 (tmm) REVERT: A 178 ARG cc_start: 0.7743 (tmm-80) cc_final: 0.7486 (tmm-80) REVERT: A 469 LEU cc_start: 0.7985 (mt) cc_final: 0.7728 (mt) REVERT: A 646 LEU cc_start: 0.8877 (tp) cc_final: 0.8652 (tp) REVERT: B 60 GLU cc_start: 0.8104 (mp0) cc_final: 0.7731 (mp0) REVERT: B 88 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5835 (tmm) REVERT: B 469 LEU cc_start: 0.7976 (mt) cc_final: 0.7720 (mt) outliers start: 38 outliers final: 32 residues processed: 210 average time/residue: 0.0766 time to fit residues: 22.9187 Evaluate side-chains 219 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 570 LYS Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 716 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 ASN B 571 ASN ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.161487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.119835 restraints weight = 9872.047| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.31 r_work: 0.2889 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9054 Z= 0.223 Angle : 0.603 11.529 12342 Z= 0.307 Chirality : 0.044 0.381 1526 Planarity : 0.004 0.041 1516 Dihedral : 5.864 69.911 1280 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.45 % Allowed : 23.83 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.25), residues: 1194 helix: 1.27 (0.18), residues: 804 sheet: 0.38 (0.59), residues: 50 loop : -1.51 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 178 TYR 0.021 0.001 TYR B 102 PHE 0.025 0.001 PHE A 394 TRP 0.005 0.001 TRP A 515 HIS 0.002 0.001 HIS A 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 ( 9054) covalent geometry : angle 0.60341 / 0.31 (12342) hydrogen bonds : bond 0.04398 / 3.03 ( 594) hydrogen bonds : angle 3.85388 / 2.76 ( 1728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.266 Fit side-chains REVERT: A 60 GLU cc_start: 0.8060 (mp0) cc_final: 0.7687 (mp0) REVERT: A 88 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.5816 (tmm) REVERT: A 127 ILE cc_start: 0.8571 (mt) cc_final: 0.8233 (mp) REVERT: A 469 LEU cc_start: 0.8011 (mt) cc_final: 0.7759 (mt) REVERT: A 646 LEU cc_start: 0.8882 (tp) cc_final: 0.8648 (tp) REVERT: B 60 GLU cc_start: 0.8065 (mp0) cc_final: 0.7689 (mp0) REVERT: B 88 MET cc_start: 0.6108 (OUTLIER) cc_final: 0.5804 (tmm) REVERT: B 127 ILE cc_start: 0.8575 (mt) cc_final: 0.8233 (mp) REVERT: B 469 LEU cc_start: 0.8008 (mt) cc_final: 0.7753 (mt) outliers start: 40 outliers final: 30 residues processed: 210 average time/residue: 0.0725 time to fit residues: 21.5902 Evaluate side-chains 216 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 570 LYS Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 716 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 65 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 547 GLN A 571 ASN B 571 ASN ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.162831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.122079 restraints weight = 9812.648| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.44 r_work: 0.2902 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9054 Z= 0.178 Angle : 0.582 11.711 12342 Z= 0.296 Chirality : 0.043 0.379 1526 Planarity : 0.003 0.041 1516 Dihedral : 4.848 36.672 1274 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.79 % Allowed : 23.94 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.25), residues: 1194 helix: 1.32 (0.18), residues: 806 sheet: 0.44 (0.60), residues: 50 loop : -1.45 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 178 TYR 0.020 0.001 TYR B 102 PHE 0.024 0.001 PHE B 394 TRP 0.005 0.001 TRP A 515 HIS 0.002 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 9054) covalent geometry : angle 0.58213 / 0.30 (12342) hydrogen bonds : bond 0.04163 / 2.87 ( 594) hydrogen bonds : angle 3.79180 / 2.72 ( 1728) =============================================================================== Job complete usr+sys time: 2292.22 seconds wall clock time: 39 minutes 56.89 seconds (2396.89 seconds total)