Starting phenix.real_space_refine on Sat Aug 23 01:05:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tnw_41427/08_2025/8tnw_41427.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tnw_41427/08_2025/8tnw_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_41427/08_2025/8tnw_41427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tnw_41427/08_2025/8tnw_41427.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tnw_41427/08_2025/8tnw_41427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tnw_41427/08_2025/8tnw_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.46, per 1000 atoms: 0.28 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: 1.05 Conformation dependent library (CDL) restraints added in 297.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.36 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: 1.51 Time building geometry restraints manager: 1.34 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: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.720 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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: 12.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 aren 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 covalent geometry : bond 0.00530 ( 9054) covalent geometry : angle 0.79858 (12342) hydrogen bonds : bond 0.14424 ( 594) hydrogen bonds : angle 5.46323 ( 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 : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 205 average time/residue: 0.0689 time to fit residues: 21.6650 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 : 0.328 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3734 r_free = 0.3734 target = 0.166177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.124793 restraints weight = 9795.274| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.42 r_work: 0.2940 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.0980 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= 0.164 Angle : 0.556 9.436 12342 Z= 0.286 Chirality : 0.042 0.253 1526 Planarity : 0.003 0.030 1516 Dihedral : 6.684 58.090 1308 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.12 % Allowed : 22.72 % Favored : 73.16 % 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 aren not related in a simple way. whole: 1.15 (0.25), residues: 1194 helix: 1.55 (0.18), residues: 810 sheet: 0.59 (0.60), residues: 54 loop : -1.16 (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 B 515 HIS 0.002 0.001 HIS A 432 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9054) covalent geometry : angle 0.55621 (12342) hydrogen bonds : bond 0.04316 ( 594) hydrogen bonds : angle 3.84942 ( 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 234 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.6237 (tmm) cc_final: 0.5996 (tmm) REVERT: A 716 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7931 (tmm) REVERT: B 88 MET cc_start: 0.6244 (tmm) cc_final: 0.5999 (tmm) REVERT: B 716 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7948 (tmm) outliers start: 37 outliers final: 21 residues processed: 216 average time/residue: 0.0790 time to fit residues: 24.8731 Evaluate side-chains 215 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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: 6.9990 chunk 18 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 547 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.165483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.123719 restraints weight = 9809.272| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.27 r_work: 0.2933 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1203 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= 0.163 Angle : 0.552 8.784 12342 Z= 0.283 Chirality : 0.042 0.265 1526 Planarity : 0.003 0.033 1516 Dihedral : 6.253 59.041 1292 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.79 % Allowed : 23.39 % Favored : 72.83 % 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 aren not related in a simple way. whole: 1.07 (0.25), residues: 1194 helix: 1.58 (0.18), residues: 794 sheet: 0.74 (0.59), residues: 50 loop : -1.33 (0.38), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 499 TYR 0.018 0.001 TYR A 102 PHE 0.015 0.001 PHE A 394 TRP 0.005 0.001 TRP B 515 HIS 0.002 0.001 HIS A 432 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9054) covalent geometry : angle 0.55242 (12342) hydrogen bonds : bond 0.04151 ( 594) hydrogen bonds : angle 3.74389 ( 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 224 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.6232 (tmm) cc_final: 0.5912 (tmm) REVERT: A 127 ILE cc_start: 0.8615 (mt) cc_final: 0.8324 (mp) REVERT: A 659 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8977 (mt) REVERT: A 716 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7754 (tmm) REVERT: B 88 MET cc_start: 0.6221 (tmm) cc_final: 0.5899 (tmm) REVERT: B 127 ILE cc_start: 0.8621 (mt) cc_final: 0.8328 (mp) REVERT: B 716 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7768 (tmm) outliers start: 34 outliers final: 20 residues processed: 214 average time/residue: 0.0749 time to fit residues: 23.3074 Evaluate side-chains 209 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 659 LEU Chi-restraints excluded: chain A residue 716 MET 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: 7.9990 chunk 62 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3706 r_free = 0.3706 target = 0.163387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.121119 restraints weight = 9893.376| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.56 r_work: 0.2865 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9054 Z= 0.230 Angle : 0.603 10.389 12342 Z= 0.309 Chirality : 0.043 0.284 1526 Planarity : 0.004 0.036 1516 Dihedral : 6.169 56.936 1288 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.45 % Allowed : 23.94 % Favored : 71.60 % 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 aren not related in a simple way. whole: 0.80 (0.25), residues: 1194 helix: 1.35 (0.18), residues: 800 sheet: 0.59 (0.58), residues: 50 loop : -1.42 (0.37), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 509 TYR 0.015 0.001 TYR A 588 PHE 0.019 0.001 PHE A 394 TRP 0.006 0.001 TRP B 515 HIS 0.003 0.001 HIS B 432 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 9054) covalent geometry : angle 0.60326 (12342) hydrogen bonds : bond 0.04587 ( 594) hydrogen bonds : angle 3.88032 ( 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 228 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.6290 (tmm) cc_final: 0.5883 (tmm) REVERT: A 469 LEU cc_start: 0.7621 (mt) cc_final: 0.7337 (mt) REVERT: A 646 LEU cc_start: 0.8820 (tp) cc_final: 0.8613 (tp) REVERT: B 88 MET cc_start: 0.6272 (tmm) cc_final: 0.5867 (tmm) REVERT: B 469 LEU cc_start: 0.7615 (mt) cc_final: 0.7333 (mt) REVERT: B 646 LEU cc_start: 0.8820 (tp) cc_final: 0.8615 (tp) outliers start: 40 outliers final: 25 residues processed: 210 average time/residue: 0.0772 time to fit residues: 23.8092 Evaluate side-chains 207 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 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 648 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 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 648 THR 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: 20.0000 chunk 23 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3695 r_free = 0.3695 target = 0.162307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.120614 restraints weight = 9850.454| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.29 r_work: 0.2890 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9054 Z= 0.204 Angle : 0.579 9.882 12342 Z= 0.297 Chirality : 0.042 0.299 1526 Planarity : 0.003 0.037 1516 Dihedral : 6.154 56.780 1288 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.12 % Allowed : 23.39 % 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 aren not related in a simple way. whole: 0.73 (0.25), residues: 1194 helix: 1.28 (0.18), residues: 804 sheet: 0.52 (0.59), residues: 50 loop : -1.42 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 158 TYR 0.012 0.001 TYR B 588 PHE 0.019 0.001 PHE B 394 TRP 0.005 0.001 TRP A 515 HIS 0.002 0.001 HIS A 363 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 9054) covalent geometry : angle 0.57869 (12342) hydrogen bonds : bond 0.04342 ( 594) hydrogen bonds : angle 3.81781 ( 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 223 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7956 (mp0) cc_final: 0.7660 (mp0) REVERT: A 88 MET cc_start: 0.6236 (tmm) cc_final: 0.5812 (tmm) REVERT: A 469 LEU cc_start: 0.7710 (mt) cc_final: 0.7443 (mt) REVERT: A 646 LEU cc_start: 0.8855 (tp) cc_final: 0.8632 (tp) REVERT: B 60 GLU cc_start: 0.7986 (mp0) cc_final: 0.7691 (mp0) REVERT: B 88 MET cc_start: 0.6204 (tmm) cc_final: 0.5779 (tmm) REVERT: B 469 LEU cc_start: 0.7709 (mt) cc_final: 0.7442 (mt) REVERT: B 646 LEU cc_start: 0.8862 (tp) cc_final: 0.8646 (tp) outliers start: 37 outliers final: 31 residues processed: 211 average time/residue: 0.0784 time to fit residues: 23.8305 Evaluate side-chains 215 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 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 573 GLN Chi-restraints excluded: chain A residue 590 ILE 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN A 571 ASN B 571 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.163426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.122344 restraints weight = 9863.619| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.35 r_work: 0.2909 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9054 Z= 0.161 Angle : 0.555 10.762 12342 Z= 0.284 Chirality : 0.042 0.313 1526 Planarity : 0.003 0.035 1516 Dihedral : 6.095 56.535 1288 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.34 % Allowed : 23.27 % 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 aren not related in a simple way. whole: 0.86 (0.25), residues: 1194 helix: 1.39 (0.18), residues: 804 sheet: 0.58 (0.60), residues: 50 loop : -1.41 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 671 TYR 0.011 0.001 TYR B 588 PHE 0.019 0.001 PHE A 394 TRP 0.004 0.001 TRP A 515 HIS 0.002 0.001 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 9054) covalent geometry : angle 0.55492 (12342) hydrogen bonds : bond 0.04071 ( 594) hydrogen bonds : angle 3.73749 ( 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: 39 poor density : 188 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7961 (mp0) cc_final: 0.7622 (mp0) REVERT: A 88 MET cc_start: 0.6232 (tmm) cc_final: 0.5792 (tmm) REVERT: A 469 LEU cc_start: 0.7776 (mt) cc_final: 0.7539 (mt) REVERT: B 60 GLU cc_start: 0.7983 (mp0) cc_final: 0.7644 (mp0) REVERT: B 88 MET cc_start: 0.6211 (tmm) cc_final: 0.5771 (tmm) REVERT: B 469 LEU cc_start: 0.7775 (mt) cc_final: 0.7537 (mt) outliers start: 39 outliers final: 37 residues processed: 213 average time/residue: 0.0783 time to fit residues: 24.0433 Evaluate side-chains 224 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 149 ILE Chi-restraints excluded: chain A residue 153 LEU 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 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 716 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 277 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 85 optimal weight: 30.0000 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN B 547 GLN B 571 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.164341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.123382 restraints weight = 9905.467| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.40 r_work: 0.2925 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9054 Z= 0.140 Angle : 0.540 11.075 12342 Z= 0.276 Chirality : 0.041 0.326 1526 Planarity : 0.003 0.036 1516 Dihedral : 6.045 56.005 1288 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.56 % Allowed : 24.39 % Favored : 72.05 % 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 aren not related in a simple way. whole: 1.01 (0.25), residues: 1194 helix: 1.51 (0.18), residues: 806 sheet: 0.63 (0.60), residues: 50 loop : -1.38 (0.38), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 671 TYR 0.011 0.001 TYR A 588 PHE 0.021 0.001 PHE A 394 TRP 0.004 0.001 TRP A 515 HIS 0.002 0.001 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9054) covalent geometry : angle 0.53977 (12342) hydrogen bonds : bond 0.03836 ( 594) hydrogen bonds : angle 3.66072 ( 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 220 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7953 (mp0) cc_final: 0.7585 (mp0) REVERT: A 88 MET cc_start: 0.6252 (tmm) cc_final: 0.5807 (tmm) REVERT: A 469 LEU cc_start: 0.7776 (mt) cc_final: 0.7551 (mt) REVERT: B 60 GLU cc_start: 0.7970 (mp0) cc_final: 0.7602 (mp0) REVERT: B 88 MET cc_start: 0.6259 (tmm) cc_final: 0.5815 (tmm) REVERT: B 469 LEU cc_start: 0.7778 (mt) cc_final: 0.7551 (mt) outliers start: 32 outliers final: 32 residues processed: 212 average time/residue: 0.0826 time to fit residues: 25.2611 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 : 0.330 ------------------------------------------------------------------------------- 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 270 LYS Chi-restraints excluded: chain A residue 277 LEU 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 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 270 LYS Chi-restraints excluded: chain B residue 277 LEU 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 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: 30.0000 chunk 45 optimal weight: 7.9990 chunk 108 optimal weight: 0.4980 chunk 72 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 28 optimal weight: 0.0020 chunk 103 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 overall best weight: 4.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3703 r_free = 0.3703 target = 0.162964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.120796 restraints weight = 9884.654| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.28 r_work: 0.2894 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1669 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= 0.179 Angle : 0.568 11.218 12342 Z= 0.289 Chirality : 0.042 0.356 1526 Planarity : 0.003 0.039 1516 Dihedral : 6.092 55.590 1288 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.34 % Allowed : 23.94 % 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 aren not related in a simple way. whole: 0.93 (0.25), residues: 1194 helix: 1.45 (0.18), residues: 806 sheet: 0.24 (0.59), residues: 54 loop : -1.37 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 178 TYR 0.010 0.001 TYR B 588 PHE 0.024 0.001 PHE A 394 TRP 0.005 0.001 TRP A 515 HIS 0.002 0.001 HIS B 432 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9054) covalent geometry : angle 0.56776 (12342) hydrogen bonds : bond 0.04113 ( 594) hydrogen bonds : angle 3.73290 ( 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 226 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8006 (mp0) cc_final: 0.7623 (mp0) REVERT: A 88 MET cc_start: 0.6243 (tmm) cc_final: 0.5792 (tmm) REVERT: A 469 LEU cc_start: 0.7854 (mt) cc_final: 0.7607 (mt) REVERT: A 646 LEU cc_start: 0.8842 (tp) cc_final: 0.8639 (tp) REVERT: B 60 GLU cc_start: 0.8038 (mp0) cc_final: 0.7657 (mp0) REVERT: B 88 MET cc_start: 0.6213 (tmm) cc_final: 0.5765 (tmm) REVERT: B 469 LEU cc_start: 0.7863 (mt) cc_final: 0.7613 (mt) outliers start: 39 outliers final: 37 residues processed: 214 average time/residue: 0.0871 time to fit residues: 26.9142 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 : 0.374 ------------------------------------------------------------------------------- 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 246 VAL 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 442 LYS Chi-restraints excluded: chain A residue 453 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 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 246 VAL 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 442 LYS Chi-restraints excluded: chain B residue 453 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 100 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 3 optimal weight: 50.0000 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 35 optimal weight: 30.0000 chunk 112 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3691 r_free = 0.3691 target = 0.161845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.119661 restraints weight = 9887.659| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.27 r_work: 0.2881 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1741 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= 0.205 Angle : 0.586 11.481 12342 Z= 0.298 Chirality : 0.043 0.367 1526 Planarity : 0.003 0.039 1516 Dihedral : 6.158 55.645 1288 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.68 % Allowed : 23.39 % Favored : 71.94 % 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 aren not related in a simple way. whole: 0.83 (0.25), residues: 1194 helix: 1.37 (0.18), residues: 806 sheet: 0.22 (0.59), residues: 54 loop : -1.38 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 178 TYR 0.011 0.001 TYR B 102 PHE 0.025 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 covalent geometry : bond 0.00479 ( 9054) covalent geometry : angle 0.58554 (12342) hydrogen bonds : bond 0.04308 ( 594) hydrogen bonds : angle 3.80025 ( 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 229 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8019 (mp0) cc_final: 0.7625 (mp0) REVERT: A 88 MET cc_start: 0.6253 (tmm) cc_final: 0.5791 (tmm) REVERT: A 178 ARG cc_start: 0.7014 (tmm-80) cc_final: 0.6806 (tmm-80) REVERT: A 469 LEU cc_start: 0.7926 (mt) cc_final: 0.7670 (mt) REVERT: A 646 LEU cc_start: 0.8870 (tp) cc_final: 0.8650 (tp) REVERT: B 60 GLU cc_start: 0.8038 (mp0) cc_final: 0.7647 (mp0) REVERT: B 88 MET cc_start: 0.6239 (tmm) cc_final: 0.5775 (tmm) REVERT: B 469 LEU cc_start: 0.7928 (mt) cc_final: 0.7671 (mt) REVERT: B 605 ASN cc_start: 0.8844 (t0) cc_final: 0.8610 (t0) outliers start: 42 outliers final: 38 residues processed: 214 average time/residue: 0.0905 time to fit residues: 27.6164 Evaluate side-chains 224 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 149 ILE 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 442 LYS Chi-restraints excluded: chain A residue 453 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 573 GLN Chi-restraints excluded: chain A residue 590 ILE 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 149 ILE 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 442 LYS Chi-restraints excluded: chain B residue 453 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 573 GLN Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 648 THR 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: 6.9990 chunk 15 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3705 r_free = 0.3705 target = 0.163148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.121900 restraints weight = 9845.290| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.36 r_work: 0.2906 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9054 Z= 0.160 Angle : 0.558 11.727 12342 Z= 0.284 Chirality : 0.041 0.297 1526 Planarity : 0.003 0.039 1516 Dihedral : 6.116 55.841 1288 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % 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 aren not related in a simple way. whole: 0.92 (0.25), residues: 1194 helix: 1.43 (0.18), residues: 806 sheet: 0.62 (0.60), residues: 50 loop : -1.39 (0.38), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 178 TYR 0.011 0.001 TYR A 588 PHE 0.024 0.001 PHE A 394 TRP 0.004 0.001 TRP A 515 HIS 0.003 0.001 HIS B 647 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9054) covalent geometry : angle 0.55817 (12342) hydrogen bonds : bond 0.04003 ( 594) hydrogen bonds : angle 3.72464 ( 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 218 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7968 (mp0) cc_final: 0.7574 (mp0) REVERT: A 88 MET cc_start: 0.6257 (tmm) cc_final: 0.5788 (tmm) REVERT: A 469 LEU cc_start: 0.7911 (mt) cc_final: 0.7666 (mt) REVERT: A 646 LEU cc_start: 0.8827 (tp) cc_final: 0.8617 (tp) REVERT: B 60 GLU cc_start: 0.7979 (mp0) cc_final: 0.7588 (mp0) REVERT: B 88 MET cc_start: 0.6275 (tmm) cc_final: 0.5805 (tmm) REVERT: B 469 LEU cc_start: 0.7908 (mt) cc_final: 0.7659 (mt) REVERT: B 605 ASN cc_start: 0.8818 (t0) cc_final: 0.8590 (t0) outliers start: 35 outliers final: 35 residues processed: 212 average time/residue: 0.0859 time to fit residues: 26.0277 Evaluate side-chains 218 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 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 415 ASN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 453 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 716 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 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 453 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: 8.9990 chunk 47 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3682 r_free = 0.3682 target = 0.161005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.120642 restraints weight = 9803.555| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.42 r_work: 0.2875 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9054 Z= 0.234 Angle : 0.610 11.575 12342 Z= 0.309 Chirality : 0.043 0.276 1526 Planarity : 0.004 0.041 1516 Dihedral : 6.225 55.767 1288 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.01 % Allowed : 24.28 % 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 aren not related in a simple way. whole: 0.71 (0.25), residues: 1194 helix: 1.26 (0.18), residues: 806 sheet: 0.17 (0.59), residues: 54 loop : -1.40 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 178 TYR 0.010 0.001 TYR A 588 PHE 0.026 0.002 PHE B 394 TRP 0.006 0.001 TRP A 515 HIS 0.002 0.001 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00551 ( 9054) covalent geometry : angle 0.60964 (12342) hydrogen bonds : bond 0.04510 ( 594) hydrogen bonds : angle 3.86597 ( 1728) =============================================================================== Job complete usr+sys time: 2539.36 seconds wall clock time: 44 minutes 6.98 seconds (2646.98 seconds total)