Starting phenix.real_space_refine on Thu Feb 13 09:55:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tnw_41427/02_2025/8tnw_41427.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tnw_41427/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tnw_41427/02_2025/8tnw_41427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tnw_41427/02_2025/8tnw_41427.map" model { file = "/net/cci-nas-00/data/ceres_data/8tnw_41427/02_2025/8tnw_41427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tnw_41427/02_2025/8tnw_41427.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 17, 'ARG:plan': 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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 17, 'ARG:plan': 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: 5.45, per 1000 atoms: 0.61 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: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.92 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: 2.60 Time building geometry restraints manager: 2.96 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: 0.04 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: 0.100 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.100 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.590 ------------------------------------------------------------------------------- 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= 0.355 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (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 TRP 0.003 0.001 TRP A 515 HIS 0.002 0.001 HIS A 647 PHE 0.016 0.001 PHE A 394 TYR 0.014 0.001 TYR A 588 ARG 0.001 0.000 ARG A 58 *********************** 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 : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 205 average time/residue: 0.1646 time to fit residues: 50.4099 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 : 1.096 ------------------------------------------------------------------------------- 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 101 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 108 optimal weight: 30.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.164921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.123549 restraints weight = 9706.953| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.33 r_work: 0.2927 rms_B_bonded: 2.98 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: 0.8335 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9054 Z= 0.294 Angle : 0.572 10.041 12342 Z= 0.295 Chirality : 0.042 0.254 1526 Planarity : 0.004 0.032 1516 Dihedral : 6.733 56.140 1308 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.90 % Allowed : 23.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1194 helix: 1.56 (0.18), residues: 794 sheet: 0.87 (0.60), residues: 50 loop : -1.24 (0.38), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 515 HIS 0.002 0.001 HIS B 432 PHE 0.015 0.001 PHE B 394 TYR 0.015 0.001 TYR A 588 ARG 0.002 0.000 ARG A 158 *********************** 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 232 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.6192 (tmm) cc_final: 0.5957 (tmm) REVERT: A 102 TYR cc_start: 0.8381 (t80) cc_final: 0.8176 (t80) REVERT: A 578 ILE cc_start: 0.9144 (mt) cc_final: 0.8922 (mt) REVERT: B 88 MET cc_start: 0.6188 (tmm) cc_final: 0.5951 (tmm) REVERT: B 102 TYR cc_start: 0.8387 (t80) cc_final: 0.8185 (t80) REVERT: B 578 ILE cc_start: 0.9146 (mt) cc_final: 0.8919 (mt) outliers start: 35 outliers final: 19 residues processed: 215 average time/residue: 0.1959 time to fit residues: 60.5109 Evaluate side-chains 207 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 125 GLN 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 36 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.163568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.121832 restraints weight = 9885.816| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.32 r_work: 0.2908 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9054 Z= 0.291 Angle : 0.571 9.690 12342 Z= 0.292 Chirality : 0.042 0.254 1526 Planarity : 0.003 0.035 1516 Dihedral : 6.248 58.739 1292 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.23 % Allowed : 24.50 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1194 helix: 1.46 (0.18), residues: 796 sheet: 0.76 (0.60), residues: 50 loop : -1.36 (0.38), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 515 HIS 0.002 0.001 HIS A 647 PHE 0.015 0.001 PHE B 394 TYR 0.014 0.001 TYR A 588 ARG 0.002 0.000 ARG A 499 *********************** 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 233 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.6177 (tmm) cc_final: 0.5811 (tmm) REVERT: A 102 TYR cc_start: 0.8448 (t80) cc_final: 0.8243 (t80) REVERT: A 127 ILE cc_start: 0.8619 (mt) cc_final: 0.8327 (mp) REVERT: A 469 LEU cc_start: 0.7477 (mt) cc_final: 0.7044 (mt) REVERT: A 646 LEU cc_start: 0.8829 (tp) cc_final: 0.8615 (tp) REVERT: B 88 MET cc_start: 0.6182 (tmm) cc_final: 0.5811 (tmm) REVERT: B 102 TYR cc_start: 0.8449 (t80) cc_final: 0.8239 (t80) REVERT: B 127 ILE cc_start: 0.8624 (mt) cc_final: 0.8329 (mp) REVERT: B 469 LEU cc_start: 0.7469 (mt) cc_final: 0.7035 (mt) REVERT: B 646 LEU cc_start: 0.8819 (tp) cc_final: 0.8610 (tp) outliers start: 38 outliers final: 28 residues processed: 221 average time/residue: 0.1721 time to fit residues: 55.5599 Evaluate side-chains 214 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 53 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.164955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.123540 restraints weight = 9748.743| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.34 r_work: 0.2935 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1364 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= 0.212 Angle : 0.539 9.814 12342 Z= 0.275 Chirality : 0.041 0.232 1526 Planarity : 0.003 0.033 1516 Dihedral : 6.031 57.555 1288 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.79 % Allowed : 24.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1194 helix: 1.47 (0.18), residues: 814 sheet: 0.62 (0.59), residues: 50 loop : -1.35 (0.38), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 515 HIS 0.002 0.001 HIS B 647 PHE 0.015 0.001 PHE A 394 TYR 0.011 0.001 TYR A 588 ARG 0.001 0.000 ARG B 178 *********************** 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 226 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.6229 (tmm) cc_final: 0.5834 (tmm) REVERT: A 127 ILE cc_start: 0.8631 (mt) cc_final: 0.8339 (mt) REVERT: A 469 LEU cc_start: 0.7457 (mt) cc_final: 0.7130 (mt) REVERT: A 716 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7789 (tmm) REVERT: B 88 MET cc_start: 0.6232 (tmm) cc_final: 0.5835 (tmm) REVERT: B 127 ILE cc_start: 0.8632 (mt) cc_final: 0.8340 (mt) REVERT: B 469 LEU cc_start: 0.7466 (mt) cc_final: 0.7136 (mt) REVERT: B 716 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7823 (tmm) outliers start: 34 outliers final: 28 residues processed: 214 average time/residue: 0.1696 time to fit residues: 53.0259 Evaluate side-chains 218 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 92 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 85 optimal weight: 40.0000 chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.164979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.123589 restraints weight = 9798.014| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.33 r_work: 0.2938 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1424 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= 0.207 Angle : 0.534 10.063 12342 Z= 0.273 Chirality : 0.040 0.217 1526 Planarity : 0.003 0.031 1516 Dihedral : 6.000 56.062 1288 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.67 % Allowed : 24.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1194 helix: 1.52 (0.18), residues: 816 sheet: 0.65 (0.59), residues: 50 loop : -1.31 (0.38), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 515 HIS 0.002 0.001 HIS B 647 PHE 0.016 0.001 PHE A 394 TYR 0.015 0.001 TYR A 102 ARG 0.001 0.000 ARG B 499 *********************** 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 220 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7912 (mp0) cc_final: 0.7614 (mp0) REVERT: A 88 MET cc_start: 0.6267 (tmm) cc_final: 0.5849 (tmm) REVERT: A 127 ILE cc_start: 0.8595 (mt) cc_final: 0.8310 (mt) REVERT: A 469 LEU cc_start: 0.7512 (mt) cc_final: 0.7206 (mt) REVERT: A 716 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7767 (tmm) REVERT: B 60 GLU cc_start: 0.7909 (mp0) cc_final: 0.7609 (mp0) REVERT: B 88 MET cc_start: 0.6268 (tmm) cc_final: 0.5851 (tmm) REVERT: B 127 ILE cc_start: 0.8596 (mt) cc_final: 0.8312 (mt) REVERT: B 469 LEU cc_start: 0.7522 (mt) cc_final: 0.7212 (mt) REVERT: B 716 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7793 (tmm) outliers start: 33 outliers final: 31 residues processed: 210 average time/residue: 0.1737 time to fit residues: 52.7578 Evaluate side-chains 220 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 172 ILE Chi-restraints excluded: chain A residue 270 LYS 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 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 172 ILE Chi-restraints excluded: chain B residue 270 LYS 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 590 ILE 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 42 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 62 optimal weight: 0.0670 chunk 36 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 64 optimal weight: 7.9990 chunk 3 optimal weight: 30.0000 chunk 53 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 overall best weight: 4.7524 ------------------------------------------------------------------------------- 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 = 0.163386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.121683 restraints weight = 9796.782| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.30 r_work: 0.2904 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1532 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= 0.275 Angle : 0.564 10.382 12342 Z= 0.287 Chirality : 0.042 0.312 1526 Planarity : 0.003 0.035 1516 Dihedral : 6.064 55.665 1288 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.01 % Allowed : 23.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1194 helix: 1.51 (0.18), residues: 806 sheet: 0.25 (0.57), residues: 54 loop : -1.33 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 515 HIS 0.002 0.001 HIS A 432 PHE 0.012 0.001 PHE A 394 TYR 0.013 0.001 TYR A 588 ARG 0.001 0.000 ARG A 158 *********************** 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 224 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 1.063 Fit side-chains REVERT: A 60 GLU cc_start: 0.7940 (mp0) cc_final: 0.7624 (mp0) REVERT: A 88 MET cc_start: 0.6257 (tmm) cc_final: 0.5822 (tmm) REVERT: A 469 LEU cc_start: 0.7692 (mt) cc_final: 0.7462 (mt) REVERT: A 716 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7902 (tmm) REVERT: B 60 GLU cc_start: 0.7970 (mp0) cc_final: 0.7656 (mp0) REVERT: B 88 MET cc_start: 0.6222 (tmm) cc_final: 0.5784 (tmm) REVERT: B 469 LEU cc_start: 0.7696 (mt) cc_final: 0.7465 (mt) REVERT: B 716 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7910 (tmm) outliers start: 36 outliers final: 28 residues processed: 214 average time/residue: 0.1939 time to fit residues: 59.0691 Evaluate side-chains 216 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 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 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 93 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 153 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 23 optimal weight: 5.9990 chunk 61 optimal weight: 0.0060 chunk 95 optimal weight: 10.0000 chunk 1 optimal weight: 0.0030 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 108 optimal weight: 0.0010 overall best weight: 0.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.168815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.127694 restraints weight = 9906.574| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.36 r_work: 0.2995 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9054 Z= 0.142 Angle : 0.521 11.631 12342 Z= 0.264 Chirality : 0.040 0.327 1526 Planarity : 0.003 0.032 1516 Dihedral : 5.354 59.482 1280 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.12 % Allowed : 24.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.26), residues: 1194 helix: 1.70 (0.18), residues: 816 sheet: 0.84 (0.62), residues: 50 loop : -1.28 (0.39), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 290 HIS 0.002 0.001 HIS A 647 PHE 0.011 0.001 PHE A 394 TYR 0.013 0.001 TYR A 102 ARG 0.002 0.000 ARG B 671 *********************** 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 234 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7876 (mp0) cc_final: 0.7616 (mp0) REVERT: A 88 MET cc_start: 0.6259 (tmm) cc_final: 0.5792 (tmm) REVERT: A 127 ILE cc_start: 0.8460 (mt) cc_final: 0.8159 (mt) REVERT: A 178 ARG cc_start: 0.7041 (tmm-80) cc_final: 0.6771 (tmm-80) REVERT: A 469 LEU cc_start: 0.7510 (mt) cc_final: 0.7240 (mt) REVERT: A 521 SER cc_start: 0.9196 (m) cc_final: 0.8895 (p) REVERT: A 716 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7753 (tmm) REVERT: B 60 GLU cc_start: 0.7907 (mp0) cc_final: 0.7649 (mp0) REVERT: B 88 MET cc_start: 0.6270 (tmm) cc_final: 0.5801 (tmm) REVERT: B 127 ILE cc_start: 0.8471 (mt) cc_final: 0.8170 (mt) REVERT: B 178 ARG cc_start: 0.7015 (tmm-80) cc_final: 0.6744 (tmm-80) REVERT: B 469 LEU cc_start: 0.7507 (mt) cc_final: 0.7239 (mt) REVERT: B 521 SER cc_start: 0.9205 (m) cc_final: 0.8904 (p) REVERT: B 716 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7764 (tmm) outliers start: 28 outliers final: 22 residues processed: 222 average time/residue: 0.1880 time to fit residues: 59.3538 Evaluate side-chains 223 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 270 LYS 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 471 ILE Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 270 LYS 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 471 ILE Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 527 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: 40.0000 chunk 49 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.163688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.121881 restraints weight = 9972.681| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.33 r_work: 0.2909 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1653 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= 0.279 Angle : 0.574 11.059 12342 Z= 0.293 Chirality : 0.042 0.351 1526 Planarity : 0.003 0.033 1516 Dihedral : 5.533 62.675 1280 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.01 % Allowed : 25.17 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1194 helix: 1.63 (0.18), residues: 806 sheet: 0.75 (0.60), residues: 50 loop : -1.34 (0.38), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 515 HIS 0.002 0.001 HIS B 432 PHE 0.018 0.001 PHE A 394 TYR 0.014 0.001 TYR B 102 ARG 0.001 0.000 ARG A 545 *********************** 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 216 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7975 (mp0) cc_final: 0.7603 (mp0) REVERT: A 88 MET cc_start: 0.6258 (tmm) cc_final: 0.5802 (tmm) REVERT: A 127 ILE cc_start: 0.8535 (mt) cc_final: 0.8191 (mp) REVERT: A 469 LEU cc_start: 0.7783 (mt) cc_final: 0.7550 (mt) REVERT: A 716 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7870 (tmm) REVERT: B 60 GLU cc_start: 0.8005 (mp0) cc_final: 0.7634 (mp0) REVERT: B 88 MET cc_start: 0.6258 (tmm) cc_final: 0.5801 (tmm) REVERT: B 127 ILE cc_start: 0.8543 (mt) cc_final: 0.8197 (mp) REVERT: B 469 LEU cc_start: 0.7776 (mt) cc_final: 0.7544 (mt) REVERT: B 716 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7863 (tmm) outliers start: 27 outliers final: 23 residues processed: 206 average time/residue: 0.1785 time to fit residues: 53.1754 Evaluate side-chains 210 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 172 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 480 LYS 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 172 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 570 LYS 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 31 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 6 optimal weight: 40.0000 chunk 90 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.160344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.118838 restraints weight = 9953.760| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.31 r_work: 0.2872 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 9054 Z= 0.437 Angle : 0.647 11.442 12342 Z= 0.330 Chirality : 0.045 0.377 1526 Planarity : 0.004 0.037 1516 Dihedral : 5.939 68.821 1280 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.34 % Allowed : 25.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1194 helix: 1.26 (0.18), residues: 806 sheet: 0.06 (0.57), residues: 54 loop : -1.42 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 376 HIS 0.003 0.001 HIS B 432 PHE 0.022 0.002 PHE B 394 TYR 0.018 0.001 TYR A 102 ARG 0.002 0.000 ARG B 158 *********************** 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 220 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.881 Fit side-chains REVERT: A 60 GLU cc_start: 0.8091 (mp0) cc_final: 0.7718 (mp0) REVERT: A 88 MET cc_start: 0.6290 (tmm) cc_final: 0.5845 (tmm) REVERT: A 127 ILE cc_start: 0.8575 (mt) cc_final: 0.8235 (mp) REVERT: A 178 ARG cc_start: 0.7074 (tmm-80) cc_final: 0.6850 (tmm-80) REVERT: A 469 LEU cc_start: 0.8078 (mt) cc_final: 0.7807 (mt) REVERT: A 645 GLU cc_start: 0.6588 (tp30) cc_final: 0.6353 (tp30) REVERT: B 60 GLU cc_start: 0.8087 (mp0) cc_final: 0.7713 (mp0) REVERT: B 88 MET cc_start: 0.6287 (tmm) cc_final: 0.5837 (tmm) REVERT: B 127 ILE cc_start: 0.8586 (mt) cc_final: 0.8243 (mp) REVERT: B 178 ARG cc_start: 0.7078 (tmm-80) cc_final: 0.6857 (tmm-80) REVERT: B 469 LEU cc_start: 0.8078 (mt) cc_final: 0.7807 (mt) REVERT: B 645 GLU cc_start: 0.6576 (tp30) cc_final: 0.6347 (tp30) outliers start: 30 outliers final: 21 residues processed: 210 average time/residue: 0.2014 time to fit residues: 58.5088 Evaluate side-chains 209 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 277 LEU 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 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 277 LEU 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 527 THR Chi-restraints excluded: chain B residue 570 LYS 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 34 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 30.0000 chunk 37 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.163515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.122157 restraints weight = 9835.633| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.30 r_work: 0.2917 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9054 Z= 0.234 Angle : 0.574 11.870 12342 Z= 0.291 Chirality : 0.042 0.300 1526 Planarity : 0.003 0.039 1516 Dihedral : 5.746 68.297 1280 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.34 % Allowed : 25.84 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1194 helix: 1.42 (0.18), residues: 806 sheet: 0.61 (0.59), residues: 50 loop : -1.40 (0.38), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 515 HIS 0.002 0.001 HIS B 647 PHE 0.019 0.001 PHE B 394 TYR 0.007 0.001 TYR A 271 ARG 0.001 0.000 ARG B 158 ********************** 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 208 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.885 Fit side-chains REVERT: A 60 GLU cc_start: 0.8015 (mp0) cc_final: 0.7609 (mp0) REVERT: A 88 MET cc_start: 0.6254 (tmm) cc_final: 0.5800 (tmm) REVERT: A 127 ILE cc_start: 0.8546 (mt) cc_final: 0.8191 (mp) REVERT: A 178 ARG cc_start: 0.6987 (tmm-80) cc_final: 0.6764 (tmm-80) REVERT: A 469 LEU cc_start: 0.7917 (mt) cc_final: 0.7668 (mt) REVERT: A 605 ASN cc_start: 0.8734 (t0) cc_final: 0.8489 (t0) REVERT: B 60 GLU cc_start: 0.8036 (mp0) cc_final: 0.7631 (mp0) REVERT: B 88 MET cc_start: 0.6255 (tmm) cc_final: 0.5804 (tmm) REVERT: B 127 ILE cc_start: 0.8548 (mt) cc_final: 0.8193 (mp) REVERT: B 178 ARG cc_start: 0.6987 (tmm-80) cc_final: 0.6765 (tmm-80) REVERT: B 469 LEU cc_start: 0.7911 (mt) cc_final: 0.7658 (mt) REVERT: B 605 ASN cc_start: 0.8741 (t0) cc_final: 0.8496 (t0) outliers start: 21 outliers final: 19 residues processed: 202 average time/residue: 0.1911 time to fit residues: 54.7555 Evaluate side-chains 206 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 570 LYS 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 277 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 480 LYS 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 716 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 20.0000 chunk 3 optimal weight: 50.0000 chunk 53 optimal weight: 1.9990 chunk 66 optimal weight: 30.0000 chunk 81 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 28 optimal weight: 0.0050 chunk 106 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.167208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.126067 restraints weight = 9897.121| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.35 r_work: 0.2973 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9054 Z= 0.160 Angle : 0.540 11.924 12342 Z= 0.274 Chirality : 0.042 0.377 1526 Planarity : 0.003 0.039 1516 Dihedral : 5.565 67.143 1280 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.45 % Allowed : 26.28 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1194 helix: 1.62 (0.18), residues: 806 sheet: 0.46 (0.59), residues: 54 loop : -1.31 (0.39), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 290 HIS 0.002 0.000 HIS B 159 PHE 0.023 0.001 PHE B 394 TYR 0.018 0.001 TYR B 102 ARG 0.001 0.000 ARG B 178 =============================================================================== Job complete usr+sys time: 5184.05 seconds wall clock time: 92 minutes 27.15 seconds (5547.15 seconds total)