Starting phenix.real_space_refine on Sat Aug 3 20:35:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnw_41427/08_2024/8tnw_41427.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnw_41427/08_2024/8tnw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnw_41427/08_2024/8tnw_41427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnw_41427/08_2024/8tnw_41427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnw_41427/08_2024/8tnw_41427.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnw_41427/08_2024/8tnw_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 Residue "A TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A ASP 511": "OD1" <-> "OD2" Residue "A PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 660": "OD1" <-> "OD2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B ASP 511": "OD1" <-> "OD2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 4.85, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 3.29 Conformation dependent library (CDL) restraints added in 1.6 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: 0.87 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: 2.50 Time building geometry restraints manager: 3.61 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: 99.92 - 106.74: 228 106.74 - 113.56: 5174 113.56 - 120.38: 3335 120.38 - 127.20: 3523 127.20 - 134.01: 82 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: 0.00 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.190 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.700 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 35 poor density : 178 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 205 average time/residue: 0.1524 time to fit residues: 46.9656 Evaluate side-chains 192 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 fitting. rotamer outliers: 35 poor density : 197 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.6421 (tmm) cc_final: 0.6166 (tmm) REVERT: B 88 MET cc_start: 0.6421 (tmm) cc_final: 0.6167 (tmm) outliers start: 35 outliers final: 19 residues processed: 215 average time/residue: 0.1814 time to fit residues: 56.1534 Evaluate side-chains 205 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 60 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 109 optimal weight: 0.5980 chunk 117 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 108 optimal weight: 30.0000 chunk 37 optimal weight: 8.9990 chunk 87 optimal weight: 40.0000 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9054 Z= 0.316 Angle : 0.584 9.940 12342 Z= 0.299 Chirality : 0.043 0.257 1526 Planarity : 0.003 0.037 1516 Dihedral : 6.302 59.666 1292 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.23 % Allowed : 25.06 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.25), residues: 1194 helix: 1.45 (0.18), residues: 794 sheet: 0.65 (0.58), residues: 50 loop : -1.38 (0.37), 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 0.016 0.001 PHE A 394 TYR 0.017 0.001 TYR A 102 ARG 0.001 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 226 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 188 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.6470 (tmm) cc_final: 0.6079 (tmm) REVERT: A 716 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7838 (tmm) REVERT: B 88 MET cc_start: 0.6465 (tmm) cc_final: 0.6076 (tmm) REVERT: B 716 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7839 (tmm) outliers start: 38 outliers final: 25 residues processed: 214 average time/residue: 0.1649 time to fit residues: 51.4103 Evaluate side-chains 208 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 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 107 optimal weight: 8.9990 chunk 82 optimal weight: 0.0270 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 73 optimal weight: 40.0000 chunk 109 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 31 optimal weight: 0.0020 overall best weight: 1.5650 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9054 Z= 0.147 Angle : 0.513 9.704 12342 Z= 0.262 Chirality : 0.040 0.220 1526 Planarity : 0.003 0.029 1516 Dihedral : 5.985 57.921 1288 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.67 % Allowed : 24.72 % Favored : 72.61 % 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: 1.18 (0.25), residues: 1194 helix: 1.61 (0.18), residues: 814 sheet: 0.47 (0.60), residues: 54 loop : -1.28 (0.39), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 290 HIS 0.002 0.000 HIS A 647 PHE 0.012 0.001 PHE A 394 TYR 0.010 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 218 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 194 time to evaluate : 0.962 Fit side-chains REVERT: A 88 MET cc_start: 0.6471 (tmm) cc_final: 0.6044 (tmm) REVERT: A 127 ILE cc_start: 0.8624 (mt) cc_final: 0.8332 (mt) REVERT: A 469 LEU cc_start: 0.7461 (mt) cc_final: 0.7071 (mt) REVERT: A 716 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7758 (tmm) REVERT: B 88 MET cc_start: 0.6468 (tmm) cc_final: 0.6041 (tmm) REVERT: B 127 ILE cc_start: 0.8621 (mt) cc_final: 0.8330 (mt) REVERT: B 469 LEU cc_start: 0.7458 (mt) cc_final: 0.7071 (mt) REVERT: B 716 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7760 (tmm) outliers start: 24 outliers final: 12 residues processed: 205 average time/residue: 0.1762 time to fit residues: 51.6589 Evaluate side-chains 204 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 190 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 392 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 86 optimal weight: 50.0000 chunk 47 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9054 Z= 0.243 Angle : 0.545 9.672 12342 Z= 0.279 Chirality : 0.041 0.236 1526 Planarity : 0.003 0.032 1516 Dihedral : 5.247 56.150 1282 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.45 % Allowed : 24.05 % 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 (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: 1.23 (0.25), residues: 1194 helix: 1.67 (0.18), residues: 806 sheet: 0.76 (0.61), residues: 50 loop : -1.28 (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 0.012 0.001 PHE B 394 TYR 0.013 0.001 TYR B 588 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 219 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 0.926 Fit side-chains REVERT: A 88 MET cc_start: 0.6543 (tmm) cc_final: 0.6094 (tmm) REVERT: A 127 ILE cc_start: 0.8621 (mt) cc_final: 0.8277 (mp) REVERT: A 469 LEU cc_start: 0.7606 (mt) cc_final: 0.7208 (mt) REVERT: A 716 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7818 (tmm) REVERT: B 88 MET cc_start: 0.6541 (tmm) cc_final: 0.6092 (tmm) REVERT: B 127 ILE cc_start: 0.8620 (mt) cc_final: 0.8274 (mp) REVERT: B 469 LEU cc_start: 0.7608 (mt) cc_final: 0.7211 (mt) REVERT: B 716 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7820 (tmm) outliers start: 31 outliers final: 25 residues processed: 208 average time/residue: 0.1698 time to fit residues: 51.0483 Evaluate side-chains 214 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 187 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 246 VAL 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 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 716 MET Chi-restraints excluded: chain B residue 93 LEU 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 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 39 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 22 optimal weight: 0.0770 chunk 68 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 116 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.4942 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1473 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= 0.145 Angle : 0.513 11.024 12342 Z= 0.262 Chirality : 0.040 0.303 1526 Planarity : 0.003 0.028 1516 Dihedral : 5.115 55.267 1282 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.12 % Allowed : 24.28 % Favored : 72.61 % 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: 1.35 (0.26), residues: 1194 helix: 1.70 (0.18), residues: 816 sheet: 0.92 (0.63), residues: 50 loop : -1.19 (0.39), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 290 HIS 0.002 0.000 HIS A 159 PHE 0.012 0.001 PHE B 394 TYR 0.011 0.001 TYR B 588 ARG 0.001 0.000 ARG A 499 *********************** 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 fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 0.871 Fit side-chains REVERT: A 60 GLU cc_start: 0.7807 (mp0) cc_final: 0.7562 (mp0) REVERT: A 88 MET cc_start: 0.6550 (tmm) cc_final: 0.6090 (tmm) REVERT: A 127 ILE cc_start: 0.8588 (mt) cc_final: 0.8288 (mt) REVERT: A 469 LEU cc_start: 0.7549 (mt) cc_final: 0.7177 (mt) REVERT: A 716 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7778 (tmm) REVERT: B 60 GLU cc_start: 0.7809 (mp0) cc_final: 0.7564 (mp0) REVERT: B 88 MET cc_start: 0.6551 (tmm) cc_final: 0.6090 (tmm) REVERT: B 127 ILE cc_start: 0.8586 (mt) cc_final: 0.8285 (mt) REVERT: B 469 LEU cc_start: 0.7548 (mt) cc_final: 0.7178 (mt) REVERT: B 716 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7780 (tmm) outliers start: 28 outliers final: 20 residues processed: 214 average time/residue: 0.1766 time to fit residues: 54.1768 Evaluate side-chains 214 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU 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 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 527 THR Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 153 LEU 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 527 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 111 optimal weight: 9.9990 chunk 13 optimal weight: 50.0000 chunk 66 optimal weight: 30.0000 chunk 84 optimal weight: 30.0000 chunk 65 optimal weight: 40.0000 chunk 97 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN A 547 GLN A 571 ASN B 415 ASN B 547 GLN B 571 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 9054 Z= 0.434 Angle : 0.638 10.864 12342 Z= 0.326 Chirality : 0.045 0.346 1526 Planarity : 0.004 0.033 1516 Dihedral : 5.467 54.437 1282 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.79 % Allowed : 24.61 % 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 (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: 0.88 (0.25), residues: 1194 helix: 1.39 (0.18), residues: 806 sheet: 0.11 (0.57), residues: 54 loop : -1.30 (0.38), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 376 HIS 0.003 0.001 HIS B 432 PHE 0.018 0.002 PHE B 394 TYR 0.015 0.002 TYR B 247 ARG 0.002 0.000 ARG B 58 *********************** 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 218 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 184 time to evaluate : 0.978 Fit side-chains REVERT: A 60 GLU cc_start: 0.7921 (mp0) cc_final: 0.7656 (mp0) REVERT: A 88 MET cc_start: 0.6581 (tmm) cc_final: 0.6083 (tmm) REVERT: A 127 ILE cc_start: 0.8669 (mt) cc_final: 0.8334 (mp) REVERT: A 262 PHE cc_start: 0.8498 (m-80) cc_final: 0.8275 (m-80) REVERT: A 469 LEU cc_start: 0.7934 (mt) cc_final: 0.7697 (mt) REVERT: A 716 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7898 (tmm) REVERT: B 60 GLU cc_start: 0.7922 (mp0) cc_final: 0.7659 (mp0) REVERT: B 88 MET cc_start: 0.6581 (tmm) cc_final: 0.6082 (tmm) REVERT: B 127 ILE cc_start: 0.8668 (mt) cc_final: 0.8332 (mp) REVERT: B 262 PHE cc_start: 0.8500 (m-80) cc_final: 0.8275 (m-80) REVERT: B 469 LEU cc_start: 0.7934 (mt) cc_final: 0.7697 (mt) REVERT: B 716 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7900 (tmm) outliers start: 34 outliers final: 25 residues processed: 206 average time/residue: 0.1985 time to fit residues: 57.9192 Evaluate side-chains 208 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 570 LYS Chi-restraints excluded: chain B residue 648 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 71 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9054 Z= 0.207 Angle : 0.565 11.531 12342 Z= 0.285 Chirality : 0.042 0.343 1526 Planarity : 0.003 0.033 1516 Dihedral : 5.304 55.085 1282 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.01 % Allowed : 25.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.25), residues: 1194 helix: 1.50 (0.18), residues: 806 sheet: 0.63 (0.58), residues: 50 loop : -1.32 (0.38), residues: 338 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 0.017 0.001 PHE B 394 TYR 0.011 0.001 TYR B 588 ARG 0.001 0.000 ARG A 671 *********************** 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 213 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 1.041 Fit side-chains REVERT: A 60 GLU cc_start: 0.7902 (mp0) cc_final: 0.7607 (mp0) REVERT: A 88 MET cc_start: 0.6541 (tmm) cc_final: 0.6051 (tmm) REVERT: A 127 ILE cc_start: 0.8637 (mt) cc_final: 0.8348 (mt) REVERT: A 716 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7804 (tmm) REVERT: B 60 GLU cc_start: 0.7903 (mp0) cc_final: 0.7610 (mp0) REVERT: B 88 MET cc_start: 0.6540 (tmm) cc_final: 0.6048 (tmm) REVERT: B 127 ILE cc_start: 0.8636 (mt) cc_final: 0.8345 (mt) REVERT: B 716 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7804 (tmm) outliers start: 27 outliers final: 23 residues processed: 206 average time/residue: 0.1844 time to fit residues: 53.7956 Evaluate side-chains 209 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 184 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 107 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 84 optimal weight: 0.0010 chunk 33 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN B 240 GLN B 571 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9054 Z= 0.138 Angle : 0.535 12.010 12342 Z= 0.269 Chirality : 0.042 0.375 1526 Planarity : 0.003 0.034 1516 Dihedral : 5.129 55.784 1282 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.78 % Allowed : 25.72 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.67 (0.18), residues: 816 sheet: 0.52 (0.61), residues: 54 loop : -1.13 (0.40), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 98 HIS 0.003 0.001 HIS B 159 PHE 0.022 0.001 PHE B 394 TYR 0.013 0.001 TYR B 588 ARG 0.001 0.000 ARG A 671 *********************** 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 221 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 196 time to evaluate : 0.948 Fit side-chains REVERT: A 60 GLU cc_start: 0.7855 (mp0) cc_final: 0.7547 (mp0) REVERT: A 88 MET cc_start: 0.6541 (tmm) cc_final: 0.6045 (tmm) REVERT: A 127 ILE cc_start: 0.8576 (mt) cc_final: 0.8308 (mt) REVERT: A 716 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7727 (tmm) REVERT: B 60 GLU cc_start: 0.7857 (mp0) cc_final: 0.7551 (mp0) REVERT: B 88 MET cc_start: 0.6542 (tmm) cc_final: 0.6044 (tmm) REVERT: B 127 ILE cc_start: 0.8575 (mt) cc_final: 0.8307 (mt) REVERT: B 716 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7728 (tmm) outliers start: 25 outliers final: 23 residues processed: 209 average time/residue: 0.1870 time to fit residues: 55.1708 Evaluate side-chains 217 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU 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 527 THR Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 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 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 54 optimal weight: 8.9990 chunk 79 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 73 optimal weight: 50.0000 chunk 58 optimal weight: 0.0270 chunk 75 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 overall best weight: 1.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN B 240 GLN B 571 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9054 Z= 0.152 Angle : 0.544 11.612 12342 Z= 0.273 Chirality : 0.042 0.374 1526 Planarity : 0.003 0.033 1516 Dihedral : 5.097 55.617 1282 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.23 % Allowed : 26.28 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.36 (0.26), residues: 1194 helix: 1.70 (0.18), residues: 816 sheet: 0.71 (0.61), residues: 54 loop : -1.12 (0.40), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 290 HIS 0.002 0.000 HIS B 159 PHE 0.020 0.001 PHE B 394 TYR 0.012 0.001 TYR A 588 ARG 0.005 0.000 ARG B 178 ********************** 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 fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 1.007 Fit side-chains REVERT: A 60 GLU cc_start: 0.7854 (mp0) cc_final: 0.7536 (mp0) REVERT: A 88 MET cc_start: 0.6501 (tmm) cc_final: 0.6016 (tmm) REVERT: A 127 ILE cc_start: 0.8587 (mt) cc_final: 0.8319 (mt) REVERT: A 716 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7725 (tmm) REVERT: B 60 GLU cc_start: 0.7858 (mp0) cc_final: 0.7539 (mp0) REVERT: B 88 MET cc_start: 0.6503 (tmm) cc_final: 0.6019 (tmm) REVERT: B 127 ILE cc_start: 0.8585 (mt) cc_final: 0.8316 (mt) REVERT: B 716 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7726 (tmm) outliers start: 29 outliers final: 27 residues processed: 204 average time/residue: 0.1762 time to fit residues: 51.6234 Evaluate side-chains 218 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 246 VAL 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 508 SER 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 153 LEU Chi-restraints excluded: chain B residue 240 GLN Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 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 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 87 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 547 GLN B 240 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.163700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.122721 restraints weight = 9812.096| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.43 r_work: 0.2914 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9054 Z= 0.330 Angle : 0.609 11.079 12342 Z= 0.308 Chirality : 0.044 0.388 1526 Planarity : 0.003 0.035 1516 Dihedral : 5.278 55.174 1282 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.67 % Allowed : 25.95 % Favored : 70.38 % 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: 1.12 (0.25), residues: 1194 helix: 1.57 (0.18), residues: 806 sheet: 0.86 (0.59), residues: 50 loop : -1.30 (0.38), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 515 HIS 0.002 0.001 HIS A 363 PHE 0.024 0.002 PHE B 394 TYR 0.025 0.002 TYR B 102 ARG 0.006 0.000 ARG A 178 =============================================================================== Job complete usr+sys time: 2029.24 seconds wall clock time: 36 minutes 52.57 seconds (2212.57 seconds total)