Starting phenix.real_space_refine on Sun Aug 4 19:33:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/08_2024/8toi_41453.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/08_2024/8toi_41453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/08_2024/8toi_41453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/08_2024/8toi_41453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/08_2024/8toi_41453.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toi_41453/08_2024/8toi_41453.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.057 sd= 0.508 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 34 5.49 5 S 40 5.16 5 C 7502 2.51 5 N 1724 2.21 5 O 2110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 87": "OD1" <-> "OD2" Residue "B ASP 87": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11414 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5160 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 28, 'TRANS': 620} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 5160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5160 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 28, 'TRANS': 620} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 547 Unusual residues: {' CA': 2, 'PGW': 18} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 394 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PGW:plan-3': 9} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 547 Unusual residues: {' CA': 2, 'PGW': 18} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 394 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PGW:plan-3': 9} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 6.70, per 1000 atoms: 0.59 Number of scatterers: 11414 At special positions: 0 Unit cell: (91.575, 137.775, 106.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 40 16.00 P 34 15.00 O 2110 8.00 N 1724 7.00 C 7502 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: 4.28 Conformation dependent library (CDL) restraints added in 1.9 seconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 73.3% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 32 through 47 removed outlier: 3.644A pdb=" N GLY A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 90 removed outlier: 3.618A pdb=" N PHE A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.833A pdb=" N LEU A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 106 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.552A pdb=" N GLU A 129 " --> pdb=" O PRO A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 165 Processing helix chain 'A' and resid 170 through 182 removed outlier: 3.813A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 199 removed outlier: 3.549A pdb=" N ALA A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'A' and resid 217 through 246 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.578A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 320 Processing helix chain 'A' and resid 330 through 358 Proline residue: A 341 - end of helix Processing helix chain 'A' and resid 362 through 392 removed outlier: 6.230A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.627A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 453 removed outlier: 3.793A pdb=" N ASN A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 452 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 466 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.584A pdb=" N GLU A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 481 " --> pdb=" O ASP A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 477 through 481' Processing helix chain 'A' and resid 482 through 493 Processing helix chain 'A' and resid 499 through 518 removed outlier: 4.318A pdb=" N ASP A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 545 removed outlier: 3.987A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.705A pdb=" N GLY A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN A 585 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 625 removed outlier: 3.506A pdb=" N LEU A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 Processing helix chain 'A' and resid 667 through 685 Processing helix chain 'A' and resid 689 through 694 Processing helix chain 'A' and resid 701 through 716 removed outlier: 3.653A pdb=" N ILE A 705 " --> pdb=" O MET A 701 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 47 removed outlier: 3.644A pdb=" N GLY B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.618A pdb=" N PHE B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.834A pdb=" N LEU B 105 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 106 " --> pdb=" O GLN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.552A pdb=" N GLU B 129 " --> pdb=" O PRO B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 165 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.813A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 199 removed outlier: 3.549A pdb=" N ALA B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 Processing helix chain 'B' and resid 217 through 246 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.578A pdb=" N ARG B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 320 Processing helix chain 'B' and resid 330 through 358 Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 362 through 392 removed outlier: 6.230A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 413 removed outlier: 3.627A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 453 removed outlier: 3.793A pdb=" N ASN B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 452 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 466 Processing helix chain 'B' and resid 477 through 481 removed outlier: 3.584A pdb=" N GLU B 480 " --> pdb=" O GLU B 477 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU B 481 " --> pdb=" O ASP B 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 477 through 481' Processing helix chain 'B' and resid 482 through 493 Processing helix chain 'B' and resid 499 through 518 removed outlier: 4.317A pdb=" N ASP B 503 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.986A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.705A pdb=" N GLY B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN B 585 " --> pdb=" O TYR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 625 removed outlier: 3.506A pdb=" N LEU B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 Processing helix chain 'B' and resid 667 through 685 Processing helix chain 'B' and resid 689 through 694 Processing helix chain 'B' and resid 701 through 716 removed outlier: 3.653A pdb=" N ILE B 705 " --> pdb=" O MET B 701 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 716 " --> pdb=" O ILE B 712 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268 removed outlier: 3.784A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 268 removed outlier: 3.784A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 2046 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: 3.16 Time building geometry restraints manager: 4.71 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: 1722 1.31 - 1.44: 3226 1.44 - 1.57: 6564 1.57 - 1.70: 68 1.70 - 1.83: 66 Bond restraints: 11646 Sorted by residual: bond pdb=" C1 PGW A 820 " pdb=" O01 PGW A 820 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C1 PGW A 809 " pdb=" O01 PGW A 809 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C1 PGW B 820 " pdb=" O01 PGW B 820 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C1 PGW B 809 " pdb=" O01 PGW B 809 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C1 PGW A 817 " pdb=" O01 PGW A 817 " ideal model delta sigma weight residual 1.332 1.427 -0.095 2.00e-02 2.50e+03 2.24e+01 ... (remaining 11641 not shown) Histogram of bond angle deviations from ideal: 80.14 - 96.20: 4 96.20 - 112.25: 6172 112.25 - 128.31: 9324 128.31 - 144.36: 120 144.36 - 160.42: 2 Bond angle restraints: 15622 Sorted by residual: angle pdb=" C2 PGW A 805 " pdb=" C1 PGW A 805 " pdb=" O01 PGW A 805 " ideal model delta sigma weight residual 110.92 160.42 -49.50 3.00e+00 1.11e-01 2.72e+02 angle pdb=" C2 PGW B 805 " pdb=" C1 PGW B 805 " pdb=" O01 PGW B 805 " ideal model delta sigma weight residual 110.92 160.38 -49.46 3.00e+00 1.11e-01 2.72e+02 angle pdb=" C2 PGW B 805 " pdb=" C1 PGW B 805 " pdb=" O02 PGW B 805 " ideal model delta sigma weight residual 125.44 80.14 45.30 3.00e+00 1.11e-01 2.28e+02 angle pdb=" C2 PGW A 805 " pdb=" C1 PGW A 805 " pdb=" O02 PGW A 805 " ideal model delta sigma weight residual 125.44 80.21 45.23 3.00e+00 1.11e-01 2.27e+02 angle pdb=" O01 PGW A 805 " pdb=" C1 PGW A 805 " pdb=" O02 PGW A 805 " ideal model delta sigma weight residual 123.63 80.21 43.42 3.00e+00 1.11e-01 2.09e+02 ... (remaining 15617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.20: 6550 33.20 - 66.41: 400 66.41 - 99.61: 58 99.61 - 132.82: 20 132.82 - 166.02: 28 Dihedral angle restraints: 7056 sinusoidal: 3268 harmonic: 3788 Sorted by residual: dihedral pdb=" CA ILE A 101 " pdb=" C ILE A 101 " pdb=" N ALA A 102 " pdb=" CA ALA A 102 " ideal model delta harmonic sigma weight residual -180.00 -156.57 -23.43 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ILE B 101 " pdb=" C ILE B 101 " pdb=" N ALA B 102 " pdb=" CA ALA B 102 " ideal model delta harmonic sigma weight residual -180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" O01 PGW B 815 " pdb=" C01 PGW B 815 " pdb=" C02 PGW B 815 " pdb=" O03 PGW B 815 " ideal model delta sinusoidal sigma weight residual 59.30 -106.72 166.02 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 7053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1242 0.054 - 0.109: 292 0.109 - 0.163: 74 0.163 - 0.217: 20 0.217 - 0.272: 4 Chirality restraints: 1632 Sorted by residual: chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA THR B 340 " pdb=" N THR B 340 " pdb=" C THR B 340 " pdb=" CB THR B 340 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB VAL B 111 " pdb=" CA VAL B 111 " pdb=" CG1 VAL B 111 " pdb=" CG2 VAL B 111 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1629 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 396 " 0.014 2.00e-02 2.50e+03 1.86e-02 6.03e+00 pdb=" CG PHE B 396 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 396 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 396 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 396 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 396 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 396 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 396 " -0.014 2.00e-02 2.50e+03 1.85e-02 5.98e+00 pdb=" CG PHE A 396 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 396 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 396 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 396 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 396 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 396 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 134 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C VAL B 134 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL B 134 " -0.016 2.00e-02 2.50e+03 pdb=" N THR B 135 " -0.014 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3412 2.83 - 3.35: 10087 3.35 - 3.87: 18858 3.87 - 4.38: 21109 4.38 - 4.90: 36789 Nonbonded interactions: 90255 Sorted by model distance: nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.318 3.040 nonbonded pdb=" OH TYR B 188 " pdb=" OD2 ASP B 539 " model vdw 2.318 3.040 nonbonded pdb=" O TRP B 570 " pdb=" OG SER B 573 " model vdw 2.353 3.040 nonbonded pdb=" O TRP A 570 " pdb=" OG SER A 573 " model vdw 2.353 3.040 nonbonded pdb=" OE2 GLU B 358 " pdb=" OH TYR B 360 " model vdw 2.360 3.040 ... (remaining 90250 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: 0.680 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 32.390 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.010 0.096 11646 Z= 0.575 Angle : 1.856 49.496 15622 Z= 0.718 Chirality : 0.054 0.272 1632 Planarity : 0.006 0.053 1914 Dihedral : 24.382 166.024 4596 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -1.60 (0.20), residues: 1274 helix: -0.55 (0.15), residues: 888 sheet: -1.94 (0.77), residues: 44 loop : -1.97 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 141 HIS 0.004 0.001 HIS B 366 PHE 0.043 0.002 PHE B 396 TYR 0.017 0.002 TYR B 457 ARG 0.003 0.000 ARG B 537 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.277 Fit side-chains REVERT: A 320 TYR cc_start: 0.8068 (t80) cc_final: 0.7754 (t80) REVERT: B 55 GLU cc_start: 0.7866 (tp30) cc_final: 0.7066 (mm-30) REVERT: B 320 TYR cc_start: 0.8143 (t80) cc_final: 0.7800 (t80) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 1.3035 time to fit residues: 233.1973 Evaluate side-chains 131 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 153 HIS A 265 HIS A 310 ASN A 366 HIS A 696 GLN A 698 GLN B 79 GLN B 153 HIS B 265 HIS B 310 ASN B 366 HIS B 696 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11646 Z= 0.197 Angle : 1.070 46.300 15622 Z= 0.417 Chirality : 0.040 0.159 1632 Planarity : 0.004 0.044 1914 Dihedral : 26.313 160.955 2250 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.59 % Allowed : 9.33 % Favored : 89.09 % 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: 0.40 (0.23), residues: 1274 helix: 1.09 (0.17), residues: 892 sheet: -1.55 (0.81), residues: 44 loop : -1.65 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 235 HIS 0.003 0.001 HIS B 479 PHE 0.022 0.001 PHE A 406 TYR 0.013 0.001 TYR A 188 ARG 0.003 0.000 ARG A 697 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.129 Fit side-chains outliers start: 17 outliers final: 6 residues processed: 138 average time/residue: 1.0998 time to fit residues: 165.9786 Evaluate side-chains 135 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 282 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 0.0470 chunk 125 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 HIS A 510 GLN A 531 ASN A 641 GLN A 696 GLN B 25 HIS ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN B 531 ASN B 641 GLN B 696 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11646 Z= 0.322 Angle : 1.079 46.193 15622 Z= 0.426 Chirality : 0.043 0.174 1632 Planarity : 0.004 0.036 1914 Dihedral : 24.800 163.168 2250 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.08 % Allowed : 11.94 % Favored : 84.98 % 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: 1.04 (0.24), residues: 1274 helix: 1.60 (0.17), residues: 902 sheet: -1.10 (0.88), residues: 44 loop : -1.64 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 235 HIS 0.005 0.001 HIS A 611 PHE 0.013 0.001 PHE A 189 TYR 0.019 0.002 TYR B 26 ARG 0.005 0.000 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 1.207 Fit side-chains REVERT: A 35 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: A 400 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6822 (pp) REVERT: B 33 ARG cc_start: 0.8368 (ttp80) cc_final: 0.8164 (ttp80) REVERT: B 400 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6877 (pp) outliers start: 33 outliers final: 6 residues processed: 154 average time/residue: 1.1396 time to fit residues: 191.4044 Evaluate side-chains 141 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 627 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 chunk 110 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 HIS A 696 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 11646 Z= 0.485 Angle : 1.115 46.109 15622 Z= 0.451 Chirality : 0.046 0.173 1632 Planarity : 0.004 0.036 1914 Dihedral : 24.194 163.505 2250 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.64 % Allowed : 12.97 % Favored : 83.40 % 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: 1.03 (0.23), residues: 1274 helix: 1.62 (0.17), residues: 896 sheet: -1.15 (0.89), residues: 44 loop : -1.69 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 235 HIS 0.005 0.001 HIS B 153 PHE 0.027 0.002 PHE B 406 TYR 0.019 0.002 TYR A 26 ARG 0.005 0.001 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 132 time to evaluate : 1.131 Fit side-chains REVERT: A 35 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: A 320 TYR cc_start: 0.8433 (t80) cc_final: 0.8119 (t80) REVERT: A 546 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8516 (m) REVERT: B 320 TYR cc_start: 0.8265 (t80) cc_final: 0.8024 (t80) outliers start: 39 outliers final: 7 residues processed: 152 average time/residue: 1.1553 time to fit residues: 190.7780 Evaluate side-chains 140 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 627 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN A 696 GLN B 310 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 HIS B 696 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11646 Z= 0.184 Angle : 1.060 46.391 15622 Z= 0.412 Chirality : 0.040 0.151 1632 Planarity : 0.004 0.034 1914 Dihedral : 23.033 165.524 2250 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.05 % Allowed : 15.39 % Favored : 82.56 % 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: 1.42 (0.24), residues: 1274 helix: 1.88 (0.17), residues: 908 sheet: -1.13 (0.89), residues: 44 loop : -1.51 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 141 HIS 0.004 0.001 HIS B 479 PHE 0.008 0.001 PHE B 379 TYR 0.017 0.002 TYR A 26 ARG 0.004 0.000 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.102 Fit side-chains REVERT: A 282 MET cc_start: 0.8068 (mmp) cc_final: 0.7840 (tpp) REVERT: B 33 ARG cc_start: 0.8373 (ttp80) cc_final: 0.8172 (ttp80) REVERT: B 282 MET cc_start: 0.8076 (mmp) cc_final: 0.7851 (tpp) REVERT: B 320 TYR cc_start: 0.8245 (t80) cc_final: 0.7954 (t80) REVERT: B 479 HIS cc_start: 0.8013 (m-70) cc_final: 0.7806 (m170) outliers start: 22 outliers final: 4 residues processed: 145 average time/residue: 1.1208 time to fit residues: 176.9424 Evaluate side-chains 132 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 153 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 102 optimal weight: 0.0370 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 overall best weight: 1.0460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11646 Z= 0.225 Angle : 1.066 46.180 15622 Z= 0.415 Chirality : 0.041 0.152 1632 Planarity : 0.004 0.034 1914 Dihedral : 22.474 166.178 2250 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.68 % Allowed : 16.88 % Favored : 81.44 % 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: 1.59 (0.24), residues: 1274 helix: 1.97 (0.17), residues: 910 sheet: -1.06 (0.86), residues: 48 loop : -1.34 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 235 HIS 0.003 0.001 HIS A 366 PHE 0.026 0.001 PHE B 406 TYR 0.016 0.002 TYR A 26 ARG 0.004 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.323 Fit side-chains REVERT: A 282 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7855 (tpp) REVERT: B 282 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7856 (tpp) REVERT: B 484 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7376 (tm-30) REVERT: B 701 MET cc_start: 0.8029 (tpp) cc_final: 0.7774 (tpt) outliers start: 18 outliers final: 7 residues processed: 137 average time/residue: 1.2352 time to fit residues: 183.7202 Evaluate side-chains 136 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 698 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 0.0870 chunk 69 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN B 479 HIS B 696 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11646 Z= 0.262 Angle : 1.075 46.107 15622 Z= 0.421 Chirality : 0.042 0.153 1632 Planarity : 0.004 0.037 1914 Dihedral : 21.990 166.224 2250 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.71 % Allowed : 16.14 % Favored : 81.16 % 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: 1.62 (0.24), residues: 1274 helix: 1.97 (0.17), residues: 912 sheet: -1.05 (0.86), residues: 48 loop : -1.28 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 141 HIS 0.004 0.001 HIS B 366 PHE 0.010 0.001 PHE A 379 TYR 0.016 0.002 TYR B 26 ARG 0.004 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.269 Fit side-chains REVERT: A 282 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7837 (tpp) REVERT: B 282 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7813 (tpp) REVERT: B 484 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7390 (tm-30) outliers start: 29 outliers final: 7 residues processed: 140 average time/residue: 1.2103 time to fit residues: 183.6829 Evaluate side-chains 133 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 153 HIS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 153 HIS Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 698 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11646 Z= 0.280 Angle : 1.082 46.143 15622 Z= 0.425 Chirality : 0.042 0.153 1632 Planarity : 0.004 0.036 1914 Dihedral : 21.513 165.736 2250 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.59 % Allowed : 17.35 % Favored : 81.06 % 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: 1.60 (0.24), residues: 1274 helix: 1.96 (0.17), residues: 912 sheet: -1.11 (0.85), residues: 48 loop : -1.29 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 141 HIS 0.004 0.001 HIS B 366 PHE 0.033 0.001 PHE A 406 TYR 0.017 0.002 TYR A 26 ARG 0.004 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.129 Fit side-chains REVERT: B 282 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7796 (tpp) REVERT: B 484 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7380 (tm-30) outliers start: 17 outliers final: 5 residues processed: 131 average time/residue: 1.1812 time to fit residues: 168.2273 Evaluate side-chains 133 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 698 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 75 optimal weight: 0.0980 chunk 121 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN B 696 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11646 Z= 0.197 Angle : 1.074 46.259 15622 Z= 0.419 Chirality : 0.041 0.149 1632 Planarity : 0.004 0.035 1914 Dihedral : 20.781 166.199 2250 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.84 % Allowed : 18.38 % Favored : 80.78 % 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: 1.73 (0.24), residues: 1274 helix: 2.05 (0.17), residues: 910 sheet: -0.99 (0.86), residues: 48 loop : -1.25 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 235 HIS 0.003 0.001 HIS A 611 PHE 0.010 0.001 PHE A 379 TYR 0.016 0.002 TYR A 457 ARG 0.004 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 1.216 Fit side-chains REVERT: A 282 MET cc_start: 0.8059 (mmp) cc_final: 0.7832 (tpp) REVERT: A 437 MET cc_start: 0.8737 (tpt) cc_final: 0.8100 (tpt) REVERT: B 282 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7814 (tpp) REVERT: B 701 MET cc_start: 0.8038 (tpp) cc_final: 0.7758 (tpt) outliers start: 9 outliers final: 2 residues processed: 138 average time/residue: 1.2152 time to fit residues: 182.1789 Evaluate side-chains 132 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 129 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 698 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11646 Z= 0.324 Angle : 1.106 46.212 15622 Z= 0.437 Chirality : 0.043 0.155 1632 Planarity : 0.004 0.034 1914 Dihedral : 20.740 164.899 2250 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.84 % Allowed : 18.56 % Favored : 80.60 % 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: 1.63 (0.24), residues: 1274 helix: 1.97 (0.17), residues: 910 sheet: -0.98 (0.86), residues: 48 loop : -1.25 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 141 HIS 0.004 0.001 HIS B 25 PHE 0.036 0.001 PHE A 406 TYR 0.016 0.002 TYR B 457 ARG 0.006 0.000 ARG B 709 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.292 Fit side-chains REVERT: B 282 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7794 (tpp) REVERT: B 437 MET cc_start: 0.8752 (tpt) cc_final: 0.8135 (tpt) REVERT: B 701 MET cc_start: 0.8087 (tpp) cc_final: 0.7825 (tpt) outliers start: 9 outliers final: 2 residues processed: 136 average time/residue: 1.2242 time to fit residues: 182.6143 Evaluate side-chains 136 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 698 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 89 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN B 696 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.127597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.091101 restraints weight = 16136.371| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.98 r_work: 0.3083 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11646 Z= 0.193 Angle : 1.084 46.255 15622 Z= 0.425 Chirality : 0.040 0.148 1632 Planarity : 0.004 0.034 1914 Dihedral : 20.129 165.160 2250 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.75 % Allowed : 19.22 % Favored : 80.04 % 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: 1.80 (0.24), residues: 1274 helix: 2.10 (0.17), residues: 910 sheet: -0.94 (0.87), residues: 48 loop : -1.20 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 235 HIS 0.003 0.001 HIS B 143 PHE 0.023 0.001 PHE B 388 TYR 0.016 0.001 TYR A 457 ARG 0.007 0.000 ARG B 709 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3889.58 seconds wall clock time: 68 minutes 51.73 seconds (4131.73 seconds total)