Starting phenix.real_space_refine on Sun Aug 4 09:00:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/08_2024/8uuk_42588.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/08_2024/8uuk_42588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/08_2024/8uuk_42588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/08_2024/8uuk_42588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/08_2024/8uuk_42588.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/08_2024/8uuk_42588.cif" } resolution = 2.5 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= 0.002 sd= 0.095 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 P 2 5.49 5 S 36 5.16 5 C 6896 2.51 5 N 1542 2.21 5 O 1766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 682": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C GLU 704": "OE1" <-> "OE2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 540": "OE1" <-> "OE2" Residue "D GLU 682": "OE1" <-> "OE2" 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: 10242 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4755 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 3 Chain: "D" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4755 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 3 Chain: "C" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 366 Unusual residues: {'AV0': 2, 'CLR': 6, 'LBN': 7} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 6} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 366 Unusual residues: {'AV0': 2, 'CLR': 6, 'LBN': 7} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 6} Unresolved non-hydrogen planarities: 68 Time building chain proxies: 6.40, per 1000 atoms: 0.62 Number of scatterers: 10242 At special positions: 0 Unit cell: (116.325, 104.775, 105.6, 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) S 36 16.00 P 2 15.00 O 1766 8.00 N 1542 7.00 C 6896 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.99 Conformation dependent library (CDL) restraints added in 1.9 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 5 sheets defined 71.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 82 through 109 removed outlier: 4.221A pdb=" N SER C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU C 107 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 108 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 131 removed outlier: 3.626A pdb=" N TYR C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Proline residue: C 123 - end of helix removed outlier: 4.038A pdb=" N ILE C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'C' and resid 157 through 162 Processing helix chain 'C' and resid 177 through 206 Processing helix chain 'C' and resid 209 through 215 removed outlier: 4.073A pdb=" N VAL C 212 " --> pdb=" O GLY C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 240 Processing helix chain 'C' and resid 251 through 264 Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 268 through 292 Processing helix chain 'C' and resid 301 through 318 Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 342 through 348 removed outlier: 4.118A pdb=" N SER C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 376 removed outlier: 3.815A pdb=" N SER C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 398 Processing helix chain 'C' and resid 406 through 416 removed outlier: 3.506A pdb=" N THR C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 446 through 458 removed outlier: 3.976A pdb=" N LEU C 450 " --> pdb=" O GLN C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 463 Processing helix chain 'C' and resid 464 through 466 No H-bonds generated for 'chain 'C' and resid 464 through 466' Processing helix chain 'C' and resid 467 through 475 Processing helix chain 'C' and resid 475 through 491 Processing helix chain 'C' and resid 493 through 515 Processing helix chain 'C' and resid 533 through 537 removed outlier: 4.217A pdb=" N LYS C 537 " --> pdb=" O THR C 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 537' Processing helix chain 'C' and resid 555 through 571 Processing helix chain 'C' and resid 573 through 585 Processing helix chain 'C' and resid 669 through 686 removed outlier: 3.742A pdb=" N ILE C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 706 Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'D' and resid 28 through 36 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 82 through 109 removed outlier: 4.215A pdb=" N SER D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU D 107 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 131 removed outlier: 3.625A pdb=" N TYR D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Proline residue: D 123 - end of helix removed outlier: 4.039A pdb=" N ILE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 156 Processing helix chain 'D' and resid 157 through 162 Processing helix chain 'D' and resid 177 through 206 Processing helix chain 'D' and resid 209 through 215 removed outlier: 4.033A pdb=" N VAL D 212 " --> pdb=" O GLY D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 240 Processing helix chain 'D' and resid 251 through 264 Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 268 through 292 Processing helix chain 'D' and resid 301 through 318 Processing helix chain 'D' and resid 318 through 323 Processing helix chain 'D' and resid 342 through 348 removed outlier: 4.111A pdb=" N SER D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 376 removed outlier: 3.809A pdb=" N SER D 355 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 398 Processing helix chain 'D' and resid 406 through 416 removed outlier: 3.505A pdb=" N THR D 416 " --> pdb=" O VAL D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 437 Processing helix chain 'D' and resid 446 through 458 removed outlier: 3.978A pdb=" N LEU D 450 " --> pdb=" O GLN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 463 Processing helix chain 'D' and resid 464 through 466 No H-bonds generated for 'chain 'D' and resid 464 through 466' Processing helix chain 'D' and resid 467 through 475 Processing helix chain 'D' and resid 475 through 491 Processing helix chain 'D' and resid 493 through 515 Processing helix chain 'D' and resid 533 through 537 removed outlier: 4.216A pdb=" N LYS D 537 " --> pdb=" O THR D 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 533 through 537' Processing helix chain 'D' and resid 555 through 571 Processing helix chain 'D' and resid 573 through 585 Processing helix chain 'D' and resid 669 through 686 removed outlier: 3.720A pdb=" N ILE D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 706 Processing helix chain 'D' and resid 723 through 731 Processing sheet with id=AA1, first strand: chain 'C' and resid 19 through 25 removed outlier: 3.643A pdb=" N VAL C 22 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 22 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 138 through 139 Processing sheet with id=AA3, first strand: chain 'C' and resid 530 through 532 removed outlier: 4.110A pdb=" N ILE C 547 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N SER C 523 " --> pdb=" O VAL C 545 " (cutoff:3.500A) removed outlier: 12.522A pdb=" N VAL C 545 " --> pdb=" O SER C 523 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS C 546 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP C 661 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 548 " --> pdb=" O ASP C 661 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N PHE C 719 " --> pdb=" O VAL C 690 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE C 692 " --> pdb=" O PHE C 719 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 138 through 139 Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 removed outlier: 4.117A pdb=" N ILE D 547 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N SER D 523 " --> pdb=" O VAL D 545 " (cutoff:3.500A) removed outlier: 12.521A pdb=" N VAL D 545 " --> pdb=" O SER D 523 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS D 546 " --> pdb=" O VAL D 659 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP D 661 " --> pdb=" O LYS D 546 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU D 548 " --> pdb=" O ASP D 661 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N PHE D 719 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE D 692 " --> pdb=" O PHE D 719 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1818 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: 3.00 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1554 1.32 - 1.44: 2596 1.44 - 1.57: 6258 1.57 - 1.69: 6 1.69 - 1.81: 56 Bond restraints: 10470 Sorted by residual: bond pdb=" O2 LBN C 806 " pdb=" P1 LBN C 806 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" O2 LBN D 806 " pdb=" P1 LBN D 806 " ideal model delta sigma weight residual 1.650 1.597 0.053 2.00e-02 2.50e+03 7.15e+00 bond pdb=" O1 LBN D 806 " pdb=" P1 LBN D 806 " ideal model delta sigma weight residual 1.632 1.595 0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" O1 LBN C 806 " pdb=" P1 LBN C 806 " ideal model delta sigma weight residual 1.632 1.596 0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" C1 LBN D 806 " pdb=" O1 LBN D 806 " ideal model delta sigma weight residual 1.410 1.444 -0.034 2.00e-02 2.50e+03 2.81e+00 ... (remaining 10465 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.29: 289 106.29 - 113.23: 6057 113.23 - 120.16: 3665 120.16 - 127.10: 4138 127.10 - 134.04: 81 Bond angle restraints: 14230 Sorted by residual: angle pdb=" CA LYS D 66 " pdb=" CB LYS D 66 " pdb=" CG LYS D 66 " ideal model delta sigma weight residual 114.10 122.36 -8.26 2.00e+00 2.50e-01 1.71e+01 angle pdb=" CA LYS C 66 " pdb=" CB LYS C 66 " pdb=" CG LYS C 66 " ideal model delta sigma weight residual 114.10 122.32 -8.22 2.00e+00 2.50e-01 1.69e+01 angle pdb=" C ILE C 491 " pdb=" N LEU C 492 " pdb=" CA LEU C 492 " ideal model delta sigma weight residual 121.54 128.79 -7.25 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C ILE D 491 " pdb=" N LEU D 492 " pdb=" CA LEU D 492 " ideal model delta sigma weight residual 121.54 128.69 -7.15 1.91e+00 2.74e-01 1.40e+01 angle pdb=" CB LYS D 66 " pdb=" CG LYS D 66 " pdb=" CD LYS D 66 " ideal model delta sigma weight residual 111.30 119.75 -8.45 2.30e+00 1.89e-01 1.35e+01 ... (remaining 14225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 6651 33.26 - 66.51: 285 66.51 - 99.77: 40 99.77 - 133.02: 56 133.02 - 166.28: 6 Dihedral angle restraints: 7038 sinusoidal: 3488 harmonic: 3550 Sorted by residual: dihedral pdb=" CA VAL D 722 " pdb=" C VAL D 722 " pdb=" N HIS D 723 " pdb=" CA HIS D 723 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA VAL C 722 " pdb=" C VAL C 722 " pdb=" N HIS C 723 " pdb=" CA HIS C 723 " ideal model delta harmonic sigma weight residual 180.00 150.98 29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CBS AV0 D 815 " pdb=" C1 AV0 D 815 " pdb=" O1 AV0 D 815 " pdb=" O5 AV0 D 815 " ideal model delta sinusoidal sigma weight residual 85.89 -80.39 166.28 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 7035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1403 0.052 - 0.105: 298 0.105 - 0.157: 42 0.157 - 0.209: 9 0.209 - 0.262: 4 Chirality restraints: 1756 Sorted by residual: chirality pdb=" CB VAL C 559 " pdb=" CA VAL C 559 " pdb=" CG1 VAL C 559 " pdb=" CG2 VAL C 559 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C2 LBN D 806 " pdb=" C1 LBN D 806 " pdb=" C3 LBN D 806 " pdb=" O7 LBN D 806 " both_signs ideal model delta sigma weight residual False -2.36 -2.59 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C2 LBN C 806 " pdb=" C1 LBN C 806 " pdb=" C3 LBN C 806 " pdb=" O7 LBN C 806 " both_signs ideal model delta sigma weight residual False -2.36 -2.58 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1753 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 141 " -0.047 5.00e-02 4.00e+02 7.15e-02 8.18e+00 pdb=" N PRO D 142 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 142 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 142 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 141 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO C 142 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 139 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO D 140 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 140 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 140 " -0.028 5.00e-02 4.00e+02 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 392 2.72 - 3.27: 10565 3.27 - 3.81: 17515 3.81 - 4.36: 21654 4.36 - 4.90: 36283 Nonbonded interactions: 86409 Sorted by model distance: nonbonded pdb=" O PRO C 553 " pdb=" ND2 ASN C 558 " model vdw 2.180 3.120 nonbonded pdb=" O PRO D 553 " pdb=" ND2 ASN D 558 " model vdw 2.188 3.120 nonbonded pdb=" OH TYR D 247 " pdb=" OE1 GLU D 259 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR C 247 " pdb=" OE1 GLU C 259 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR D 78 " pdb=" OD2 ASP D 87 " model vdw 2.240 3.040 ... (remaining 86404 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 'C' selection = chain 'D' } 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.100 Process input model: 30.380 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.004 0.054 10470 Z= 0.256 Angle : 0.665 10.383 14230 Z= 0.325 Chirality : 0.045 0.262 1756 Planarity : 0.004 0.072 1628 Dihedral : 21.914 166.280 4750 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.53 % Allowed : 17.02 % Favored : 81.45 % 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: 1.07 (0.24), residues: 1210 helix: 1.74 (0.19), residues: 788 sheet: 1.90 (0.71), residues: 34 loop : -1.65 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 74 HIS 0.003 0.001 HIS C 656 PHE 0.017 0.001 PHE D 141 TYR 0.012 0.001 TYR D 371 ARG 0.009 0.000 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.159 Fit side-chains REVERT: C 187 LEU cc_start: 0.8288 (mt) cc_final: 0.7987 (mm) REVERT: D 187 LEU cc_start: 0.8299 (mt) cc_final: 0.7992 (mm) outliers start: 16 outliers final: 14 residues processed: 141 average time/residue: 0.6699 time to fit residues: 108.2856 Evaluate side-chains 141 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 559 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 0.3980 chunk 71 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN C 684 GLN C 689 HIS D 248 ASN D 684 GLN D 689 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10470 Z= 0.266 Angle : 0.688 10.448 14230 Z= 0.335 Chirality : 0.046 0.231 1756 Planarity : 0.005 0.080 1628 Dihedral : 17.407 160.161 2621 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.21 % Favored : 94.63 % Rotamer: Outliers : 3.35 % Allowed : 14.72 % Favored : 81.93 % 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: 1.08 (0.25), residues: 1210 helix: 1.64 (0.18), residues: 798 sheet: 0.95 (0.68), residues: 50 loop : -1.44 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 74 HIS 0.002 0.001 HIS C 656 PHE 0.022 0.002 PHE D 141 TYR 0.015 0.002 TYR C 371 ARG 0.005 0.001 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.053 Fit side-chains REVERT: C 187 LEU cc_start: 0.8303 (mt) cc_final: 0.8005 (mm) REVERT: D 187 LEU cc_start: 0.8313 (mt) cc_final: 0.8009 (mm) outliers start: 35 outliers final: 15 residues processed: 159 average time/residue: 0.8238 time to fit residues: 146.3811 Evaluate side-chains 131 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 684 GLN C 689 HIS D 684 GLN D 689 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10470 Z= 0.359 Angle : 0.691 9.079 14230 Z= 0.342 Chirality : 0.048 0.266 1756 Planarity : 0.005 0.081 1628 Dihedral : 16.324 158.994 2613 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.96 % Favored : 94.88 % Rotamer: Outliers : 4.11 % Allowed : 14.91 % Favored : 80.98 % 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: 0.89 (0.24), residues: 1210 helix: 1.45 (0.18), residues: 806 sheet: 0.87 (0.66), residues: 50 loop : -1.47 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 74 HIS 0.003 0.001 HIS D 656 PHE 0.022 0.002 PHE D 161 TYR 0.019 0.002 TYR C 371 ARG 0.005 0.001 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 1.183 Fit side-chains REVERT: C 103 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8412 (mtp) REVERT: C 187 LEU cc_start: 0.8320 (mt) cc_final: 0.8025 (mm) REVERT: C 560 ASP cc_start: 0.7387 (m-30) cc_final: 0.7129 (m-30) REVERT: D 103 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8453 (mtp) REVERT: D 187 LEU cc_start: 0.8331 (mt) cc_final: 0.8030 (mm) REVERT: D 217 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7913 (m-30) outliers start: 43 outliers final: 24 residues processed: 151 average time/residue: 0.9186 time to fit residues: 153.1567 Evaluate side-chains 140 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 459 LYS Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 678 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 0.0770 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 689 HIS D 684 GLN D 689 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10470 Z= 0.186 Angle : 0.637 15.918 14230 Z= 0.309 Chirality : 0.045 0.324 1756 Planarity : 0.005 0.085 1628 Dihedral : 15.071 154.253 2613 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 3.54 % Allowed : 16.63 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1210 helix: 1.70 (0.18), residues: 808 sheet: 0.82 (0.64), residues: 50 loop : -1.43 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 74 HIS 0.002 0.001 HIS D 656 PHE 0.023 0.001 PHE C 141 TYR 0.014 0.001 TYR D 371 ARG 0.008 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 1.195 Fit side-chains REVERT: C 103 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8340 (mtp) REVERT: C 187 LEU cc_start: 0.8314 (mt) cc_final: 0.8020 (mm) REVERT: C 560 ASP cc_start: 0.7293 (m-30) cc_final: 0.6936 (m-30) REVERT: D 103 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8355 (mtp) REVERT: D 187 LEU cc_start: 0.8325 (mt) cc_final: 0.8025 (mm) REVERT: D 704 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7752 (pt0) outliers start: 37 outliers final: 21 residues processed: 149 average time/residue: 0.8325 time to fit residues: 138.2672 Evaluate side-chains 139 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 689 HIS D 689 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10470 Z= 0.187 Angle : 0.625 12.195 14230 Z= 0.304 Chirality : 0.046 0.334 1756 Planarity : 0.005 0.083 1628 Dihedral : 14.474 151.735 2613 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.12 % Rotamer: Outliers : 3.82 % Allowed : 16.73 % Favored : 79.45 % 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: 1.24 (0.24), residues: 1210 helix: 1.77 (0.18), residues: 802 sheet: 0.69 (0.64), residues: 50 loop : -1.38 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 74 HIS 0.002 0.001 HIS D 656 PHE 0.022 0.001 PHE D 141 TYR 0.014 0.001 TYR D 371 ARG 0.007 0.000 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 118 time to evaluate : 1.170 Fit side-chains REVERT: C 66 LYS cc_start: 0.6223 (tppt) cc_final: 0.6017 (tppt) REVERT: C 103 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8335 (mtp) REVERT: C 187 LEU cc_start: 0.8329 (mt) cc_final: 0.8030 (mm) REVERT: C 560 ASP cc_start: 0.7355 (m-30) cc_final: 0.6959 (m-30) REVERT: D 66 LYS cc_start: 0.6271 (tppt) cc_final: 0.6032 (tppt) REVERT: D 103 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8348 (mtp) REVERT: D 187 LEU cc_start: 0.8319 (mt) cc_final: 0.8014 (mm) REVERT: D 704 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7751 (pt0) outliers start: 40 outliers final: 27 residues processed: 144 average time/residue: 0.8658 time to fit residues: 138.6146 Evaluate side-chains 146 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.0970 chunk 118 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.1980 chunk 61 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 684 GLN C 689 HIS D 689 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10470 Z= 0.162 Angle : 0.589 9.570 14230 Z= 0.289 Chirality : 0.044 0.298 1756 Planarity : 0.005 0.079 1628 Dihedral : 13.374 148.811 2613 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.04 % Favored : 94.79 % Rotamer: Outliers : 3.35 % Allowed : 17.02 % Favored : 79.64 % 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: 1.38 (0.25), residues: 1210 helix: 1.88 (0.18), residues: 802 sheet: 0.66 (0.64), residues: 50 loop : -1.34 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 482 HIS 0.002 0.001 HIS D 656 PHE 0.022 0.001 PHE C 141 TYR 0.012 0.001 TYR D 371 ARG 0.007 0.000 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 1.095 Fit side-chains REVERT: C 103 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8294 (mtp) REVERT: C 187 LEU cc_start: 0.8310 (mt) cc_final: 0.8005 (mm) REVERT: C 320 GLU cc_start: 0.7907 (tp30) cc_final: 0.6977 (pm20) REVERT: D 103 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8302 (mtp) REVERT: D 187 LEU cc_start: 0.8316 (mt) cc_final: 0.8005 (mm) REVERT: D 701 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7524 (mm-30) outliers start: 35 outliers final: 25 residues processed: 148 average time/residue: 0.8354 time to fit residues: 137.4659 Evaluate side-chains 144 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 678 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 117 optimal weight: 0.0970 chunk 73 optimal weight: 0.0000 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 689 HIS D 689 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10470 Z= 0.168 Angle : 0.595 8.273 14230 Z= 0.290 Chirality : 0.044 0.339 1756 Planarity : 0.005 0.079 1628 Dihedral : 12.825 146.913 2613 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 3.35 % Allowed : 17.30 % Favored : 79.35 % 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: 1.49 (0.25), residues: 1210 helix: 1.96 (0.18), residues: 800 sheet: 0.58 (0.63), residues: 50 loop : -1.22 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 PHE 0.022 0.001 PHE D 141 TYR 0.013 0.001 TYR D 371 ARG 0.006 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 1.153 Fit side-chains REVERT: C 66 LYS cc_start: 0.5936 (mmmt) cc_final: 0.5274 (tppt) REVERT: C 187 LEU cc_start: 0.8316 (mt) cc_final: 0.8011 (mm) REVERT: C 320 GLU cc_start: 0.7879 (tp30) cc_final: 0.7047 (pm20) REVERT: D 66 LYS cc_start: 0.6025 (mmmt) cc_final: 0.5375 (tppt) REVERT: D 187 LEU cc_start: 0.8322 (mt) cc_final: 0.8008 (mm) outliers start: 35 outliers final: 23 residues processed: 146 average time/residue: 0.7940 time to fit residues: 129.5939 Evaluate side-chains 141 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 678 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 689 HIS D 684 GLN D 689 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10470 Z= 0.228 Angle : 0.629 8.813 14230 Z= 0.308 Chirality : 0.046 0.356 1756 Planarity : 0.005 0.078 1628 Dihedral : 12.759 145.296 2611 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.96 % Favored : 94.88 % Rotamer: Outliers : 3.25 % Allowed : 17.69 % Favored : 79.06 % 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: 1.34 (0.25), residues: 1210 helix: 1.80 (0.18), residues: 812 sheet: 0.56 (0.63), residues: 50 loop : -1.29 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 74 HIS 0.002 0.001 HIS D 656 PHE 0.021 0.001 PHE C 141 TYR 0.015 0.001 TYR C 371 ARG 0.008 0.001 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 1.160 Fit side-chains REVERT: C 66 LYS cc_start: 0.6028 (mmmt) cc_final: 0.5411 (tppt) REVERT: C 187 LEU cc_start: 0.8340 (mt) cc_final: 0.8030 (mm) REVERT: C 217 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: C 320 GLU cc_start: 0.7901 (tp30) cc_final: 0.7124 (pm20) REVERT: C 560 ASP cc_start: 0.7353 (m-30) cc_final: 0.6962 (m-30) REVERT: D 66 LYS cc_start: 0.6083 (mmmt) cc_final: 0.5451 (tppt) REVERT: D 187 LEU cc_start: 0.8351 (mt) cc_final: 0.8033 (mm) REVERT: D 320 GLU cc_start: 0.7955 (tp30) cc_final: 0.7087 (pm20) outliers start: 34 outliers final: 21 residues processed: 145 average time/residue: 1.0103 time to fit residues: 160.2884 Evaluate side-chains 136 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 678 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9980 chunk 102 optimal weight: 0.3980 chunk 109 optimal weight: 0.0970 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 689 HIS D 684 GLN D 689 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10470 Z= 0.165 Angle : 0.592 8.320 14230 Z= 0.291 Chirality : 0.044 0.359 1756 Planarity : 0.005 0.081 1628 Dihedral : 12.213 144.445 2609 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.04 % Favored : 94.79 % Rotamer: Outliers : 2.87 % Allowed : 17.88 % Favored : 79.25 % 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 (0.25), residues: 1210 helix: 1.85 (0.18), residues: 814 sheet: 0.57 (0.63), residues: 50 loop : -1.23 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 PHE 0.023 0.001 PHE C 141 TYR 0.013 0.001 TYR C 371 ARG 0.007 0.000 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 1.080 Fit side-chains REVERT: C 66 LYS cc_start: 0.5894 (mmmt) cc_final: 0.5353 (tppt) REVERT: C 187 LEU cc_start: 0.8326 (mt) cc_final: 0.8026 (mm) REVERT: C 217 ASP cc_start: 0.8102 (m-30) cc_final: 0.7815 (m-30) REVERT: C 320 GLU cc_start: 0.7879 (tp30) cc_final: 0.7180 (pm20) REVERT: D 66 LYS cc_start: 0.5897 (mmmt) cc_final: 0.5362 (tppt) REVERT: D 187 LEU cc_start: 0.8316 (mt) cc_final: 0.8010 (mm) outliers start: 30 outliers final: 21 residues processed: 143 average time/residue: 0.8253 time to fit residues: 131.4884 Evaluate side-chains 138 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 678 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 80 optimal weight: 8.9990 chunk 121 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 689 HIS D 684 GLN D 689 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10470 Z= 0.175 Angle : 0.596 8.153 14230 Z= 0.294 Chirality : 0.044 0.341 1756 Planarity : 0.005 0.079 1628 Dihedral : 11.977 142.253 2609 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.04 % Favored : 94.79 % Rotamer: Outliers : 2.01 % Allowed : 19.12 % Favored : 78.87 % 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: 1.38 (0.25), residues: 1210 helix: 1.84 (0.18), residues: 816 sheet: 0.55 (0.63), residues: 50 loop : -1.32 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 74 HIS 0.002 0.001 HIS C 656 PHE 0.022 0.001 PHE D 141 TYR 0.014 0.001 TYR D 371 ARG 0.007 0.000 ARG D 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.103 Fit side-chains REVERT: C 66 LYS cc_start: 0.5828 (mmmt) cc_final: 0.5339 (tppt) REVERT: C 187 LEU cc_start: 0.8328 (mt) cc_final: 0.8019 (mm) REVERT: C 217 ASP cc_start: 0.8101 (m-30) cc_final: 0.7823 (m-30) REVERT: C 318 ASN cc_start: 0.8244 (t0) cc_final: 0.7999 (t0) REVERT: C 320 GLU cc_start: 0.7883 (tp30) cc_final: 0.7182 (pm20) REVERT: C 701 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7337 (pt0) REVERT: D 66 LYS cc_start: 0.5832 (mmmt) cc_final: 0.5322 (tppt) REVERT: D 187 LEU cc_start: 0.8328 (mt) cc_final: 0.8011 (mm) REVERT: D 701 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7326 (pt0) outliers start: 21 outliers final: 20 residues processed: 134 average time/residue: 0.8894 time to fit residues: 132.5211 Evaluate side-chains 137 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 678 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.5980 chunk 89 optimal weight: 0.0170 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 689 HIS D 684 GLN D 689 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.145750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113897 restraints weight = 12670.904| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.15 r_work: 0.3359 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10470 Z= 0.157 Angle : 0.576 8.157 14230 Z= 0.285 Chirality : 0.043 0.269 1756 Planarity : 0.005 0.078 1628 Dihedral : 11.550 139.507 2609 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.71 % Rotamer: Outliers : 2.29 % Allowed : 18.83 % Favored : 78.87 % 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: 1.47 (0.25), residues: 1210 helix: 1.91 (0.18), residues: 814 sheet: 0.56 (0.63), residues: 50 loop : -1.26 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 482 HIS 0.002 0.001 HIS C 698 PHE 0.022 0.001 PHE D 141 TYR 0.012 0.001 TYR D 371 ARG 0.007 0.000 ARG C 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3311.02 seconds wall clock time: 59 minutes 13.03 seconds (3553.03 seconds total)