Starting phenix.real_space_refine on Sat Jul 20 06:27:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/07_2024/8uuk_42588.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/07_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_42588/07_2024/8uuk_42588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/07_2024/8uuk_42588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/07_2024/8uuk_42588.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uuk_42588/07_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-5388/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: 6.81, per 1000 atoms: 0.66 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: 4.37 Conformation dependent library (CDL) restraints added in 2.0 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: 1.11 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: 3.33 Time building geometry restraints manager: 4.64 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 2.520 nonbonded pdb=" O PRO D 553 " pdb=" ND2 ASN D 558 " model vdw 2.188 2.520 nonbonded pdb=" OH TYR D 247 " pdb=" OE1 GLU D 259 " model vdw 2.229 2.440 nonbonded pdb=" OH TYR C 247 " pdb=" OE1 GLU C 259 " model vdw 2.233 2.440 nonbonded pdb=" OH TYR D 78 " pdb=" OD2 ASP D 87 " model vdw 2.240 2.440 ... (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 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: 1.300 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.820 Find NCS groups from input model: 0.410 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:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.980 ------------------------------------------------------------------------------- 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 : 1.101 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: 0.6483 time to fit residues: 104.6081 Evaluate side-chains 141 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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: 0.8980 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8040 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10470 Z= 0.227 Angle : 0.654 9.675 14230 Z= 0.316 Chirality : 0.045 0.232 1756 Planarity : 0.005 0.079 1628 Dihedral : 16.961 159.496 2621 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.37 % Favored : 94.46 % Rotamer: Outliers : 3.73 % Allowed : 14.53 % Favored : 81.74 % 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: 1.21 (0.25), residues: 1210 helix: 1.76 (0.19), residues: 798 sheet: 0.94 (0.68), residues: 50 loop : -1.45 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 74 HIS 0.002 0.001 HIS D 689 PHE 0.024 0.002 PHE D 141 TYR 0.013 0.002 TYR C 371 ARG 0.005 0.000 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 174 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 1.222 Fit side-chains REVERT: C 187 LEU cc_start: 0.8295 (mt) cc_final: 0.8005 (mm) REVERT: C 560 ASP cc_start: 0.7288 (m-30) cc_final: 0.7003 (m-30) REVERT: D 187 LEU cc_start: 0.8306 (mt) cc_final: 0.8010 (mm) REVERT: D 503 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7609 (mmp) outliers start: 39 outliers final: 20 residues processed: 164 average time/residue: 0.8376 time to fit residues: 152.6912 Evaluate side-chains 142 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 333 ARG Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR 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 252 SER Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 503 MET 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 704 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 0.0000 overall best weight: 1.9992 ------------------------------------------------------------------------------- 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 ** C 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 684 GLN D 689 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10470 Z= 0.321 Angle : 0.673 9.094 14230 Z= 0.332 Chirality : 0.047 0.274 1756 Planarity : 0.005 0.080 1628 Dihedral : 16.172 158.822 2613 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.04 % Favored : 94.79 % Rotamer: Outliers : 4.21 % Allowed : 15.49 % Favored : 80.31 % 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: 0.99 (0.24), residues: 1210 helix: 1.53 (0.18), residues: 806 sheet: 0.87 (0.66), residues: 50 loop : -1.44 (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 698 PHE 0.021 0.002 PHE C 141 TYR 0.018 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 164 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 120 time to evaluate : 1.133 Fit side-chains REVERT: C 103 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8414 (mtp) REVERT: C 187 LEU cc_start: 0.8302 (mt) cc_final: 0.8007 (mm) REVERT: C 333 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7982 (mmt-90) REVERT: C 560 ASP cc_start: 0.7361 (m-30) cc_final: 0.7023 (m-30) REVERT: D 103 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8431 (mtp) REVERT: D 187 LEU cc_start: 0.8312 (mt) cc_final: 0.8013 (mm) REVERT: D 333 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7970 (mmt-90) outliers start: 44 outliers final: 20 residues processed: 151 average time/residue: 0.9489 time to fit residues: 158.1468 Evaluate side-chains 138 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 333 ARG Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR 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 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 333 ARG Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 6.9990 chunk 57 optimal weight: 0.0770 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 ASN C 684 GLN C 689 HIS D 684 GLN D 689 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10470 Z= 0.197 Angle : 0.639 16.615 14230 Z= 0.305 Chirality : 0.045 0.345 1756 Planarity : 0.005 0.086 1628 Dihedral : 14.881 154.072 2613 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 3.82 % Allowed : 17.69 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1210 helix: 1.77 (0.19), residues: 802 sheet: 0.90 (0.65), residues: 50 loop : -1.40 (0.32), residues: 358 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 0.023 0.001 PHE C 141 TYR 0.015 0.001 TYR D 371 ARG 0.005 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 165 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 125 time to evaluate : 0.999 Fit side-chains REVERT: C 103 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8356 (mtp) REVERT: C 187 LEU cc_start: 0.8299 (mt) cc_final: 0.7998 (mm) REVERT: C 560 ASP cc_start: 0.7276 (m-30) cc_final: 0.6961 (m-30) REVERT: C 704 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7747 (pt0) REVERT: D 103 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8371 (mtp) REVERT: D 187 LEU cc_start: 0.8308 (mt) cc_final: 0.8006 (mm) REVERT: D 704 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7759 (pt0) outliers start: 40 outliers final: 19 residues processed: 148 average time/residue: 0.8320 time to fit residues: 136.9740 Evaluate side-chains 143 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 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 103 MET 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 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: 7.9990 chunk 1 optimal weight: 0.4980 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.8069 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10470 Z= 0.208 Angle : 0.626 11.525 14230 Z= 0.302 Chirality : 0.045 0.341 1756 Planarity : 0.005 0.084 1628 Dihedral : 14.276 150.943 2613 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.63 % Favored : 95.21 % Rotamer: Outliers : 3.35 % Allowed : 18.16 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1210 helix: 1.79 (0.18), residues: 802 sheet: 0.79 (0.64), residues: 50 loop : -1.34 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 74 HIS 0.002 0.001 HIS C 656 PHE 0.021 0.001 PHE C 141 TYR 0.015 0.001 TYR D 371 ARG 0.006 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 161 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 1.172 Fit side-chains REVERT: C 103 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8386 (mtp) REVERT: C 187 LEU cc_start: 0.8306 (mt) cc_final: 0.8006 (mm) REVERT: C 560 ASP cc_start: 0.7338 (m-30) cc_final: 0.6939 (m-30) REVERT: C 704 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7763 (pt0) REVERT: D 103 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8400 (mtp) REVERT: D 187 LEU cc_start: 0.8314 (mt) cc_final: 0.8010 (mm) REVERT: D 704 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7756 (pt0) outliers start: 35 outliers final: 21 residues processed: 145 average time/residue: 0.8954 time to fit residues: 143.9309 Evaluate side-chains 146 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 385 PHE Chi-restraints excluded: chain C residue 404 THR 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 678 MET 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 103 MET 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 404 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 0.0000 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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: 0.8041 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10470 Z= 0.175 Angle : 0.596 10.467 14230 Z= 0.289 Chirality : 0.044 0.280 1756 Planarity : 0.005 0.082 1628 Dihedral : 13.492 148.285 2613 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.12 % Rotamer: Outliers : 3.15 % Allowed : 18.55 % Favored : 78.30 % 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: 1.44 (0.25), residues: 1210 helix: 1.89 (0.19), residues: 806 sheet: 0.75 (0.63), residues: 50 loop : -1.25 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 74 HIS 0.002 0.001 HIS C 656 PHE 0.022 0.001 PHE C 141 TYR 0.013 0.001 TYR D 371 ARG 0.008 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 163 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 130 time to evaluate : 1.166 Fit side-chains REVERT: C 66 LYS cc_start: 0.6202 (tppt) cc_final: 0.5984 (tppt) REVERT: C 103 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8324 (mtp) REVERT: C 187 LEU cc_start: 0.8305 (mt) cc_final: 0.7997 (mm) REVERT: C 701 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7412 (mm-30) REVERT: C 704 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7811 (pt0) REVERT: D 66 LYS cc_start: 0.6211 (tppt) cc_final: 0.6007 (tppt) REVERT: D 187 LEU cc_start: 0.8313 (mt) cc_final: 0.8001 (mm) REVERT: D 329 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8265 (ttmm) REVERT: D 704 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7805 (pt0) outliers start: 33 outliers final: 21 residues processed: 145 average time/residue: 0.8607 time to fit residues: 138.4268 Evaluate side-chains 152 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 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 556 TYR Chi-restraints excluded: chain C residue 678 MET 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 248 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 329 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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: 0.8093 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10470 Z= 0.258 Angle : 0.640 8.661 14230 Z= 0.312 Chirality : 0.046 0.280 1756 Planarity : 0.005 0.080 1628 Dihedral : 13.626 146.249 2613 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 3.82 % Allowed : 18.45 % Favored : 77.72 % 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: 1.26 (0.25), residues: 1210 helix: 1.71 (0.18), residues: 810 sheet: 0.72 (0.63), residues: 50 loop : -1.25 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 74 HIS 0.003 0.001 HIS D 698 PHE 0.021 0.002 PHE C 141 TYR 0.017 0.002 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 155 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 115 time to evaluate : 1.144 Fit side-chains REVERT: C 66 LYS cc_start: 0.6263 (tppt) cc_final: 0.5911 (tppt) REVERT: C 187 LEU cc_start: 0.8325 (mt) cc_final: 0.8022 (mm) REVERT: C 560 ASP cc_start: 0.7396 (m-30) cc_final: 0.7031 (m-30) REVERT: C 704 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7771 (pt0) REVERT: D 66 LYS cc_start: 0.6350 (tppt) cc_final: 0.6019 (tppt) REVERT: D 187 LEU cc_start: 0.8334 (mt) cc_final: 0.8027 (mm) REVERT: D 329 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8307 (ttmm) REVERT: D 704 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7793 (pt0) outliers start: 40 outliers final: 22 residues processed: 140 average time/residue: 1.0113 time to fit residues: 154.7302 Evaluate side-chains 141 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR 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 678 MET 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 248 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.4980 chunk 70 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.8056 moved from start: 0.1886 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= 0.184 Angle : 0.597 8.231 14230 Z= 0.292 Chirality : 0.044 0.303 1756 Planarity : 0.005 0.083 1628 Dihedral : 13.119 145.891 2613 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 3.06 % Allowed : 18.93 % Favored : 78.01 % 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 (0.19), residues: 806 sheet: 0.72 (0.62), residues: 50 loop : -1.20 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 74 HIS 0.002 0.001 HIS C 656 PHE 0.023 0.001 PHE D 141 TYR 0.014 0.001 TYR D 371 ARG 0.006 0.000 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 153 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 1.113 Fit side-chains REVERT: C 187 LEU cc_start: 0.8306 (mt) cc_final: 0.7999 (mm) REVERT: C 560 ASP cc_start: 0.7244 (m-30) cc_final: 0.6916 (m-30) REVERT: C 704 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7802 (pt0) REVERT: D 187 LEU cc_start: 0.8311 (mt) cc_final: 0.8000 (mm) REVERT: D 217 ASP cc_start: 0.8169 (m-30) cc_final: 0.7888 (m-30) REVERT: D 320 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: D 704 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7763 (pt0) outliers start: 32 outliers final: 18 residues processed: 141 average time/residue: 0.9164 time to fit residues: 142.0452 Evaluate side-chains 139 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 678 MET 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 248 ASN Chi-restraints excluded: chain D residue 320 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.8980 chunk 102 optimal weight: 0.0870 chunk 109 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 0.0270 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 689 HIS D 266 ASN D 689 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10470 Z= 0.161 Angle : 0.586 9.332 14230 Z= 0.286 Chirality : 0.043 0.362 1756 Planarity : 0.005 0.081 1628 Dihedral : 12.335 144.133 2613 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 2.58 % Allowed : 19.60 % Favored : 77.82 % 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: 1.52 (0.25), residues: 1210 helix: 1.94 (0.19), residues: 806 sheet: 0.65 (0.62), residues: 50 loop : -1.19 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.002 0.001 HIS C 656 PHE 0.022 0.001 PHE C 141 TYR 0.012 0.001 TYR D 371 ARG 0.008 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 154 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 1.083 Fit side-chains REVERT: C 66 LYS cc_start: 0.6018 (mmmt) cc_final: 0.5477 (tppt) REVERT: C 187 LEU cc_start: 0.8296 (mt) cc_final: 0.7989 (mm) REVERT: C 320 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7252 (pm20) REVERT: D 66 LYS cc_start: 0.6131 (mmmt) cc_final: 0.5566 (tppt) REVERT: D 187 LEU cc_start: 0.8306 (mt) cc_final: 0.7995 (mm) REVERT: D 320 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7370 (pm20) outliers start: 27 outliers final: 18 residues processed: 143 average time/residue: 0.8793 time to fit residues: 139.8336 Evaluate side-chains 143 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 320 GLU 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 678 MET 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 320 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10470 Z= 0.194 Angle : 0.599 9.037 14230 Z= 0.292 Chirality : 0.044 0.363 1756 Planarity : 0.005 0.081 1628 Dihedral : 12.213 142.021 2613 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.04 % Favored : 94.79 % Rotamer: Outliers : 2.49 % Allowed : 19.89 % Favored : 77.63 % 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: 1.50 (0.25), residues: 1210 helix: 1.93 (0.19), residues: 806 sheet: 0.65 (0.63), residues: 50 loop : -1.20 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 74 HIS 0.002 0.001 HIS D 698 PHE 0.021 0.001 PHE C 141 TYR 0.013 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 145 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 1.158 Fit side-chains REVERT: C 66 LYS cc_start: 0.6079 (mmmt) cc_final: 0.5511 (tppt) REVERT: C 187 LEU cc_start: 0.8315 (mt) cc_final: 0.7996 (mm) REVERT: C 320 GLU cc_start: 0.7920 (tp30) cc_final: 0.7236 (pm20) REVERT: D 66 LYS cc_start: 0.6114 (mmmt) cc_final: 0.5596 (tppt) REVERT: D 187 LEU cc_start: 0.8324 (mt) cc_final: 0.8001 (mm) REVERT: D 320 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7373 (pm20) outliers start: 26 outliers final: 18 residues processed: 137 average time/residue: 0.8336 time to fit residues: 127.1127 Evaluate side-chains 139 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 678 MET 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 320 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.0470 chunk 89 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112488 restraints weight = 12678.515| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.15 r_work: 0.3342 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10470 Z= 0.171 Angle : 0.576 8.872 14230 Z= 0.284 Chirality : 0.043 0.310 1756 Planarity : 0.005 0.081 1628 Dihedral : 11.841 140.620 2613 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 2.10 % Allowed : 20.17 % Favored : 77.72 % 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: 1.53 (0.25), residues: 1210 helix: 1.95 (0.19), residues: 810 sheet: 0.66 (0.62), residues: 50 loop : -1.22 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.002 0.001 HIS C 656 PHE 0.022 0.001 PHE C 141 TYR 0.012 0.001 TYR D 371 ARG 0.007 0.000 ARG D 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3401.33 seconds wall clock time: 60 minutes 41.63 seconds (3641.63 seconds total)