Starting phenix.real_space_refine on Fri Jan 19 00:04:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msw_23970/01_2024/7msw_23970.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msw_23970/01_2024/7msw_23970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msw_23970/01_2024/7msw_23970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msw_23970/01_2024/7msw_23970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msw_23970/01_2024/7msw_23970.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7msw_23970/01_2024/7msw_23970.pdb" } resolution = 3.76 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= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 S 37 5.16 5 C 3133 2.51 5 N 817 2.21 5 O 932 1.98 5 H 4959 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9881 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 9881 Unusual residues: {' ZN': 3} Inner-chain residues flagged as termini: ['pdbres="GLY A 638 "'] Classifications: {'peptide': 635, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 612, None: 3} Not linked: pdbres="GLY A 638 " pdbres=" ZN A 701 " Not linked: pdbres=" ZN A 701 " pdbres=" ZN A 702 " Not linked: pdbres=" ZN A 702 " pdbres=" ZN A 703 " List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2239 SG CYS A 143 47.628 57.591 57.381 1.00 70.33 S ATOM 2279 SG CYS A 146 49.040 58.391 61.057 1.00 79.12 S ATOM 2493 SG CYS A 161 46.730 54.355 58.766 1.00 64.88 S ATOM 2539 SG CYS A 164 45.709 57.421 60.597 1.00 64.69 S ATOM 2922 SG CYS A 190 25.012 58.630 43.266 1.00 82.05 S ATOM 2957 SG CYS A 193 21.329 59.123 44.523 1.00116.32 S ATOM 3590 SG CYS A 236 23.238 55.260 42.398 1.00102.03 S ATOM 247 SG CYS A 20 49.958 45.672 18.693 1.00 90.92 S ATOM 727 SG CYS A 51 52.351 44.160 16.412 1.00126.07 S Time building chain proxies: 4.83, per 1000 atoms: 0.49 Number of scatterers: 9881 At special positions: 0 Unit cell: (72.558, 80.064, 145.116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 37 16.00 O 932 8.00 N 817 7.00 C 3133 6.00 H 4959 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.24 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 146 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 143 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 164 " pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 202 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 190 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 236 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 193 " pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" ND1 HIS A 54 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 56 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 51 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 20 " Number of angles added : 11 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 36.1% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 18 through 28 Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 114 through 124 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.530A pdb=" N HIS A 194 " --> pdb=" O CYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 262 through 275 removed outlier: 3.525A pdb=" N LEU A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 315 through 325 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 378 through 394 Processing helix chain 'A' and resid 396 through 408 removed outlier: 3.538A pdb=" N SER A 408 " --> pdb=" O MET A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 444 through 455 removed outlier: 3.986A pdb=" N LEU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 460 removed outlier: 6.653A pdb=" N VAL A 459 " --> pdb=" O LYS A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 492 through 508 Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 removed outlier: 7.399A pdb=" N VAL A 6 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR A 61 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ALA A 59 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LYS A 82 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR A 61 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA A 80 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU A 63 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYS A 78 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ALA A 184 " --> pdb=" O PRO A 245 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASN A 133 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LYS A 187 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 6 through 7 removed outlier: 7.399A pdb=" N VAL A 6 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR A 61 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ALA A 59 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LYS A 82 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR A 61 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA A 80 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU A 63 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYS A 78 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 235 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 244 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR A 233 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ARG A 246 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N PHE A 231 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER A 248 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N CYS A 229 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYR A 233 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ARG A 222 " --> pdb=" O TYR A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.817A pdb=" N LEU A 137 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 334 removed outlier: 6.152A pdb=" N VAL A 279 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N THR A 332 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE A 281 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLY A 334 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE A 283 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 478 through 480 Processing sheet with id=AA6, first strand: chain 'A' and resid 510 through 515 Processing sheet with id=AA7, first strand: chain 'A' and resid 566 through 567 removed outlier: 4.173A pdb=" N VAL A 628 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ALA A 621 " --> pdb=" O THR A 629 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN A 631 " --> pdb=" O TYR A 619 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TYR A 619 " --> pdb=" O ASN A 631 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N MET A 609 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 577 " --> pdb=" O CYS A 604 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 566 through 567 removed outlier: 4.173A pdb=" N VAL A 628 " --> pdb=" O LEU A 567 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 597 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: 3.80 Time building geometry restraints manager: 8.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 4932 1.13 - 1.30: 833 1.30 - 1.47: 1932 1.47 - 1.64: 2226 1.64 - 1.81: 47 Bond restraints: 9970 Sorted by residual: bond pdb=" CD2 PHE A 300 " pdb=" HD2 PHE A 300 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" CD1 PHE A 368 " pdb=" HD1 PHE A 368 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" CD2 PHE A 83 " pdb=" HD2 PHE A 83 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" CD2 PHE A 307 " pdb=" HD2 PHE A 307 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" CD2 PHE A 86 " pdb=" HD2 PHE A 86 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.48e+01 ... (remaining 9965 not shown) Histogram of bond angle deviations from ideal: 95.93 - 103.54: 74 103.54 - 111.14: 11183 111.14 - 118.74: 2317 118.74 - 126.34: 4423 126.34 - 133.94: 77 Bond angle restraints: 18074 Sorted by residual: angle pdb=" CA LEU A 506 " pdb=" C LEU A 506 " pdb=" N ALA A 507 " ideal model delta sigma weight residual 117.39 122.99 -5.60 1.24e+00 6.50e-01 2.04e+01 angle pdb=" CA ALA A 596 " pdb=" C ALA A 596 " pdb=" N PRO A 597 " ideal model delta sigma weight residual 118.44 125.38 -6.94 1.59e+00 3.96e-01 1.90e+01 angle pdb=" CA ASN A 168 " pdb=" C ASN A 168 " pdb=" O ASN A 168 " ideal model delta sigma weight residual 121.44 116.84 4.60 1.17e+00 7.31e-01 1.55e+01 angle pdb=" CA ALA A 596 " pdb=" C ALA A 596 " pdb=" O ALA A 596 " ideal model delta sigma weight residual 120.16 114.99 5.17 1.37e+00 5.33e-01 1.43e+01 angle pdb=" C PHE A 499 " pdb=" N LYS A 500 " pdb=" CA LYS A 500 " ideal model delta sigma weight residual 120.29 115.01 5.28 1.42e+00 4.96e-01 1.38e+01 ... (remaining 18069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 4382 15.89 - 31.77: 133 31.77 - 47.66: 44 47.66 - 63.54: 13 63.54 - 79.43: 4 Dihedral angle restraints: 4576 sinusoidal: 2461 harmonic: 2115 Sorted by residual: dihedral pdb=" CA PHE A 633 " pdb=" C PHE A 633 " pdb=" N THR A 634 " pdb=" CA THR A 634 " ideal model delta harmonic sigma weight residual 180.00 163.68 16.32 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ASP A 114 " pdb=" CB ASP A 114 " pdb=" CG ASP A 114 " pdb=" OD1 ASP A 114 " ideal model delta sinusoidal sigma weight residual -30.00 -85.42 55.42 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CB GLU A 570 " pdb=" CG GLU A 570 " pdb=" CD GLU A 570 " pdb=" OE1 GLU A 570 " ideal model delta sinusoidal sigma weight residual 0.00 -79.43 79.43 1 3.00e+01 1.11e-03 8.71e+00 ... (remaining 4573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 576 0.046 - 0.092: 117 0.092 - 0.138: 64 0.138 - 0.184: 19 0.184 - 0.230: 1 Chirality restraints: 777 Sorted by residual: chirality pdb=" CA VAL A 594 " pdb=" N VAL A 594 " pdb=" C VAL A 594 " pdb=" CB VAL A 594 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA VAL A 480 " pdb=" N VAL A 480 " pdb=" C VAL A 480 " pdb=" CB VAL A 480 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA VAL A 530 " pdb=" N VAL A 530 " pdb=" C VAL A 530 " pdb=" CB VAL A 530 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 774 not shown) Planarity restraints: 1475 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 145 " 0.017 2.00e-02 2.50e+03 1.89e-02 8.03e+00 pdb=" CG HIS A 145 " 0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS A 145 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 HIS A 145 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 145 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS A 145 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 HIS A 145 " -0.044 2.00e-02 2.50e+03 pdb=" HD2 HIS A 145 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 HIS A 145 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 56 " -0.017 2.00e-02 2.50e+03 1.89e-02 8.00e+00 pdb=" CG HIS A 56 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS A 56 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 HIS A 56 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 56 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS A 56 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 HIS A 56 " 0.044 2.00e-02 2.50e+03 pdb=" HD2 HIS A 56 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 HIS A 56 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 202 " -0.017 2.00e-02 2.50e+03 1.88e-02 7.95e+00 pdb=" CG HIS A 202 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS A 202 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 HIS A 202 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 202 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 HIS A 202 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 HIS A 202 " 0.043 2.00e-02 2.50e+03 pdb=" HD2 HIS A 202 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 HIS A 202 " -0.013 2.00e-02 2.50e+03 ... (remaining 1472 not shown) Histogram of nonbonded interaction distances: 1.33 - 1.99: 234 1.99 - 2.64: 12033 2.64 - 3.29: 30670 3.29 - 3.95: 38844 3.95 - 4.60: 58361 Nonbonded interactions: 140142 Sorted by model distance: nonbonded pdb=" HG CYS A 143 " pdb="HD21 ASN A 168 " model vdw 1.334 2.270 nonbonded pdb=" HG CYS A 164 " pdb=" H THR A 166 " model vdw 1.433 2.270 nonbonded pdb=" O ALA A 403 " pdb=" HG1 THR A 407 " model vdw 1.496 1.850 nonbonded pdb=" HG CYS A 477 " pdb="HG22 THR A 486 " model vdw 1.540 2.440 nonbonded pdb=" OE1 GLN A 38 " pdb=" H TYR A 69 " model vdw 1.601 1.850 ... (remaining 140137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 5.200 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 38.190 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 : 0.009 0.071 5011 Z= 0.577 Angle : 0.659 6.936 6775 Z= 0.424 Chirality : 0.054 0.230 777 Planarity : 0.003 0.022 863 Dihedral : 10.616 79.428 1848 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.53 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -0.01 (0.30), residues: 633 helix: 0.26 (0.33), residues: 196 sheet: -0.47 (0.42), residues: 126 loop : 0.22 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 466 HIS 0.001 0.000 HIS A 208 PHE 0.006 0.001 PHE A 461 TYR 0.007 0.000 TYR A 420 ARG 0.004 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8962 (p0) cc_final: 0.8712 (p0) REVERT: A 405 MET cc_start: 0.8350 (tpt) cc_final: 0.8041 (tpp) REVERT: A 443 LYS cc_start: 0.8749 (mmtt) cc_final: 0.8295 (mttt) REVERT: A 534 LYS cc_start: 0.7425 (mttt) cc_final: 0.6909 (tttm) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.4423 time to fit residues: 66.2108 Evaluate side-chains 60 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5011 Z= 0.171 Angle : 0.476 5.062 6775 Z= 0.261 Chirality : 0.040 0.140 777 Planarity : 0.004 0.042 863 Dihedral : 3.983 16.341 672 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.92 % Allowed : 6.63 % Favored : 92.45 % 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: 0.55 (0.31), residues: 633 helix: 1.40 (0.36), residues: 195 sheet: -0.49 (0.40), residues: 126 loop : 0.22 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 432 HIS 0.005 0.001 HIS A 145 PHE 0.010 0.001 PHE A 471 TYR 0.008 0.001 TYR A 396 ARG 0.002 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.6710 (mm-30) cc_final: 0.6322 (mp0) REVERT: A 443 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8431 (mttt) REVERT: A 534 LYS cc_start: 0.7514 (mttt) cc_final: 0.6988 (tmtt) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 0.3471 time to fit residues: 31.7059 Evaluate side-chains 55 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 451 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5011 Z= 0.276 Angle : 0.517 4.350 6775 Z= 0.285 Chirality : 0.041 0.201 777 Planarity : 0.004 0.047 863 Dihedral : 4.074 15.354 672 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.03 % Allowed : 7.18 % Favored : 90.79 % 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: 0.41 (0.31), residues: 633 helix: 1.50 (0.37), residues: 196 sheet: -0.39 (0.42), residues: 108 loop : -0.17 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 432 HIS 0.004 0.001 HIS A 202 PHE 0.015 0.002 PHE A 499 TYR 0.032 0.002 TYR A 124 ARG 0.002 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 CYS cc_start: 0.8157 (m) cc_final: 0.7919 (m) REVERT: A 443 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8432 (mttt) REVERT: A 534 LYS cc_start: 0.7505 (mttt) cc_final: 0.6976 (tmtt) outliers start: 11 outliers final: 10 residues processed: 59 average time/residue: 0.3292 time to fit residues: 26.2314 Evaluate side-chains 52 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 566 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5011 Z= 0.201 Angle : 0.462 4.477 6775 Z= 0.251 Chirality : 0.040 0.166 777 Planarity : 0.004 0.050 863 Dihedral : 3.909 14.332 672 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.84 % Allowed : 8.66 % Favored : 89.50 % 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: 0.57 (0.32), residues: 633 helix: 1.91 (0.37), residues: 189 sheet: -0.50 (0.43), residues: 112 loop : -0.13 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 432 HIS 0.003 0.001 HIS A 145 PHE 0.012 0.001 PHE A 41 TYR 0.024 0.001 TYR A 124 ARG 0.007 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8526 (mttt) REVERT: A 534 LYS cc_start: 0.7475 (mttt) cc_final: 0.6945 (tmtt) outliers start: 10 outliers final: 9 residues processed: 54 average time/residue: 0.3781 time to fit residues: 26.7183 Evaluate side-chains 52 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 501 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 168 ASN ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5011 Z= 0.409 Angle : 0.594 4.363 6775 Z= 0.328 Chirality : 0.042 0.154 777 Planarity : 0.004 0.051 863 Dihedral : 4.506 15.925 672 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.58 % Allowed : 9.21 % Favored : 88.21 % 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: -0.37 (0.31), residues: 633 helix: 0.74 (0.36), residues: 196 sheet: -0.54 (0.45), residues: 109 loop : -0.69 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 432 HIS 0.006 0.002 HIS A 202 PHE 0.017 0.002 PHE A 471 TYR 0.020 0.002 TYR A 124 ARG 0.003 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 38 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.7013 (m110) cc_final: 0.6713 (m110) REVERT: A 210 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6499 (mp0) REVERT: A 405 MET cc_start: 0.8563 (tpt) cc_final: 0.8311 (tpt) REVERT: A 534 LYS cc_start: 0.7430 (mttt) cc_final: 0.6965 (tmtt) outliers start: 14 outliers final: 13 residues processed: 49 average time/residue: 0.3739 time to fit residues: 24.5584 Evaluate side-chains 49 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 36 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 566 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 60 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5011 Z= 0.180 Angle : 0.459 4.355 6775 Z= 0.250 Chirality : 0.039 0.151 777 Planarity : 0.003 0.052 863 Dihedral : 4.056 15.294 672 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.39 % Allowed : 9.76 % Favored : 87.85 % 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: -0.01 (0.32), residues: 633 helix: 1.23 (0.37), residues: 197 sheet: -0.65 (0.43), residues: 129 loop : -0.46 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.003 0.001 HIS A 202 PHE 0.011 0.001 PHE A 471 TYR 0.020 0.001 TYR A 124 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.7080 (m110) cc_final: 0.6812 (m110) REVERT: A 210 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6462 (mp0) REVERT: A 405 MET cc_start: 0.8526 (tpt) cc_final: 0.8185 (tpt) REVERT: A 443 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8571 (mttt) REVERT: A 534 LYS cc_start: 0.7455 (mttt) cc_final: 0.6977 (tmtt) REVERT: A 551 MET cc_start: 0.4380 (tpt) cc_final: 0.4134 (tpt) outliers start: 13 outliers final: 11 residues processed: 51 average time/residue: 0.3530 time to fit residues: 24.0069 Evaluate side-chains 52 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 566 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 28 optimal weight: 0.0060 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5011 Z= 0.140 Angle : 0.431 4.299 6775 Z= 0.232 Chirality : 0.039 0.145 777 Planarity : 0.003 0.051 863 Dihedral : 3.787 15.214 672 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.58 % Allowed : 10.31 % Favored : 87.11 % 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: 0.17 (0.33), residues: 633 helix: 1.63 (0.37), residues: 199 sheet: -0.74 (0.42), residues: 129 loop : -0.45 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 432 HIS 0.003 0.001 HIS A 202 PHE 0.008 0.001 PHE A 471 TYR 0.017 0.001 TYR A 124 ARG 0.002 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8578 (mttt) REVERT: A 534 LYS cc_start: 0.7438 (mttt) cc_final: 0.6952 (tmtt) outliers start: 14 outliers final: 12 residues processed: 53 average time/residue: 0.3726 time to fit residues: 25.9767 Evaluate side-chains 55 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 566 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5011 Z= 0.136 Angle : 0.429 4.279 6775 Z= 0.231 Chirality : 0.039 0.141 777 Planarity : 0.003 0.050 863 Dihedral : 3.679 14.598 672 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.84 % Allowed : 11.05 % Favored : 87.11 % 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: 0.31 (0.33), residues: 633 helix: 1.78 (0.37), residues: 200 sheet: -0.72 (0.43), residues: 127 loop : -0.37 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 432 HIS 0.002 0.001 HIS A 202 PHE 0.008 0.001 PHE A 471 TYR 0.018 0.001 TYR A 124 ARG 0.002 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8612 (mttt) REVERT: A 534 LYS cc_start: 0.7407 (mttt) cc_final: 0.6905 (tmtt) outliers start: 10 outliers final: 9 residues processed: 52 average time/residue: 0.3861 time to fit residues: 26.6374 Evaluate side-chains 52 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 501 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5011 Z= 0.195 Angle : 0.457 4.272 6775 Z= 0.248 Chirality : 0.039 0.141 777 Planarity : 0.003 0.049 863 Dihedral : 3.804 14.589 672 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.21 % Allowed : 10.68 % Favored : 87.11 % 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: 0.18 (0.32), residues: 633 helix: 1.71 (0.37), residues: 199 sheet: -0.78 (0.42), residues: 131 loop : -0.48 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.003 0.001 HIS A 202 PHE 0.009 0.001 PHE A 471 TYR 0.015 0.001 TYR A 124 ARG 0.002 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8602 (mttt) REVERT: A 534 LYS cc_start: 0.7421 (mttt) cc_final: 0.6941 (tmtt) outliers start: 12 outliers final: 11 residues processed: 52 average time/residue: 0.3721 time to fit residues: 25.6206 Evaluate side-chains 55 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 566 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5011 Z= 0.182 Angle : 0.449 4.197 6775 Z= 0.243 Chirality : 0.039 0.143 777 Planarity : 0.003 0.050 863 Dihedral : 3.779 15.851 672 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.03 % Allowed : 10.50 % Favored : 87.48 % 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: 0.16 (0.32), residues: 633 helix: 1.72 (0.37), residues: 201 sheet: -0.75 (0.43), residues: 128 loop : -0.55 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.003 0.001 HIS A 202 PHE 0.009 0.001 PHE A 471 TYR 0.016 0.001 TYR A 124 ARG 0.002 0.000 ARG A 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8603 (mttt) REVERT: A 534 LYS cc_start: 0.7411 (mttt) cc_final: 0.6924 (tmtt) REVERT: A 610 LEU cc_start: 0.7330 (mp) cc_final: 0.7039 (mt) outliers start: 11 outliers final: 11 residues processed: 54 average time/residue: 0.3708 time to fit residues: 26.2902 Evaluate side-chains 57 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 566 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.113079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.085020 restraints weight = 34327.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.088697 restraints weight = 13968.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.090869 restraints weight = 8201.359| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5011 Z= 0.134 Angle : 0.434 4.876 6775 Z= 0.232 Chirality : 0.039 0.140 777 Planarity : 0.003 0.049 863 Dihedral : 3.683 15.001 672 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.03 % Allowed : 10.68 % Favored : 87.29 % 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: 0.31 (0.32), residues: 633 helix: 1.92 (0.37), residues: 201 sheet: -0.72 (0.44), residues: 124 loop : -0.51 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.003 0.001 HIS A 202 PHE 0.007 0.001 PHE A 471 TYR 0.017 0.001 TYR A 124 ARG 0.009 0.001 ARG A 538 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2932.45 seconds wall clock time: 52 minutes 42.01 seconds (3162.01 seconds total)