Starting phenix.real_space_refine on Fri Feb 14 07:18:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7msw_23970/02_2025/7msw_23970.cif Found real_map, /net/cci-nas-00/data/ceres_data/7msw_23970/02_2025/7msw_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/cci-nas-00/data/ceres_data/7msw_23970/02_2025/7msw_23970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7msw_23970/02_2025/7msw_23970.map" model { file = "/net/cci-nas-00/data/ceres_data/7msw_23970/02_2025/7msw_23970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7msw_23970/02_2025/7msw_23970.cif" } 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. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9881 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 9878 Classifications: {'peptide': 635} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 612} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 5.06, per 1000 atoms: 0.51 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 - 3.00 Amino acid : True - 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: 2.65 Conformation dependent library (CDL) restraints added in 657.4 milliseconds 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: 1.00 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: 3.92 Time building geometry restraints manager: 3.16 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: 0.00 - 2.61: 16536 2.61 - 5.23: 989 5.23 - 7.84: 519 7.84 - 10.45: 3 10.45 - 13.07: 27 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: 4405 15.89 - 31.77: 158 31.77 - 47.66: 63 47.66 - 63.54: 44 63.54 - 79.43: 4 Dihedral angle restraints: 4674 sinusoidal: 2559 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 4671 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 2.450 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 2.450 ... (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: 1.280 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: 0.160 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.590 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.470 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.825 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: 0.4452 time to fit residues: 66.5778 Evaluate side-chains 60 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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: 0.9980 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 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: 0.9180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.118210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.089241 restraints weight = 35109.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.093231 restraints weight = 14459.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.095605 restraints weight = 8532.610| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5011 Z= 0.189 Angle : 0.497 5.138 6775 Z= 0.272 Chirality : 0.041 0.142 777 Planarity : 0.004 0.042 863 Dihedral : 4.071 16.988 672 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.74 % Allowed : 6.63 % Favored : 92.63 % 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: 0.52 (0.32), residues: 633 helix: 1.45 (0.36), residues: 195 sheet: -0.58 (0.40), residues: 126 loop : 0.17 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 432 HIS 0.004 0.001 HIS A 145 PHE 0.012 0.001 PHE A 471 TYR 0.011 0.001 TYR A 207 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 to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.774 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: A 210 GLU cc_start: 0.6662 (mm-30) cc_final: 0.6177 (mp0) REVERT: A 534 LYS cc_start: 0.7394 (mttt) cc_final: 0.6894 (tmtt) outliers start: 4 outliers final: 3 residues processed: 69 average time/residue: 0.3546 time to fit residues: 32.4195 Evaluate side-chains 56 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS 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 62 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 24 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.114385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.084659 restraints weight = 35987.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.088439 restraints weight = 15003.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.090709 restraints weight = 8995.065| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5011 Z= 0.234 Angle : 0.497 4.172 6775 Z= 0.273 Chirality : 0.040 0.191 777 Planarity : 0.004 0.045 863 Dihedral : 3.999 16.468 672 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.47 % Allowed : 7.92 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.32), residues: 633 helix: 1.61 (0.37), residues: 196 sheet: -0.82 (0.39), residues: 126 loop : -0.03 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 432 HIS 0.004 0.001 HIS A 255 PHE 0.011 0.001 PHE A 499 TYR 0.027 0.001 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 59 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.811 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: A 534 LYS cc_start: 0.7460 (mttt) cc_final: 0.6924 (tmtt) outliers start: 8 outliers final: 7 residues processed: 57 average time/residue: 0.3839 time to fit residues: 28.6803 Evaluate side-chains 51 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 126 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 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 19 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 55 optimal weight: 0.0270 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.115319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.085737 restraints weight = 35272.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.089554 restraints weight = 14583.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.091868 restraints weight = 8688.982| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4274 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 : 0.438 4.387 6775 Z= 0.235 Chirality : 0.040 0.173 777 Planarity : 0.004 0.048 863 Dihedral : 3.748 13.966 672 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.47 % Allowed : 8.29 % Favored : 90.24 % 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: 0.59 (0.32), residues: 633 helix: 1.98 (0.38), residues: 195 sheet: -0.72 (0.41), residues: 116 loop : -0.08 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.002 0.001 HIS A 255 PHE 0.009 0.001 PHE A 499 TYR 0.020 0.001 TYR A 124 ARG 0.005 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 60 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.710 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 117 MET cc_start: 0.7470 (mmm) cc_final: 0.7190 (tpt) REVERT: A 534 LYS cc_start: 0.7413 (mttt) cc_final: 0.6890 (tmtt) outliers start: 8 outliers final: 4 residues processed: 58 average time/residue: 0.3226 time to fit residues: 24.9869 Evaluate side-chains 49 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 428 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 9 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.112808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.083109 restraints weight = 35763.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.086832 restraints weight = 14958.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.089076 restraints weight = 8979.720| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5011 Z= 0.225 Angle : 0.474 4.789 6775 Z= 0.257 Chirality : 0.040 0.151 777 Planarity : 0.004 0.048 863 Dihedral : 3.827 14.508 672 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.66 % Allowed : 8.66 % Favored : 89.69 % 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: 0.36 (0.32), residues: 633 helix: 1.77 (0.38), residues: 197 sheet: -0.85 (0.42), residues: 116 loop : -0.23 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 432 HIS 0.003 0.001 HIS A 202 PHE 0.013 0.001 PHE A 499 TYR 0.024 0.001 TYR A 124 ARG 0.002 0.000 ARG A 365 *********************** 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 to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.7416 (mttt) cc_final: 0.6942 (tmtt) outliers start: 9 outliers final: 7 residues processed: 50 average time/residue: 0.3779 time to fit residues: 25.0353 Evaluate side-chains 47 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 126 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 501 LEU 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 32 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 0.0370 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.114208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.084391 restraints weight = 35345.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.088214 restraints weight = 14703.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.090459 restraints weight = 8757.109| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4806 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= 0.142 Angle : 0.437 4.305 6775 Z= 0.234 Chirality : 0.040 0.152 777 Planarity : 0.003 0.048 863 Dihedral : 3.711 17.608 672 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.10 % Allowed : 9.58 % Favored : 89.32 % 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: 0.36 (0.33), residues: 633 helix: 1.79 (0.38), residues: 201 sheet: -0.85 (0.43), residues: 118 loop : -0.26 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 432 HIS 0.002 0.001 HIS A 255 PHE 0.009 0.001 PHE A 471 TYR 0.028 0.001 TYR A 124 ARG 0.004 0.000 ARG A 538 *********************** 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 52 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.7662 (mmm) cc_final: 0.7083 (tpt) REVERT: A 534 LYS cc_start: 0.7401 (mttt) cc_final: 0.6907 (tmtt) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.3866 time to fit residues: 25.7137 Evaluate side-chains 48 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 126 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 501 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 57 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.110536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.080787 restraints weight = 35868.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.084455 restraints weight = 15147.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.086645 restraints weight = 9071.640| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5011 Z= 0.305 Angle : 0.525 4.310 6775 Z= 0.288 Chirality : 0.041 0.143 777 Planarity : 0.004 0.046 863 Dihedral : 4.090 15.521 672 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.84 % Allowed : 9.02 % Favored : 89.13 % 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: -0.12 (0.31), residues: 633 helix: 1.36 (0.37), residues: 197 sheet: -0.73 (0.47), residues: 102 loop : -0.71 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 432 HIS 0.005 0.001 HIS A 202 PHE 0.016 0.002 PHE A 471 TYR 0.024 0.002 TYR A 124 ARG 0.003 0.001 ARG A 365 *********************** 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 53 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.7390 (mttt) cc_final: 0.6963 (tmtt) outliers start: 10 outliers final: 10 residues processed: 50 average time/residue: 0.3583 time to fit residues: 23.8722 Evaluate side-chains 51 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 126 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 509 CYS Chi-restraints excluded: chain A residue 532 HIS 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 10 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 62 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.112792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.083283 restraints weight = 35237.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.087008 restraints weight = 14789.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.089280 restraints weight = 8845.948| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5283 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= 0.176 Angle : 0.451 4.226 6775 Z= 0.244 Chirality : 0.039 0.148 777 Planarity : 0.003 0.046 863 Dihedral : 3.881 16.931 672 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.29 % Allowed : 10.31 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.32), residues: 633 helix: 1.52 (0.37), residues: 200 sheet: -0.73 (0.43), residues: 125 loop : -0.62 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 432 HIS 0.002 0.001 HIS A 202 PHE 0.012 0.001 PHE A 471 TYR 0.022 0.001 TYR A 124 ARG 0.001 0.000 ARG A 107 *********************** 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 50 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.846 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 405 MET cc_start: 0.8357 (tpt) cc_final: 0.7976 (tpt) REVERT: A 534 LYS cc_start: 0.7327 (mttt) cc_final: 0.6906 (tmtt) outliers start: 7 outliers final: 7 residues processed: 48 average time/residue: 0.3787 time to fit residues: 23.8646 Evaluate side-chains 47 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 126 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 509 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 39 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.112511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.083116 restraints weight = 35218.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.086822 restraints weight = 14981.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.089063 restraints weight = 9037.348| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5011 Z= 0.200 Angle : 0.475 5.821 6775 Z= 0.258 Chirality : 0.040 0.145 777 Planarity : 0.003 0.046 863 Dihedral : 3.892 17.210 672 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.03 % Allowed : 10.13 % 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: 1.55 (0.37), residues: 200 sheet: -0.71 (0.43), residues: 125 loop : -0.70 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 432 HIS 0.003 0.001 HIS A 202 PHE 0.012 0.001 PHE A 471 TYR 0.021 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 51 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.7296 (mttt) cc_final: 0.6879 (tmtt) outliers start: 11 outliers final: 10 residues processed: 48 average time/residue: 0.3703 time to fit residues: 23.5524 Evaluate side-chains 49 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 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 444 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 509 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 52 optimal weight: 4.9990 chunk 4 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.114116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.084738 restraints weight = 35407.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.088504 restraints weight = 14948.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.090819 restraints weight = 9017.290| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5011 Z= 0.140 Angle : 0.450 5.199 6775 Z= 0.241 Chirality : 0.039 0.144 777 Planarity : 0.003 0.046 863 Dihedral : 3.780 17.474 672 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.66 % Allowed : 10.31 % Favored : 88.03 % 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: 0.13 (0.32), residues: 633 helix: 1.76 (0.37), residues: 199 sheet: -0.75 (0.43), residues: 123 loop : -0.62 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 432 HIS 0.002 0.001 HIS A 202 PHE 0.010 0.001 PHE A 471 TYR 0.022 0.001 TYR A 124 ARG 0.001 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 55 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.8373 (tpt) cc_final: 0.7919 (tpt) REVERT: A 443 LYS cc_start: 0.8072 (mttt) cc_final: 0.7838 (mtmt) REVERT: A 534 LYS cc_start: 0.7225 (mttt) cc_final: 0.6824 (tmtt) outliers start: 9 outliers final: 9 residues processed: 51 average time/residue: 0.3556 time to fit residues: 23.8948 Evaluate side-chains 51 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 54 HIS 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 444 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 509 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.113586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.084391 restraints weight = 34936.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.088089 restraints weight = 14699.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.090373 restraints weight = 8812.972| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5011 Z= 0.151 Angle : 0.471 9.947 6775 Z= 0.248 Chirality : 0.039 0.143 777 Planarity : 0.003 0.045 863 Dihedral : 3.693 18.804 672 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.66 % Allowed : 10.50 % 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: 0.17 (0.32), residues: 633 helix: 1.81 (0.37), residues: 200 sheet: -0.74 (0.43), residues: 123 loop : -0.62 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.002 0.001 HIS A 255 PHE 0.009 0.001 PHE A 471 TYR 0.022 0.001 TYR A 124 ARG 0.001 0.000 ARG A 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3708.48 seconds wall clock time: 66 minutes 13.71 seconds (3973.71 seconds total)