Starting phenix.real_space_refine on Mon Jul 28 02:06:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7msw_23970/07_2025/7msw_23970.cif Found real_map, /net/cci-nas-00/data/ceres_data/7msw_23970/07_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_23970/07_2025/7msw_23970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7msw_23970/07_2025/7msw_23970.map" model { file = "/net/cci-nas-00/data/ceres_data/7msw_23970/07_2025/7msw_23970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7msw_23970/07_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-5711/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: 6.47, per 1000 atoms: 0.65 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: 2.82 Conformation dependent library (CDL) restraints added in 749.0 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: 0.93 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: 3.65 Time building geometry restraints manager: 3.41 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: 2.310 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: 0.260 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.340 Find NCS groups from input model: 0.050 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.250 ------------------------------------------------------------------------------- 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 : 0.017 0.544 5023 Z= 0.697 Angle : 1.293 54.312 6786 Z= 0.477 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 Details of bonding type rmsd hydrogen bonds : bond 0.17629 ( 210) hydrogen bonds : angle 7.42166 ( 597) metal coordination : bond 0.29856 ( 12) metal coordination : angle 27.63473 ( 11) covalent geometry : bond 0.00868 ( 5011) covalent geometry : angle 0.65865 ( 6775) *********************** 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 : 0.692 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: 0.4407 time to fit residues: 66.2119 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 : 0.748 ------------------------------------------------------------------------------- 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: 5.9990 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 = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.089247 restraints weight = 35109.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.093211 restraints weight = 14447.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.095605 restraints weight = 8548.284| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 0.040 5023 Z= 0.135 Angle : 0.618 20.584 6786 Z= 0.281 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 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 210) hydrogen bonds : angle 5.59970 ( 597) metal coordination : bond 0.01499 ( 12) metal coordination : angle 9.15374 ( 11) covalent geometry : bond 0.00292 ( 5011) covalent geometry : angle 0.49651 ( 6775) *********************** 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 : 0.716 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: 0.6661 (mm-30) cc_final: 0.6176 (mp0) REVERT: A 534 LYS cc_start: 0.7390 (mttt) cc_final: 0.6892 (tmtt) outliers start: 4 outliers final: 3 residues processed: 69 average time/residue: 0.3318 time to fit residues: 30.2605 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 : 0.722 ------------------------------------------------------------------------------- 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: 10.0000 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.0050 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: 0.7980 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.115605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.085931 restraints weight = 35891.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.089770 restraints weight = 14903.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.092079 restraints weight = 8875.134| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5023 Z= 0.133 Angle : 0.543 16.677 6786 Z= 0.260 Chirality : 0.040 0.193 777 Planarity : 0.004 0.045 863 Dihedral : 3.893 15.613 672 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.14 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: 0.52 (0.32), residues: 633 helix: 1.77 (0.38), residues: 196 sheet: -0.79 (0.40), residues: 126 loop : 0.01 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.004 0.001 HIS A 255 PHE 0.009 0.001 PHE A 499 TYR 0.027 0.001 TYR A 124 ARG 0.002 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 210) hydrogen bonds : angle 5.14229 ( 597) metal coordination : bond 0.01352 ( 12) metal coordination : angle 6.82623 ( 11) covalent geometry : bond 0.00281 ( 5011) covalent geometry : angle 0.46859 ( 6775) *********************** 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 61 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.778 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: A 534 LYS cc_start: 0.7452 (mttt) cc_final: 0.6927 (tmtt) outliers start: 8 outliers final: 6 residues processed: 58 average time/residue: 0.3340 time to fit residues: 26.3282 Evaluate side-chains 51 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 48 optimal weight: 0.0040 chunk 16 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.115784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.086249 restraints weight = 35203.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.090084 restraints weight = 14542.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.092411 restraints weight = 8645.418| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5023 Z= 0.101 Angle : 0.486 12.972 6786 Z= 0.237 Chirality : 0.040 0.174 777 Planarity : 0.004 0.047 863 Dihedral : 3.719 14.142 672 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: 0.56 (0.32), residues: 633 helix: 1.93 (0.38), residues: 195 sheet: -0.74 (0.41), residues: 116 loop : -0.09 (0.33), residues: 322 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 499 TYR 0.021 0.001 TYR A 124 ARG 0.002 0.000 ARG A 107 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 210) hydrogen bonds : angle 4.82782 ( 597) metal coordination : bond 0.01119 ( 12) metal coordination : angle 5.38214 ( 11) covalent geometry : bond 0.00217 ( 5011) covalent geometry : angle 0.43571 ( 6775) *********************** 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: 9 poor density : 51 time to evaluate : 0.720 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 534 LYS cc_start: 0.7410 (mttt) cc_final: 0.6896 (tmtt) outliers start: 9 outliers final: 5 residues processed: 58 average time/residue: 0.2904 time to fit residues: 23.5226 Evaluate side-chains 52 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.110304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.080479 restraints weight = 35897.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.083980 restraints weight = 15377.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.086156 restraints weight = 9397.507| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 5023 Z= 0.265 Angle : 0.644 19.971 6786 Z= 0.320 Chirality : 0.042 0.151 777 Planarity : 0.004 0.047 863 Dihedral : 4.259 17.131 672 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.21 % Allowed : 9.02 % Favored : 88.77 % 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: -0.10 (0.31), residues: 633 helix: 1.28 (0.37), residues: 190 sheet: -0.80 (0.46), residues: 102 loop : -0.56 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 432 HIS 0.006 0.002 HIS A 202 PHE 0.018 0.002 PHE A 499 TYR 0.026 0.002 TYR A 124 ARG 0.003 0.001 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 210) hydrogen bonds : angle 5.25144 ( 597) metal coordination : bond 0.02936 ( 12) metal coordination : angle 7.48921 ( 11) covalent geometry : bond 0.00573 ( 5011) covalent geometry : angle 0.56903 ( 6775) *********************** 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 57 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.7410 (mttt) cc_final: 0.6945 (tmtt) outliers start: 12 outliers final: 9 residues processed: 56 average time/residue: 0.4554 time to fit residues: 33.6669 Evaluate side-chains 49 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 451 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 532 HIS 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: 5.9990 chunk 17 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.111861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.082040 restraints weight = 35362.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.085663 restraints weight = 15050.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.087864 restraints weight = 9095.280| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5023 Z= 0.145 Angle : 0.526 14.395 6786 Z= 0.260 Chirality : 0.040 0.152 777 Planarity : 0.004 0.049 863 Dihedral : 4.010 16.066 672 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % 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: -0.00 (0.32), residues: 633 helix: 1.48 (0.37), residues: 192 sheet: -0.97 (0.41), residues: 135 loop : -0.41 (0.34), residues: 306 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 0.012 0.001 PHE A 471 TYR 0.029 0.002 TYR A 124 ARG 0.002 0.000 ARG A 107 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 210) hydrogen bonds : angle 4.94538 ( 597) metal coordination : bond 0.01782 ( 12) metal coordination : angle 5.69621 ( 11) covalent geometry : bond 0.00311 ( 5011) covalent geometry : angle 0.47408 ( 6775) *********************** 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 53 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.7289 (mttt) cc_final: 0.6849 (tmtt) outliers start: 9 outliers final: 8 residues processed: 51 average time/residue: 0.6593 time to fit residues: 47.1822 Evaluate side-chains 51 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 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 57 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.109365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.079639 restraints weight = 36042.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.083167 restraints weight = 15476.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.085293 restraints weight = 9413.798| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 5023 Z= 0.251 Angle : 0.607 17.547 6786 Z= 0.306 Chirality : 0.041 0.146 777 Planarity : 0.004 0.049 863 Dihedral : 4.302 15.671 672 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.21 % Allowed : 10.31 % 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: -0.49 (0.32), residues: 633 helix: 0.97 (0.36), residues: 197 sheet: -1.05 (0.42), residues: 131 loop : -0.77 (0.33), residues: 305 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 0.021 0.002 TYR A 124 ARG 0.003 0.000 ARG A 370 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 210) hydrogen bonds : angle 5.18934 ( 597) metal coordination : bond 0.02847 ( 12) metal coordination : angle 6.64320 ( 11) covalent geometry : bond 0.00546 ( 5011) covalent geometry : angle 0.54560 ( 6775) *********************** 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: 12 poor density : 41 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6500 (mp0) REVERT: A 534 LYS cc_start: 0.7313 (mttt) cc_final: 0.6885 (tmtt) outliers start: 12 outliers final: 11 residues processed: 50 average time/residue: 0.3654 time to fit residues: 24.3365 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 : 0.802 ------------------------------------------------------------------------------- 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 444 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 501 LEU 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: 1.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.112170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.082977 restraints weight = 35108.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.086554 restraints weight = 14873.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.088746 restraints weight = 9034.791| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.003 0.051 5023 Z= 0.130 Angle : 0.515 13.214 6786 Z= 0.257 Chirality : 0.040 0.151 777 Planarity : 0.003 0.049 863 Dihedral : 4.062 16.960 672 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.29 % Allowed : 11.60 % 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: -0.27 (0.32), residues: 633 helix: 1.31 (0.37), residues: 198 sheet: -1.16 (0.40), residues: 139 loop : -0.63 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.002 0.001 HIS A 202 PHE 0.011 0.001 PHE A 471 TYR 0.022 0.001 TYR A 124 ARG 0.001 0.000 ARG A 107 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 210) hydrogen bonds : angle 4.85405 ( 597) metal coordination : bond 0.01561 ( 12) metal coordination : angle 5.33823 ( 11) covalent geometry : bond 0.00281 ( 5011) covalent geometry : angle 0.46887 ( 6775) *********************** 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 : 0.720 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: 0.7190 (mttt) cc_final: 0.6792 (tmtt) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.3770 time to fit residues: 24.2106 Evaluate side-chains 46 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 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 39 optimal weight: 0.8980 chunk 37 optimal weight: 0.0770 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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 = 0.113110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.083852 restraints weight = 35015.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.087524 restraints weight = 14828.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.089722 restraints weight = 8917.810| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5023 Z= 0.105 Angle : 0.501 12.155 6786 Z= 0.249 Chirality : 0.040 0.149 777 Planarity : 0.003 0.048 863 Dihedral : 3.936 18.714 672 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.74 % Allowed : 12.34 % Favored : 86.92 % 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: -0.11 (0.33), residues: 633 helix: 1.46 (0.37), residues: 200 sheet: -1.08 (0.41), residues: 135 loop : -0.57 (0.34), residues: 298 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 0.009 0.001 PHE A 471 TYR 0.021 0.001 TYR A 124 ARG 0.008 0.000 ARG A 538 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 210) hydrogen bonds : angle 4.66184 ( 597) metal coordination : bond 0.01250 ( 12) metal coordination : angle 4.94193 ( 11) covalent geometry : bond 0.00230 ( 5011) covalent geometry : angle 0.45972 ( 6775) *********************** 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 48 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.7234 (mttt) cc_final: 0.6848 (tmtt) outliers start: 4 outliers final: 4 residues processed: 47 average time/residue: 0.3918 time to fit residues: 24.2243 Evaluate side-chains 44 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 501 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 52 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.112709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.083373 restraints weight = 35263.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.086973 restraints weight = 14986.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.089177 restraints weight = 9109.183| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5023 Z= 0.127 Angle : 0.526 12.408 6786 Z= 0.259 Chirality : 0.040 0.149 777 Planarity : 0.003 0.047 863 Dihedral : 3.894 17.947 672 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.92 % Allowed : 12.71 % Favored : 86.37 % 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: -0.15 (0.33), residues: 633 helix: 1.56 (0.37), residues: 198 sheet: -1.14 (0.40), residues: 139 loop : -0.64 (0.34), residues: 296 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 0.009 0.001 PHE A 471 TYR 0.021 0.001 TYR A 124 ARG 0.005 0.000 ARG A 538 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 210) hydrogen bonds : angle 4.63963 ( 597) metal coordination : bond 0.01401 ( 12) metal coordination : angle 4.93302 ( 11) covalent geometry : bond 0.00277 ( 5011) covalent geometry : angle 0.48789 ( 6775) ********************** 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 49 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.7232 (mttt) cc_final: 0.6852 (tmtt) REVERT: A 538 ARG cc_start: 0.7346 (mpt180) cc_final: 0.7029 (mpt180) outliers start: 5 outliers final: 5 residues processed: 47 average time/residue: 0.4065 time to fit residues: 24.9302 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 : 0.728 ------------------------------------------------------------------------------- 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 444 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 501 LEU 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: 1.9990 chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.112621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.083040 restraints weight = 35368.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.086678 restraints weight = 15103.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.088907 restraints weight = 9214.724| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5023 Z= 0.128 Angle : 0.523 12.521 6786 Z= 0.259 Chirality : 0.040 0.146 777 Planarity : 0.003 0.047 863 Dihedral : 3.873 19.174 672 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.29 % Allowed : 11.97 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.32), residues: 633 helix: 1.54 (0.37), residues: 198 sheet: -1.20 (0.40), residues: 139 loop : -0.70 (0.34), residues: 296 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 0.010 0.001 PHE A 471 TYR 0.022 0.001 TYR A 124 ARG 0.003 0.000 ARG A 538 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 210) hydrogen bonds : angle 4.59988 ( 597) metal coordination : bond 0.01442 ( 12) metal coordination : angle 4.92997 ( 11) covalent geometry : bond 0.00281 ( 5011) covalent geometry : angle 0.48458 ( 6775) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4255.28 seconds wall clock time: 76 minutes 1.23 seconds (4561.23 seconds total)