Starting phenix.real_space_refine on Wed Mar 4 01:41:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7msw_23970/03_2026/7msw_23970.cif Found real_map, /net/cci-nas-00/data/ceres_data/7msw_23970/03_2026/7msw_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_23970/03_2026/7msw_23970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7msw_23970/03_2026/7msw_23970.map" model { file = "/net/cci-nas-00/data/ceres_data/7msw_23970/03_2026/7msw_23970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7msw_23970/03_2026/7msw_23970.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.98, per 1000 atoms: 0.20 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: 0.88 Conformation dependent library (CDL) restraints added in 236.9 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: 0.30 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: 2.28 Time building geometry restraints manager: 1.25 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: 2.090 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: 0.060 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.760 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.490 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG A 52 TYR 0.007 0.000 TYR A 420 PHE 0.006 0.001 PHE A 461 TRP 0.013 0.001 TRP A 466 HIS 0.001 0.000 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00868 ( 5011) covalent geometry : angle 0.65865 ( 6775) hydrogen bonds : bond 0.17629 ( 210) hydrogen bonds : angle 7.42166 ( 597) metal coordination : bond 0.29856 ( 12) metal coordination : angle 27.63473 ( 11) *********************** 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 : 0.270 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: 0.2120 time to fit residues: 31.4169 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 : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.118306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.089281 restraints weight = 35577.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.093287 restraints weight = 14632.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.095688 restraints weight = 8619.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.097059 restraints weight = 6377.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.097780 restraints weight = 5416.583| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5023 Z= 0.135 Angle : 0.620 20.563 6786 Z= 0.281 Chirality : 0.041 0.144 777 Planarity : 0.004 0.046 863 Dihedral : 4.075 17.357 672 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.92 % Allowed : 6.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.32), residues: 633 helix: 1.40 (0.36), residues: 196 sheet: -0.59 (0.40), residues: 126 loop : 0.20 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 365 TYR 0.011 0.001 TYR A 207 PHE 0.012 0.001 PHE A 471 TRP 0.018 0.001 TRP A 432 HIS 0.005 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5011) covalent geometry : angle 0.49461 ( 6775) hydrogen bonds : bond 0.04696 ( 210) hydrogen bonds : angle 5.63760 ( 597) metal coordination : bond 0.01564 ( 12) metal coordination : angle 9.29696 ( 11) *********************** 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: 5 poor density : 65 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.7333 (mttt) cc_final: 0.6874 (tmtt) outliers start: 5 outliers final: 2 residues processed: 68 average time/residue: 0.1639 time to fit residues: 14.6171 Evaluate side-chains 53 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 10 optimal weight: 0.0670 chunk 37 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.114196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.084326 restraints weight = 35883.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.088106 restraints weight = 14977.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.090365 restraints weight = 8997.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.091626 restraints weight = 6735.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.092295 restraints weight = 5770.011| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5023 Z= 0.175 Angle : 0.581 18.209 6786 Z= 0.279 Chirality : 0.041 0.196 777 Planarity : 0.004 0.045 863 Dihedral : 4.009 16.497 672 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.32), residues: 633 helix: 1.56 (0.37), residues: 196 sheet: -0.89 (0.40), residues: 120 loop : -0.07 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.032 0.002 TYR A 124 PHE 0.012 0.001 PHE A 499 TRP 0.011 0.001 TRP A 432 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 5011) covalent geometry : angle 0.50022 ( 6775) hydrogen bonds : bond 0.04229 ( 210) hydrogen bonds : angle 5.25658 ( 597) metal coordination : bond 0.01878 ( 12) metal coordination : angle 7.33518 ( 11) *********************** 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 : 0.266 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 534 LYS cc_start: 0.7415 (mttt) cc_final: 0.6910 (tmtt) outliers start: 8 outliers final: 7 residues processed: 57 average time/residue: 0.2027 time to fit residues: 14.4843 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 : 0.327 ------------------------------------------------------------------------------- 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 36 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.112486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.082873 restraints weight = 35698.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.086642 restraints weight = 14910.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.088883 restraints weight = 8853.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.090158 restraints weight = 6596.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.090762 restraints weight = 5628.381| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5023 Z= 0.158 Angle : 0.533 15.106 6786 Z= 0.262 Chirality : 0.040 0.168 777 Planarity : 0.004 0.048 863 Dihedral : 3.942 15.520 672 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.84 % Allowed : 8.29 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.32), residues: 633 helix: 1.56 (0.37), residues: 196 sheet: -0.92 (0.41), residues: 116 loop : -0.17 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 246 TYR 0.021 0.001 TYR A 124 PHE 0.014 0.001 PHE A 499 TRP 0.010 0.001 TRP A 432 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 5011) covalent geometry : angle 0.47692 ( 6775) hydrogen bonds : bond 0.03772 ( 210) hydrogen bonds : angle 4.96544 ( 597) metal coordination : bond 0.01903 ( 12) metal coordination : angle 5.94069 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.269 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: 0.7389 (mttt) cc_final: 0.6910 (tmtt) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.1672 time to fit residues: 12.1173 Evaluate side-chains 48 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.110084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.080287 restraints weight = 35869.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.083812 restraints weight = 15324.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.085982 restraints weight = 9352.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.087187 restraints weight = 7052.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.087863 restraints weight = 6053.893| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 5023 Z= 0.228 Angle : 0.586 15.880 6786 Z= 0.295 Chirality : 0.041 0.151 777 Planarity : 0.004 0.049 863 Dihedral : 4.249 16.037 672 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.03 % Allowed : 9.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.32), residues: 633 helix: 1.08 (0.37), residues: 197 sheet: -0.72 (0.45), residues: 115 loop : -0.58 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 365 TYR 0.022 0.002 TYR A 124 PHE 0.016 0.002 PHE A 499 TRP 0.009 0.002 TRP A 432 HIS 0.005 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 5011) covalent geometry : angle 0.53106 ( 6775) hydrogen bonds : bond 0.04103 ( 210) hydrogen bonds : angle 5.14384 ( 597) metal coordination : bond 0.02525 ( 12) metal coordination : angle 6.19224 ( 11) *********************** 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: 11 poor density : 46 time to evaluate : 0.192 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: 0.7403 (mttt) cc_final: 0.6983 (tmtt) outliers start: 11 outliers final: 10 residues processed: 54 average time/residue: 0.1681 time to fit residues: 11.9074 Evaluate side-chains 52 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 501 LEU 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 49 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.111347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.081637 restraints weight = 35751.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.085265 restraints weight = 15106.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.087463 restraints weight = 9133.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.088700 restraints weight = 6858.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.089385 restraints weight = 5866.202| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5023 Z= 0.146 Angle : 0.512 12.218 6786 Z= 0.258 Chirality : 0.040 0.151 777 Planarity : 0.004 0.050 863 Dihedral : 4.055 16.019 672 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.66 % Allowed : 9.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.32), residues: 633 helix: 1.28 (0.37), residues: 198 sheet: -0.93 (0.43), residues: 125 loop : -0.60 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 246 TYR 0.027 0.002 TYR A 124 PHE 0.011 0.001 PHE A 471 TRP 0.008 0.001 TRP A 432 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5011) covalent geometry : angle 0.47111 ( 6775) hydrogen bonds : bond 0.03527 ( 210) hydrogen bonds : angle 4.84231 ( 597) metal coordination : bond 0.01771 ( 12) metal coordination : angle 5.02018 ( 11) *********************** 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 50 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.278 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: 0.7313 (mttt) cc_final: 0.6901 (tmtt) outliers start: 9 outliers final: 8 residues processed: 48 average time/residue: 0.1776 time to fit residues: 11.1609 Evaluate side-chains 47 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 31 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 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 = 0.3741 r_free = 0.3741 target = 0.111652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.082385 restraints weight = 35279.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.086045 restraints weight = 14917.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.088247 restraints weight = 8941.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.089422 restraints weight = 6683.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.090009 restraints weight = 5733.453| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5023 Z= 0.143 Angle : 0.503 11.730 6786 Z= 0.254 Chirality : 0.039 0.146 777 Planarity : 0.003 0.049 863 Dihedral : 4.002 15.768 672 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.32), residues: 633 helix: 1.37 (0.37), residues: 198 sheet: -0.95 (0.42), residues: 127 loop : -0.67 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 538 TYR 0.022 0.002 TYR A 124 PHE 0.009 0.001 PHE A 471 TRP 0.009 0.001 TRP A 432 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 5011) covalent geometry : angle 0.46489 ( 6775) hydrogen bonds : bond 0.03419 ( 210) hydrogen bonds : angle 4.73975 ( 597) metal coordination : bond 0.01669 ( 12) metal coordination : angle 4.77763 ( 11) *********************** 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: 9 poor density : 44 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.7283 (mttt) cc_final: 0.6904 (tmtt) REVERT: A 538 ARG cc_start: 0.7368 (mpt180) cc_final: 0.6979 (mpt180) outliers start: 9 outliers final: 9 residues processed: 50 average time/residue: 0.1691 time to fit residues: 11.0538 Evaluate side-chains 50 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 451 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 566 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 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 = 0.3697 r_free = 0.3697 target = 0.109168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.079569 restraints weight = 35935.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083123 restraints weight = 15390.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085253 restraints weight = 9373.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.086444 restraints weight = 7072.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.086972 restraints weight = 6083.715| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 5023 Z= 0.217 Angle : 0.566 13.740 6786 Z= 0.290 Chirality : 0.040 0.145 777 Planarity : 0.004 0.049 863 Dihedral : 4.266 16.732 672 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.66 % Allowed : 10.68 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.31), residues: 633 helix: 1.07 (0.36), residues: 198 sheet: -1.04 (0.46), residues: 113 loop : -0.95 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 538 TYR 0.021 0.002 TYR A 124 PHE 0.014 0.001 PHE A 471 TRP 0.009 0.001 TRP A 432 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 5011) covalent geometry : angle 0.52223 ( 6775) hydrogen bonds : bond 0.03841 ( 210) hydrogen bonds : angle 4.99901 ( 597) metal coordination : bond 0.02406 ( 12) metal coordination : angle 5.42542 ( 11) *********************** 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 53 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 LYS cc_start: 0.7279 (mttt) cc_final: 0.6903 (tmtt) outliers start: 9 outliers final: 9 residues processed: 51 average time/residue: 0.1702 time to fit residues: 11.3779 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 : 0.279 ------------------------------------------------------------------------------- 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 451 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 566 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.110953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.081755 restraints weight = 35136.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.085365 restraints weight = 15035.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.087511 restraints weight = 9078.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.088726 restraints weight = 6835.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.089241 restraints weight = 5859.005| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5023 Z= 0.152 Angle : 0.512 11.755 6786 Z= 0.261 Chirality : 0.040 0.145 777 Planarity : 0.003 0.049 863 Dihedral : 4.133 16.512 672 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.03 % Allowed : 10.31 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.31), residues: 633 helix: 1.31 (0.36), residues: 198 sheet: -1.02 (0.46), residues: 115 loop : -1.00 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 107 TYR 0.023 0.002 TYR A 124 PHE 0.011 0.001 PHE A 471 TRP 0.009 0.001 TRP A 432 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5011) covalent geometry : angle 0.47484 ( 6775) hydrogen bonds : bond 0.03463 ( 210) hydrogen bonds : angle 4.84113 ( 597) metal coordination : bond 0.01852 ( 12) metal coordination : angle 4.77402 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.272 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: 0.7222 (mttt) cc_final: 0.6853 (tmtt) outliers start: 11 outliers final: 10 residues processed: 53 average time/residue: 0.1802 time to fit residues: 12.3309 Evaluate side-chains 55 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 451 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 566 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.111290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.082437 restraints weight = 34773.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.086033 restraints weight = 14776.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.088166 restraints weight = 8911.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.089317 restraints weight = 6695.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.090020 restraints weight = 5756.336| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5023 Z= 0.143 Angle : 0.506 11.319 6786 Z= 0.257 Chirality : 0.039 0.145 777 Planarity : 0.003 0.048 863 Dihedral : 4.081 17.859 672 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.84 % Allowed : 10.50 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.32), residues: 633 helix: 1.41 (0.36), residues: 198 sheet: -1.15 (0.46), residues: 113 loop : -1.01 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 370 TYR 0.024 0.002 TYR A 124 PHE 0.009 0.001 PHE A 471 TRP 0.009 0.001 TRP A 432 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 5011) covalent geometry : angle 0.47149 ( 6775) hydrogen bonds : bond 0.03305 ( 210) hydrogen bonds : angle 4.73997 ( 597) metal coordination : bond 0.01608 ( 12) metal coordination : angle 4.59707 ( 11) ********************** 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 57 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.261 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: 0.7181 (mttt) cc_final: 0.6841 (tmtt) outliers start: 10 outliers final: 10 residues processed: 54 average time/residue: 0.1680 time to fit residues: 11.7906 Evaluate side-chains 57 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 451 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 566 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.111713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.082828 restraints weight = 35201.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.086506 restraints weight = 14854.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.088679 restraints weight = 8880.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.089906 restraints weight = 6628.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.090497 restraints weight = 5660.031| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.5854 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= 0.128 Angle : 0.489 10.565 6786 Z= 0.249 Chirality : 0.039 0.144 777 Planarity : 0.003 0.048 863 Dihedral : 3.973 15.777 672 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.84 % Allowed : 10.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.32), residues: 633 helix: 1.47 (0.37), residues: 200 sheet: -1.20 (0.45), residues: 119 loop : -0.87 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 246 TYR 0.024 0.001 TYR A 124 PHE 0.008 0.001 PHE A 471 TRP 0.010 0.001 TRP A 432 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5011) covalent geometry : angle 0.45776 ( 6775) hydrogen bonds : bond 0.03179 ( 210) hydrogen bonds : angle 4.61992 ( 597) metal coordination : bond 0.01416 ( 12) metal coordination : angle 4.30527 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2159.26 seconds wall clock time: 37 minutes 20.89 seconds (2240.89 seconds total)