Starting phenix.real_space_refine on Tue Feb 11 21:34:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nus_0521/02_2025/6nus_0521.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nus_0521/02_2025/6nus_0521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nus_0521/02_2025/6nus_0521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nus_0521/02_2025/6nus_0521.map" model { file = "/net/cci-nas-00/data/ceres_data/6nus_0521/02_2025/6nus_0521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nus_0521/02_2025/6nus_0521.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 54 5.16 5 C 4235 2.51 5 N 1115 2.21 5 O 1226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6632 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5767 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 689} Chain breaks: 6 Chain: "B" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 863 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 106} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1481 SG CYS A 301 37.503 61.634 35.610 1.00 36.78 S ATOM 1522 SG CYS A 306 37.698 60.632 32.501 1.00 62.98 S ATOM 1554 SG CYS A 310 41.314 60.514 34.574 1.00 33.81 S ATOM 2658 SG CYS A 487 19.463 58.580 43.739 1.00 37.60 S ATOM 3783 SG CYS A 645 18.191 58.310 40.576 1.00 36.07 S ATOM 3789 SG CYS A 646 21.574 60.826 41.973 1.00 36.63 S Time building chain proxies: 4.31, per 1000 atoms: 0.65 Number of scatterers: 6632 At special positions: 0 Unit cell: (86.25, 93.15, 97.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 54 16.00 O 1226 8.00 N 1115 7.00 C 4235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.74 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " Number of angles added : 6 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 7 sheets defined 52.4% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 199 Processing helix chain 'A' and resid 234 through 242 Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.763A pdb=" N SER A 255 " --> pdb=" O ALA A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.517A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.505A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 581 removed outlier: 5.213A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 4.206A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.804A pdb=" N ILE A 715 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 729 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 778 through 790 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 833 through 840 Processing helix chain 'A' and resid 855 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 891 removed outlier: 4.068A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 915 Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'B' and resid 81 through 99 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 180 Processing sheet with id=AA1, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.589A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ILE A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY A 203 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.533A pdb=" N VAL A 335 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL A 341 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE A 333 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N SER A 343 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG A 331 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 345 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 390 removed outlier: 6.281A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 390 removed outlier: 6.281A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 400 removed outlier: 6.189A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA7, first strand: chain 'A' and resid 816 through 821 319 hydrogen bonds defined for protein. 864 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: 2.22 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1232 1.32 - 1.45: 1957 1.45 - 1.58: 3498 1.58 - 1.70: 15 1.70 - 1.83: 81 Bond restraints: 6783 Sorted by residual: bond pdb=" CB TYR A 884 " pdb=" CG TYR A 884 " ideal model delta sigma weight residual 1.512 1.424 0.088 2.20e-02 2.07e+03 1.60e+01 bond pdb=" NE ARG A 365 " pdb=" CZ ARG A 365 " ideal model delta sigma weight residual 1.326 1.370 -0.044 1.10e-02 8.26e+03 1.58e+01 bond pdb=" CB ILE B 107 " pdb=" CG1 ILE B 107 " ideal model delta sigma weight residual 1.530 1.609 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" CB LEU B 91 " pdb=" CG LEU B 91 " ideal model delta sigma weight residual 1.530 1.606 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" NE1 TRP A 290 " pdb=" CE2 TRP A 290 " ideal model delta sigma weight residual 1.370 1.329 0.041 1.10e-02 8.26e+03 1.38e+01 ... (remaining 6778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 7482 1.86 - 3.72: 1410 3.72 - 5.58: 266 5.58 - 7.44: 43 7.44 - 9.30: 9 Bond angle restraints: 9210 Sorted by residual: angle pdb=" C ASP A 377 " pdb=" N PRO A 378 " pdb=" CA PRO A 378 " ideal model delta sigma weight residual 119.56 127.07 -7.51 1.02e+00 9.61e-01 5.42e+01 angle pdb=" C MET A 626 " pdb=" N PRO A 627 " pdb=" CA PRO A 627 " ideal model delta sigma weight residual 119.78 127.04 -7.26 1.03e+00 9.43e-01 4.96e+01 angle pdb=" C ASN A 168 " pdb=" N PRO A 169 " pdb=" CA PRO A 169 " ideal model delta sigma weight residual 119.82 126.63 -6.81 9.80e-01 1.04e+00 4.83e+01 angle pdb=" CA ASP A 194 " pdb=" CB ASP A 194 " pdb=" CG ASP A 194 " ideal model delta sigma weight residual 112.60 119.47 -6.87 1.00e+00 1.00e+00 4.72e+01 angle pdb=" N ILE A 757 " pdb=" CA ILE A 757 " pdb=" C ILE A 757 " ideal model delta sigma weight residual 108.11 117.41 -9.30 1.40e+00 5.10e-01 4.41e+01 ... (remaining 9205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 3896 17.22 - 34.44: 103 34.44 - 51.66: 16 51.66 - 68.88: 9 68.88 - 86.11: 5 Dihedral angle restraints: 4029 sinusoidal: 1576 harmonic: 2453 Sorted by residual: dihedral pdb=" C HIS A 295 " pdb=" N HIS A 295 " pdb=" CA HIS A 295 " pdb=" CB HIS A 295 " ideal model delta harmonic sigma weight residual -122.60 -113.98 -8.62 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CA ILE B 120 " pdb=" CB ILE B 120 " ideal model delta harmonic sigma weight residual 123.40 131.72 -8.32 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" CA PRO A 830 " pdb=" C PRO A 830 " pdb=" N TYR A 831 " pdb=" CA TYR A 831 " ideal model delta harmonic sigma weight residual 180.00 163.43 16.57 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 4026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 623 0.070 - 0.140: 281 0.140 - 0.210: 89 0.210 - 0.279: 29 0.279 - 0.349: 4 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CA TYR A 867 " pdb=" N TYR A 867 " pdb=" C TYR A 867 " pdb=" CB TYR A 867 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA PHE B 92 " pdb=" N PHE B 92 " pdb=" C PHE B 92 " pdb=" CB PHE B 92 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA MET A 242 " pdb=" N MET A 242 " pdb=" C MET A 242 " pdb=" CB MET A 242 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 1023 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 619 " 0.072 2.00e-02 2.50e+03 3.93e-02 3.09e+01 pdb=" CG TYR A 619 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 619 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR A 619 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR A 619 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 619 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 619 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 619 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 509 " -0.046 2.00e-02 2.50e+03 2.25e-02 1.26e+01 pdb=" CG TRP A 509 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 509 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 509 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP A 509 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 509 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 509 " 0.029 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 509 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 509 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 509 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 237 " 0.048 2.00e-02 2.50e+03 2.50e-02 1.25e+01 pdb=" CG TYR A 237 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 237 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 237 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 237 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 237 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 237 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 237 " 0.034 2.00e-02 2.50e+03 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1997 2.82 - 3.34: 6272 3.34 - 3.86: 11632 3.86 - 4.38: 14206 4.38 - 4.90: 22527 Nonbonded interactions: 56634 Sorted by model distance: nonbonded pdb=" OH TYR A 175 " pdb=" OH TYR A 787 " model vdw 2.301 3.040 nonbonded pdb=" OG1 THR A 189 " pdb=" OH TYR A 237 " model vdw 2.418 3.040 nonbonded pdb=" NZ LYS A 478 " pdb=" OD1 ASP A 743 " model vdw 2.458 3.120 nonbonded pdb=" N ASP A 258 " pdb=" OD1 ASP A 258 " model vdw 2.460 3.120 nonbonded pdb=" N ASP B 112 " pdb=" OD1 ASP B 112 " model vdw 2.464 3.120 ... (remaining 56629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.950 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 21.060 Find NCS groups from input model: 0.070 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:4.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 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 : 0.016 0.094 6783 Z= 1.029 Angle : 1.568 9.299 9210 Z= 1.081 Chirality : 0.090 0.349 1026 Planarity : 0.009 0.039 1176 Dihedral : 9.782 86.106 2445 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.30 (0.28), residues: 811 helix: -0.34 (0.24), residues: 354 sheet: 0.55 (0.60), residues: 63 loop : 0.94 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.011 TRP A 509 HIS 0.017 0.002 HIS A 613 PHE 0.032 0.006 PHE A 859 TYR 0.072 0.008 TYR A 619 ARG 0.008 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 263 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 GLN cc_start: 0.7702 (mt0) cc_final: 0.7485 (mt0) outliers start: 1 outliers final: 1 residues processed: 264 average time/residue: 0.2122 time to fit residues: 71.8005 Evaluate side-chains 168 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 HIS ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A 752 HIS ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.194264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.171564 restraints weight = 8636.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.176244 restraints weight = 4034.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.179140 restraints weight = 2344.380| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6783 Z= 0.230 Angle : 0.615 6.492 9210 Z= 0.336 Chirality : 0.044 0.235 1026 Planarity : 0.005 0.043 1176 Dihedral : 4.805 35.610 909 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.19 % Allowed : 10.84 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.78 (0.29), residues: 811 helix: 0.73 (0.27), residues: 360 sheet: 0.31 (0.59), residues: 74 loop : 0.56 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 917 HIS 0.006 0.001 HIS A 872 PHE 0.026 0.002 PHE A 471 TYR 0.023 0.002 TYR A 530 ARG 0.003 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7673 (tttm) cc_final: 0.7145 (mmmt) REVERT: A 173 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7679 (ptt90) REVERT: A 509 TRP cc_start: 0.7379 (m-10) cc_final: 0.6937 (m-90) REVERT: A 666 MET cc_start: 0.5935 (mmm) cc_final: 0.4956 (mmm) REVERT: A 763 VAL cc_start: 0.8050 (m) cc_final: 0.7842 (p) REVERT: A 913 THR cc_start: 0.7915 (m) cc_final: 0.7640 (t) outliers start: 16 outliers final: 9 residues processed: 182 average time/residue: 0.1853 time to fit residues: 44.9431 Evaluate side-chains 154 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 483 TYR Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 18 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 0.0870 chunk 22 optimal weight: 0.6980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.187152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.164590 restraints weight = 8947.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.169174 restraints weight = 4219.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.171930 restraints weight = 2456.365| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6783 Z= 0.214 Angle : 0.565 6.182 9210 Z= 0.304 Chirality : 0.043 0.152 1026 Planarity : 0.005 0.042 1176 Dihedral : 4.736 31.057 909 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.61 % Allowed : 12.62 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.72 (0.29), residues: 811 helix: 0.84 (0.27), residues: 359 sheet: 0.38 (0.58), residues: 73 loop : 0.32 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 154 HIS 0.005 0.001 HIS A 599 PHE 0.028 0.002 PHE A 753 TYR 0.024 0.002 TYR A 530 ARG 0.003 0.000 ARG A 735 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7565 (tttm) cc_final: 0.7110 (mmmt) REVERT: A 173 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7763 (ptt90) REVERT: A 324 THR cc_start: 0.8442 (p) cc_final: 0.8060 (t) REVERT: A 343 SER cc_start: 0.8065 (m) cc_final: 0.7654 (m) REVERT: A 509 TRP cc_start: 0.7494 (m-10) cc_final: 0.6867 (m-90) REVERT: A 513 ARG cc_start: 0.6438 (ttm110) cc_final: 0.6104 (ttm110) REVERT: A 666 MET cc_start: 0.6039 (mmm) cc_final: 0.4979 (mmm) REVERT: A 668 MET cc_start: 0.8134 (mtp) cc_final: 0.7660 (mtp) REVERT: A 714 LYS cc_start: 0.7718 (mmtm) cc_final: 0.6853 (tptp) REVERT: A 763 VAL cc_start: 0.8032 (m) cc_final: 0.7735 (p) REVERT: A 794 MET cc_start: 0.6041 (ttp) cc_final: 0.5757 (ptm) outliers start: 19 outliers final: 11 residues processed: 171 average time/residue: 0.1696 time to fit residues: 39.7110 Evaluate side-chains 153 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 17 optimal weight: 0.0770 chunk 80 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.187769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.165176 restraints weight = 9073.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.169698 restraints weight = 4362.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.172489 restraints weight = 2567.471| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6783 Z= 0.187 Angle : 0.518 5.962 9210 Z= 0.278 Chirality : 0.041 0.128 1026 Planarity : 0.004 0.044 1176 Dihedral : 4.491 23.640 907 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.02 % Allowed : 14.40 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.79 (0.29), residues: 811 helix: 0.91 (0.28), residues: 360 sheet: 0.43 (0.57), residues: 73 loop : 0.34 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 917 HIS 0.008 0.001 HIS A 309 PHE 0.024 0.002 PHE A 753 TYR 0.024 0.001 TYR A 530 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7559 (tttm) cc_final: 0.7098 (mmmt) REVERT: A 324 THR cc_start: 0.8422 (p) cc_final: 0.8110 (t) REVERT: A 343 SER cc_start: 0.8064 (m) cc_final: 0.7619 (m) REVERT: A 509 TRP cc_start: 0.7474 (m-10) cc_final: 0.6790 (m-90) REVERT: A 540 THR cc_start: 0.8014 (t) cc_final: 0.7729 (t) REVERT: A 666 MET cc_start: 0.5931 (mmm) cc_final: 0.4924 (mmm) REVERT: A 668 MET cc_start: 0.8057 (mtp) cc_final: 0.7855 (mtp) REVERT: A 714 LYS cc_start: 0.7727 (mmtm) cc_final: 0.6832 (tptp) REVERT: A 794 MET cc_start: 0.6005 (ttp) cc_final: 0.5586 (ptm) REVERT: A 855 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.5491 (ptt) REVERT: B 96 ARG cc_start: 0.6422 (mmm160) cc_final: 0.6113 (mtp-110) outliers start: 22 outliers final: 14 residues processed: 161 average time/residue: 0.1859 time to fit residues: 40.3080 Evaluate side-chains 157 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.1980 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** 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 = 0.4120 r_free = 0.4120 target = 0.183566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.160094 restraints weight = 8973.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164497 restraints weight = 4318.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.167087 restraints weight = 2560.009| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6783 Z= 0.187 Angle : 0.525 6.187 9210 Z= 0.279 Chirality : 0.041 0.139 1026 Planarity : 0.004 0.043 1176 Dihedral : 4.423 23.900 907 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.61 % Allowed : 13.99 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.83 (0.30), residues: 811 helix: 0.97 (0.28), residues: 360 sheet: 0.38 (0.57), residues: 73 loop : 0.34 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 917 HIS 0.006 0.001 HIS A 309 PHE 0.026 0.002 PHE A 753 TYR 0.014 0.001 TYR A 619 ARG 0.006 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7670 (tttm) cc_final: 0.7201 (mmmt) REVERT: A 324 THR cc_start: 0.8441 (p) cc_final: 0.8093 (t) REVERT: A 343 SER cc_start: 0.8072 (m) cc_final: 0.7635 (m) REVERT: A 509 TRP cc_start: 0.7437 (m-90) cc_final: 0.6757 (m-90) REVERT: A 540 THR cc_start: 0.8058 (t) cc_final: 0.7750 (t) REVERT: A 666 MET cc_start: 0.5831 (mmm) cc_final: 0.4828 (mmm) REVERT: A 668 MET cc_start: 0.8138 (mtp) cc_final: 0.7897 (mtp) REVERT: A 714 LYS cc_start: 0.7814 (mmtm) cc_final: 0.6838 (tptp) REVERT: A 794 MET cc_start: 0.6220 (ttp) cc_final: 0.5698 (ptm) REVERT: A 855 MET cc_start: 0.5600 (OUTLIER) cc_final: 0.5389 (ptt) outliers start: 19 outliers final: 16 residues processed: 159 average time/residue: 0.1536 time to fit residues: 34.0786 Evaluate side-chains 161 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 9 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 5 optimal weight: 0.0370 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.179929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.157036 restraints weight = 8886.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.161291 restraints weight = 4307.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.163858 restraints weight = 2579.828| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6783 Z= 0.217 Angle : 0.548 6.610 9210 Z= 0.286 Chirality : 0.042 0.181 1026 Planarity : 0.004 0.046 1176 Dihedral : 4.474 23.595 907 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.16 % Allowed : 13.85 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.74 (0.30), residues: 811 helix: 0.91 (0.28), residues: 362 sheet: 0.24 (0.57), residues: 73 loop : 0.29 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 917 HIS 0.005 0.001 HIS A 309 PHE 0.018 0.002 PHE A 753 TYR 0.026 0.002 TYR A 530 ARG 0.003 0.000 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7720 (tttm) cc_final: 0.7235 (mmmt) REVERT: A 291 ASP cc_start: 0.7930 (p0) cc_final: 0.7671 (p0) REVERT: A 324 THR cc_start: 0.8438 (p) cc_final: 0.8152 (t) REVERT: A 343 SER cc_start: 0.8142 (m) cc_final: 0.7723 (m) REVERT: A 509 TRP cc_start: 0.7436 (m-90) cc_final: 0.6770 (m-90) REVERT: A 540 THR cc_start: 0.8225 (t) cc_final: 0.7962 (t) REVERT: A 666 MET cc_start: 0.5851 (mmm) cc_final: 0.4735 (mmm) REVERT: A 714 LYS cc_start: 0.7773 (mmtm) cc_final: 0.6819 (tptp) REVERT: A 794 MET cc_start: 0.6324 (ttp) cc_final: 0.5778 (ptm) REVERT: A 825 ASP cc_start: 0.6867 (t70) cc_final: 0.6493 (p0) REVERT: B 96 ARG cc_start: 0.6835 (tpt170) cc_final: 0.6441 (mmm160) outliers start: 23 outliers final: 19 residues processed: 164 average time/residue: 0.1817 time to fit residues: 41.3120 Evaluate side-chains 168 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 HIS ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.181892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.158929 restraints weight = 8833.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.163181 restraints weight = 4325.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.165745 restraints weight = 2610.986| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 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 0.030 6783 Z= 0.184 Angle : 0.548 8.698 9210 Z= 0.282 Chirality : 0.041 0.144 1026 Planarity : 0.004 0.045 1176 Dihedral : 4.432 23.141 907 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.02 % Allowed : 15.50 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.73 (0.30), residues: 811 helix: 0.94 (0.28), residues: 372 sheet: 0.12 (0.57), residues: 73 loop : 0.25 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 917 HIS 0.005 0.001 HIS A 309 PHE 0.026 0.001 PHE A 753 TYR 0.022 0.001 TYR A 530 ARG 0.004 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7809 (tttm) cc_final: 0.7298 (mmmt) REVERT: A 257 MET cc_start: 0.5355 (ppp) cc_final: 0.4958 (ttp) REVERT: A 324 THR cc_start: 0.8384 (p) cc_final: 0.8163 (t) REVERT: A 380 MET cc_start: 0.6802 (mmp) cc_final: 0.6269 (mtp) REVERT: A 509 TRP cc_start: 0.7425 (m-90) cc_final: 0.6804 (m-90) REVERT: A 540 THR cc_start: 0.8196 (t) cc_final: 0.7971 (t) REVERT: A 666 MET cc_start: 0.5759 (mmm) cc_final: 0.4628 (mmm) REVERT: A 714 LYS cc_start: 0.7717 (mmtm) cc_final: 0.6892 (tptp) REVERT: A 825 ASP cc_start: 0.6881 (t70) cc_final: 0.6510 (p0) REVERT: B 96 ARG cc_start: 0.6711 (tpt170) cc_final: 0.6382 (mmm160) outliers start: 22 outliers final: 19 residues processed: 162 average time/residue: 0.1599 time to fit residues: 36.4002 Evaluate side-chains 166 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 HIS ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.182172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.159185 restraints weight = 8919.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.163454 restraints weight = 4327.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.166206 restraints weight = 2596.193| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6783 Z= 0.176 Angle : 0.532 7.037 9210 Z= 0.277 Chirality : 0.041 0.132 1026 Planarity : 0.004 0.043 1176 Dihedral : 4.393 22.914 907 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.61 % Allowed : 16.19 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.78 (0.30), residues: 811 helix: 0.99 (0.28), residues: 372 sheet: 0.04 (0.57), residues: 73 loop : 0.28 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 917 HIS 0.005 0.001 HIS A 309 PHE 0.022 0.001 PHE A 753 TYR 0.020 0.001 TYR A 530 ARG 0.003 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7823 (tttm) cc_final: 0.7330 (mmmt) REVERT: A 257 MET cc_start: 0.5258 (ppp) cc_final: 0.4846 (ttp) REVERT: A 324 THR cc_start: 0.8371 (p) cc_final: 0.8158 (t) REVERT: A 343 SER cc_start: 0.8139 (m) cc_final: 0.7709 (m) REVERT: A 509 TRP cc_start: 0.7438 (m-90) cc_final: 0.6824 (m-90) REVERT: A 540 THR cc_start: 0.8212 (t) cc_final: 0.7999 (t) REVERT: A 666 MET cc_start: 0.5667 (mmm) cc_final: 0.4568 (mmm) REVERT: A 714 LYS cc_start: 0.7773 (mmtm) cc_final: 0.6941 (tptp) REVERT: A 825 ASP cc_start: 0.6739 (t70) cc_final: 0.6426 (p0) outliers start: 19 outliers final: 17 residues processed: 154 average time/residue: 0.1596 time to fit residues: 34.5143 Evaluate side-chains 158 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** 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 = 0.4091 r_free = 0.4091 target = 0.181338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.158453 restraints weight = 8927.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.162725 restraints weight = 4330.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.165373 restraints weight = 2600.711| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6783 Z= 0.186 Angle : 0.550 6.960 9210 Z= 0.288 Chirality : 0.042 0.304 1026 Planarity : 0.004 0.044 1176 Dihedral : 4.376 22.382 907 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.74 % Allowed : 16.32 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.74 (0.30), residues: 811 helix: 0.96 (0.28), residues: 373 sheet: 0.12 (0.58), residues: 71 loop : 0.24 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 917 HIS 0.005 0.001 HIS A 309 PHE 0.023 0.001 PHE A 753 TYR 0.019 0.001 TYR A 530 ARG 0.003 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7831 (tttm) cc_final: 0.7347 (mmmt) REVERT: A 343 SER cc_start: 0.8195 (m) cc_final: 0.7792 (m) REVERT: A 497 ASN cc_start: 0.8459 (t0) cc_final: 0.7937 (t0) REVERT: A 509 TRP cc_start: 0.7474 (m-90) cc_final: 0.6851 (m-90) REVERT: A 540 THR cc_start: 0.8228 (t) cc_final: 0.8027 (t) REVERT: A 666 MET cc_start: 0.5615 (mmm) cc_final: 0.4526 (mmm) REVERT: A 714 LYS cc_start: 0.7727 (mmtm) cc_final: 0.6978 (tptp) REVERT: A 825 ASP cc_start: 0.6797 (t70) cc_final: 0.6439 (p0) REVERT: B 149 TYR cc_start: 0.7433 (t80) cc_final: 0.7041 (t80) outliers start: 20 outliers final: 19 residues processed: 152 average time/residue: 0.1496 time to fit residues: 32.3955 Evaluate side-chains 162 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 31 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 3 optimal weight: 0.0020 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 HIS ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.182209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.159183 restraints weight = 9009.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.163468 restraints weight = 4366.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.166181 restraints weight = 2624.588| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6783 Z= 0.170 Angle : 0.537 7.409 9210 Z= 0.281 Chirality : 0.043 0.316 1026 Planarity : 0.004 0.052 1176 Dihedral : 4.347 22.055 907 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.74 % Allowed : 16.60 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.80 (0.30), residues: 811 helix: 1.03 (0.28), residues: 373 sheet: 0.08 (0.56), residues: 77 loop : 0.26 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 268 HIS 0.005 0.001 HIS A 309 PHE 0.021 0.001 PHE A 753 TYR 0.019 0.001 TYR A 530 ARG 0.003 0.000 ARG A 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1622 Ramachandran restraints generated. 811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7836 (tttm) cc_final: 0.7363 (mmmt) REVERT: A 257 MET cc_start: 0.5533 (ppp) cc_final: 0.5297 (ttt) REVERT: A 343 SER cc_start: 0.8192 (m) cc_final: 0.7795 (m) REVERT: A 497 ASN cc_start: 0.8418 (t0) cc_final: 0.7902 (t0) REVERT: A 509 TRP cc_start: 0.7500 (m-90) cc_final: 0.6899 (m-90) REVERT: A 666 MET cc_start: 0.5591 (mmm) cc_final: 0.4521 (mmm) REVERT: A 714 LYS cc_start: 0.7719 (mmtm) cc_final: 0.7018 (tptp) REVERT: A 825 ASP cc_start: 0.6844 (t70) cc_final: 0.6481 (p0) REVERT: B 149 TYR cc_start: 0.7395 (t80) cc_final: 0.6966 (t80) outliers start: 20 outliers final: 18 residues processed: 150 average time/residue: 0.1618 time to fit residues: 33.6941 Evaluate side-chains 158 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 10.0000 chunk 59 optimal weight: 0.0670 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 11 optimal weight: 0.0870 chunk 40 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 ASN ** 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 = 0.4140 r_free = 0.4140 target = 0.186231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.163479 restraints weight = 8853.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.167807 restraints weight = 4283.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170567 restraints weight = 2559.340| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.6205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6783 Z= 0.137 Angle : 0.526 9.066 9210 Z= 0.274 Chirality : 0.041 0.271 1026 Planarity : 0.004 0.045 1176 Dihedral : 4.181 21.157 907 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.92 % Allowed : 17.70 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.98 (0.30), residues: 811 helix: 1.15 (0.28), residues: 373 sheet: 0.14 (0.57), residues: 77 loop : 0.39 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 917 HIS 0.005 0.001 HIS A 309 PHE 0.021 0.001 PHE A 753 TYR 0.018 0.001 TYR A 530 ARG 0.004 0.000 ARG A 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2195.37 seconds wall clock time: 40 minutes 23.08 seconds (2423.08 seconds total)