Starting phenix.real_space_refine on Sun Apr 27 23:44:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nus_0521/04_2025/6nus_0521.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nus_0521/04_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_0521/04_2025/6nus_0521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nus_0521/04_2025/6nus_0521.map" model { file = "/net/cci-nas-00/data/ceres_data/6nus_0521/04_2025/6nus_0521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nus_0521/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 6.00, per 1000 atoms: 0.90 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: 1.86 Conformation dependent library (CDL) restraints added in 1.6 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: 1.13 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: 2.33 Time building geometry restraints manager: 2.18 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: 1.350 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.790 Find NCS groups from input model: 0.090 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:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.130 ------------------------------------------------------------------------------- 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 : 0.019 0.721 6791 Z= 0.874 Angle : 1.646 25.451 9216 Z= 1.088 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 Details of bonding type rmsd hydrogen bonds : bond 0.16731 ( 310) hydrogen bonds : angle 6.70815 ( 864) metal coordination : bond 0.31958 ( 8) metal coordination : angle 19.78734 ( 6) covalent geometry : bond 0.01603 ( 6783) covalent geometry : angle 1.56754 ( 9210) *********************** 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 : 0.687 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: 0.3142 time to fit residues: 106.7953 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 : 0.733 ------------------------------------------------------------------------------- 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: 0.9980 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.4210 r_free = 0.4210 target = 0.193114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170455 restraints weight = 8656.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.175156 restraints weight = 4057.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.178057 restraints weight = 2347.566| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6791 Z= 0.157 Angle : 0.621 5.977 9216 Z= 0.338 Chirality : 0.044 0.222 1026 Planarity : 0.005 0.042 1176 Dihedral : 4.825 35.123 909 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.19 % Allowed : 11.11 % Favored : 86.69 % 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 (0.29), residues: 811 helix: 0.71 (0.27), residues: 360 sheet: 0.45 (0.60), residues: 72 loop : 0.59 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 917 HIS 0.006 0.001 HIS A 872 PHE 0.028 0.002 PHE A 471 TYR 0.024 0.002 TYR A 530 ARG 0.004 0.001 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.04664 ( 310) hydrogen bonds : angle 5.13195 ( 864) metal coordination : bond 0.01355 ( 8) metal coordination : angle 2.72194 ( 6) covalent geometry : bond 0.00344 ( 6783) covalent geometry : angle 0.61697 ( 9210) *********************** 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 189 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7679 (tttm) cc_final: 0.7147 (mmmt) REVERT: A 173 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7764 (ptt90) REVERT: A 509 TRP cc_start: 0.7403 (m-10) cc_final: 0.6960 (m-90) REVERT: A 666 MET cc_start: 0.5944 (mmm) cc_final: 0.4874 (mmm) REVERT: A 807 LYS cc_start: 0.7846 (ptpt) cc_final: 0.6973 (tmtt) REVERT: A 913 THR cc_start: 0.7919 (m) cc_final: 0.7651 (t) outliers start: 16 outliers final: 9 residues processed: 181 average time/residue: 0.1970 time to fit residues: 47.3889 Evaluate side-chains 155 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 820 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 129 MET 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: 1.9990 chunk 45 optimal weight: 0.0970 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4172 r_free = 0.4172 target = 0.189098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.166822 restraints weight = 8933.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.171394 restraints weight = 4204.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.174222 restraints weight = 2441.080| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6791 Z= 0.138 Angle : 0.555 6.416 9216 Z= 0.299 Chirality : 0.042 0.150 1026 Planarity : 0.004 0.043 1176 Dihedral : 4.710 31.846 909 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.19 % Allowed : 12.89 % Favored : 84.91 % 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: 0.81 (0.29), residues: 811 helix: 0.89 (0.27), residues: 360 sheet: 0.48 (0.57), residues: 73 loop : 0.37 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 917 HIS 0.003 0.001 HIS A 599 PHE 0.029 0.002 PHE A 753 TYR 0.023 0.001 TYR A 530 ARG 0.003 0.000 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 310) hydrogen bonds : angle 4.88447 ( 864) metal coordination : bond 0.00506 ( 8) metal coordination : angle 1.83993 ( 6) covalent geometry : bond 0.00305 ( 6783) covalent geometry : angle 0.55358 ( 9210) *********************** 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 173 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7517 (tttm) cc_final: 0.7044 (mmmt) REVERT: A 173 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7750 (ptt90) REVERT: A 324 THR cc_start: 0.8403 (p) cc_final: 0.8029 (t) REVERT: A 343 SER cc_start: 0.8006 (m) cc_final: 0.7586 (m) REVERT: A 509 TRP cc_start: 0.7497 (m-10) cc_final: 0.6913 (m-90) REVERT: A 666 MET cc_start: 0.5973 (mmm) cc_final: 0.4921 (mmm) REVERT: A 668 MET cc_start: 0.8141 (mtp) cc_final: 0.7667 (mtp) REVERT: A 714 LYS cc_start: 0.7753 (mmtm) cc_final: 0.6857 (tptp) REVERT: A 794 MET cc_start: 0.6082 (ttp) cc_final: 0.5724 (ptm) outliers start: 16 outliers final: 10 residues processed: 166 average time/residue: 0.1904 time to fit residues: 43.3452 Evaluate side-chains 150 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 649 SER 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 B residue 83 VAL 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: 0.9990 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 80 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.188512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.166303 restraints weight = 9014.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.170743 restraints weight = 4244.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.173444 restraints weight = 2493.354| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6791 Z= 0.125 Angle : 0.522 5.916 9216 Z= 0.281 Chirality : 0.042 0.143 1026 Planarity : 0.004 0.044 1176 Dihedral : 4.496 24.133 907 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.57 % Allowed : 13.85 % 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: 0.78 (0.29), residues: 811 helix: 0.91 (0.28), residues: 359 sheet: 0.46 (0.59), residues: 61 loop : 0.32 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 917 HIS 0.008 0.001 HIS A 309 PHE 0.027 0.002 PHE A 471 TYR 0.023 0.001 TYR A 530 ARG 0.006 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 310) hydrogen bonds : angle 4.81886 ( 864) metal coordination : bond 0.00480 ( 8) metal coordination : angle 1.60754 ( 6) covalent geometry : bond 0.00283 ( 6783) covalent geometry : angle 0.52061 ( 9210) *********************** 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 188 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7588 (tttm) cc_final: 0.7096 (mmmt) REVERT: A 324 THR cc_start: 0.8404 (p) cc_final: 0.8078 (t) REVERT: A 343 SER cc_start: 0.8055 (m) cc_final: 0.7596 (m) REVERT: A 509 TRP cc_start: 0.7456 (m-10) cc_final: 0.6742 (m-90) REVERT: A 540 THR cc_start: 0.8000 (t) cc_final: 0.7707 (t) REVERT: A 666 MET cc_start: 0.5947 (mmm) cc_final: 0.4941 (mmm) REVERT: A 668 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7896 (mtp) REVERT: A 714 LYS cc_start: 0.7739 (mmtm) cc_final: 0.6818 (tptp) REVERT: A 794 MET cc_start: 0.6036 (ttp) cc_final: 0.5633 (ptm) REVERT: B 87 MET cc_start: 0.7799 (mtm) cc_final: 0.7585 (mtm) REVERT: B 89 THR cc_start: 0.8163 (m) cc_final: 0.7869 (p) outliers start: 26 outliers final: 17 residues processed: 172 average time/residue: 0.1756 time to fit residues: 41.0918 Evaluate side-chains 162 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 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 668 MET 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 856 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 913 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.182613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.159726 restraints weight = 8996.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.164097 restraints weight = 4308.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.166725 restraints weight = 2547.746| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6791 Z= 0.138 Angle : 0.538 6.380 9216 Z= 0.284 Chirality : 0.042 0.128 1026 Planarity : 0.004 0.044 1176 Dihedral : 4.475 24.409 907 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.47 % Allowed : 15.64 % Favored : 81.89 % 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: 0.75 (0.30), residues: 811 helix: 0.95 (0.28), residues: 359 sheet: 0.43 (0.58), residues: 73 loop : 0.22 (0.33), residues: 379 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 0.029 0.002 PHE A 753 TYR 0.015 0.001 TYR A 619 ARG 0.005 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 310) hydrogen bonds : angle 4.66392 ( 864) metal coordination : bond 0.00527 ( 8) metal coordination : angle 2.13372 ( 6) covalent geometry : bond 0.00321 ( 6783) covalent geometry : angle 0.53541 ( 9210) *********************** 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 168 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7703 (tttm) cc_final: 0.7124 (mmmt) REVERT: A 324 THR cc_start: 0.8464 (p) cc_final: 0.8114 (t) REVERT: A 343 SER cc_start: 0.8081 (m) cc_final: 0.7635 (m) REVERT: A 509 TRP cc_start: 0.7429 (m-90) cc_final: 0.6759 (m-90) REVERT: A 540 THR cc_start: 0.8055 (t) cc_final: 0.7733 (t) REVERT: A 666 MET cc_start: 0.5874 (mmm) cc_final: 0.4877 (mmm) REVERT: A 714 LYS cc_start: 0.7809 (mmtm) cc_final: 0.6848 (tptp) REVERT: A 794 MET cc_start: 0.6263 (ttp) cc_final: 0.5714 (ptm) REVERT: B 94 MET cc_start: 0.7948 (mmt) cc_final: 0.7733 (tpt) outliers start: 18 outliers final: 17 residues processed: 157 average time/residue: 0.1463 time to fit residues: 32.7030 Evaluate side-chains 160 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 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 856 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 913 THR 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: 3.9990 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 5 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.183525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.160503 restraints weight = 8798.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.164801 restraints weight = 4289.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.167558 restraints weight = 2576.764| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6791 Z= 0.111 Angle : 0.520 6.350 9216 Z= 0.269 Chirality : 0.041 0.164 1026 Planarity : 0.004 0.044 1176 Dihedral : 4.335 23.494 907 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: 0.82 (0.30), residues: 811 helix: 0.95 (0.28), residues: 364 sheet: 0.37 (0.57), residues: 73 loop : 0.33 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 917 HIS 0.005 0.001 HIS A 309 PHE 0.021 0.001 PHE A 753 TYR 0.026 0.001 TYR A 530 ARG 0.009 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03277 ( 310) hydrogen bonds : angle 4.56708 ( 864) metal coordination : bond 0.00503 ( 8) metal coordination : angle 1.72037 ( 6) covalent geometry : bond 0.00254 ( 6783) covalent geometry : angle 0.51819 ( 9210) *********************** 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 173 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7684 (tttm) cc_final: 0.7191 (mmmt) REVERT: A 291 ASP cc_start: 0.7927 (p0) cc_final: 0.7685 (p0) REVERT: A 324 THR cc_start: 0.8414 (p) cc_final: 0.8089 (t) REVERT: A 343 SER cc_start: 0.8085 (m) cc_final: 0.7627 (m) REVERT: A 509 TRP cc_start: 0.7421 (m-90) cc_final: 0.6779 (m-90) REVERT: A 540 THR cc_start: 0.8136 (t) cc_final: 0.7839 (t) REVERT: A 666 MET cc_start: 0.5712 (mmm) cc_final: 0.4637 (mmm) REVERT: A 714 LYS cc_start: 0.7763 (mmtm) cc_final: 0.6828 (tptp) REVERT: A 794 MET cc_start: 0.6157 (ttp) cc_final: 0.5726 (ptm) REVERT: A 825 ASP cc_start: 0.6839 (t70) cc_final: 0.6520 (p0) outliers start: 19 outliers final: 15 residues processed: 161 average time/residue: 0.1592 time to fit residues: 35.8589 Evaluate side-chains 158 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 495 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 80 optimal weight: 0.0970 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.185697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.162672 restraints weight = 8798.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.166958 restraints weight = 4243.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.169686 restraints weight = 2532.931| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6791 Z= 0.103 Angle : 0.531 8.894 9216 Z= 0.271 Chirality : 0.042 0.321 1026 Planarity : 0.004 0.045 1176 Dihedral : 4.232 23.326 907 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.61 % Allowed : 16.60 % Favored : 80.80 % 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: 0.95 (0.30), residues: 811 helix: 1.00 (0.28), residues: 373 sheet: 0.31 (0.57), residues: 71 loop : 0.50 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 917 HIS 0.005 0.001 HIS A 309 PHE 0.019 0.001 PHE A 753 TYR 0.028 0.001 TYR A 530 ARG 0.003 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 310) hydrogen bonds : angle 4.50035 ( 864) metal coordination : bond 0.00415 ( 8) metal coordination : angle 1.45723 ( 6) covalent geometry : bond 0.00231 ( 6783) covalent geometry : angle 0.52997 ( 9210) *********************** 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 175 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7763 (tttm) cc_final: 0.7213 (mmmt) REVERT: A 324 THR cc_start: 0.8406 (p) cc_final: 0.8077 (t) REVERT: A 509 TRP cc_start: 0.7415 (m-90) cc_final: 0.6744 (m-90) REVERT: A 540 THR cc_start: 0.8148 (t) cc_final: 0.7926 (t) REVERT: A 714 LYS cc_start: 0.7747 (mmtm) cc_final: 0.6898 (tptp) REVERT: A 794 MET cc_start: 0.6274 (ttp) cc_final: 0.6065 (ttm) REVERT: A 825 ASP cc_start: 0.6848 (t70) cc_final: 0.6507 (p0) outliers start: 19 outliers final: 17 residues processed: 163 average time/residue: 0.1582 time to fit residues: 36.0708 Evaluate side-chains 165 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 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 153 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.0070 chunk 44 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** 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 ** 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 = 0.4091 r_free = 0.4091 target = 0.181256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.158046 restraints weight = 8875.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.162198 restraints weight = 4339.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.164862 restraints weight = 2646.641| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6791 Z= 0.147 Angle : 0.581 11.526 9216 Z= 0.295 Chirality : 0.043 0.305 1026 Planarity : 0.004 0.051 1176 Dihedral : 4.334 22.946 907 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.02 % Allowed : 16.60 % 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: 0.78 (0.30), residues: 811 helix: 0.90 (0.28), residues: 372 sheet: 0.33 (0.59), residues: 71 loop : 0.33 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.005 0.001 HIS A 309 PHE 0.026 0.002 PHE A 753 TYR 0.025 0.002 TYR A 530 ARG 0.007 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 310) hydrogen bonds : angle 4.68452 ( 864) metal coordination : bond 0.00777 ( 8) metal coordination : angle 1.78412 ( 6) covalent geometry : bond 0.00342 ( 6783) covalent geometry : angle 0.57979 ( 9210) *********************** 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 163 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7827 (tttm) cc_final: 0.7323 (mmmt) REVERT: A 343 SER cc_start: 0.8138 (m) cc_final: 0.7716 (m) REVERT: A 509 TRP cc_start: 0.7492 (m-90) cc_final: 0.6851 (m-90) REVERT: A 540 THR cc_start: 0.8213 (t) cc_final: 0.7984 (t) REVERT: A 666 MET cc_start: 0.5722 (mmm) cc_final: 0.4661 (mmm) REVERT: A 714 LYS cc_start: 0.7719 (mmtm) cc_final: 0.6941 (tptp) REVERT: A 794 MET cc_start: 0.6268 (ttp) cc_final: 0.6035 (ttm) REVERT: A 825 ASP cc_start: 0.6896 (t70) cc_final: 0.6554 (p0) outliers start: 22 outliers final: 20 residues processed: 150 average time/residue: 0.1592 time to fit residues: 33.4955 Evaluate side-chains 158 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 668 MET 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 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 164 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.183520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.160512 restraints weight = 8879.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.164769 restraints weight = 4311.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.167466 restraints weight = 2593.292| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6791 Z= 0.113 Angle : 0.548 10.427 9216 Z= 0.279 Chirality : 0.042 0.276 1026 Planarity : 0.004 0.045 1176 Dihedral : 4.250 21.983 907 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.61 % Allowed : 17.28 % Favored : 80.11 % 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: 0.87 (0.30), residues: 811 helix: 1.01 (0.28), residues: 372 sheet: 0.28 (0.58), residues: 71 loop : 0.36 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 917 HIS 0.005 0.001 HIS A 381 PHE 0.024 0.001 PHE A 753 TYR 0.023 0.001 TYR A 530 ARG 0.003 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 310) hydrogen bonds : angle 4.57655 ( 864) metal coordination : bond 0.00463 ( 8) metal coordination : angle 1.60196 ( 6) covalent geometry : bond 0.00261 ( 6783) covalent geometry : angle 0.54636 ( 9210) *********************** 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 159 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7805 (tttm) cc_final: 0.7324 (mmmt) REVERT: A 343 SER cc_start: 0.8120 (m) cc_final: 0.7697 (m) REVERT: A 380 MET cc_start: 0.6845 (mmp) cc_final: 0.6418 (mmm) REVERT: A 497 ASN cc_start: 0.8465 (t0) cc_final: 0.7966 (t0) REVERT: A 509 TRP cc_start: 0.7507 (m-90) cc_final: 0.6879 (m-90) REVERT: A 540 THR cc_start: 0.8229 (t) cc_final: 0.8025 (t) REVERT: A 714 LYS cc_start: 0.7784 (mmtm) cc_final: 0.6986 (tptp) REVERT: A 825 ASP cc_start: 0.6881 (t70) cc_final: 0.6511 (p0) REVERT: B 149 TYR cc_start: 0.7423 (t80) cc_final: 0.7079 (t80) outliers start: 19 outliers final: 18 residues processed: 147 average time/residue: 0.1443 time to fit residues: 30.0787 Evaluate side-chains 154 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 668 MET 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 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: 1.9990 chunk 74 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 48 optimal weight: 0.0060 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.182406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.159410 restraints weight = 9002.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.163669 restraints weight = 4353.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.166421 restraints weight = 2601.930| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6791 Z= 0.120 Angle : 0.573 10.068 9216 Z= 0.290 Chirality : 0.042 0.274 1026 Planarity : 0.004 0.044 1176 Dihedral : 4.259 22.198 907 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.88 % Allowed : 17.28 % Favored : 79.84 % 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: 0.87 (0.30), residues: 811 helix: 1.03 (0.28), residues: 372 sheet: 0.23 (0.59), residues: 71 loop : 0.35 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 268 HIS 0.005 0.001 HIS A 309 PHE 0.022 0.001 PHE A 753 TYR 0.023 0.001 TYR A 530 ARG 0.010 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 310) hydrogen bonds : angle 4.59212 ( 864) metal coordination : bond 0.00536 ( 8) metal coordination : angle 1.77041 ( 6) covalent geometry : bond 0.00282 ( 6783) covalent geometry : angle 0.57181 ( 9210) ********************** 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 162 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7816 (tttm) cc_final: 0.7347 (mmmt) REVERT: A 343 SER cc_start: 0.8152 (m) cc_final: 0.7719 (m) REVERT: A 380 MET cc_start: 0.6837 (mmp) cc_final: 0.6178 (mmm) REVERT: A 497 ASN cc_start: 0.8461 (t0) cc_final: 0.7969 (t0) REVERT: A 509 TRP cc_start: 0.7518 (m-90) cc_final: 0.6896 (m-90) REVERT: A 666 MET cc_start: 0.5622 (mmm) cc_final: 0.4574 (mmm) REVERT: A 714 LYS cc_start: 0.7725 (mmtm) cc_final: 0.7004 (tptp) REVERT: A 825 ASP cc_start: 0.6903 (t70) cc_final: 0.6543 (p0) REVERT: B 149 TYR cc_start: 0.7361 (t80) cc_final: 0.6965 (t80) outliers start: 21 outliers final: 19 residues processed: 151 average time/residue: 0.1410 time to fit residues: 30.4078 Evaluate side-chains 156 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 663 LEU Chi-restraints excluded: chain A residue 668 MET 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 820 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain B residue 129 MET 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: 0.5980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 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 572 HIS ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 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 = 0.4094 r_free = 0.4094 target = 0.181768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.159017 restraints weight = 8899.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.163181 restraints weight = 4303.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.165840 restraints weight = 2585.713| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6791 Z= 0.125 Angle : 0.574 10.110 9216 Z= 0.292 Chirality : 0.043 0.263 1026 Planarity : 0.004 0.043 1176 Dihedral : 4.270 22.340 907 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.02 % Allowed : 16.46 % Favored : 80.52 % 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: 0.87 (0.30), residues: 811 helix: 1.04 (0.28), residues: 372 sheet: 0.21 (0.58), residues: 71 loop : 0.34 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 268 HIS 0.005 0.001 HIS A 309 PHE 0.023 0.001 PHE A 753 TYR 0.022 0.001 TYR A 530 ARG 0.006 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 310) hydrogen bonds : angle 4.58583 ( 864) metal coordination : bond 0.00572 ( 8) metal coordination : angle 1.74145 ( 6) covalent geometry : bond 0.00297 ( 6783) covalent geometry : angle 0.57252 ( 9210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2629.09 seconds wall clock time: 47 minutes 18.90 seconds (2838.90 seconds total)