Starting phenix.real_space_refine on Sat May 10 17:59:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nus_0521/05_2025/6nus_0521.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nus_0521/05_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_0521/05_2025/6nus_0521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nus_0521/05_2025/6nus_0521.map" model { file = "/net/cci-nas-00/data/ceres_data/6nus_0521/05_2025/6nus_0521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nus_0521/05_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-5687/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: 4.34, 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: 1.57 Conformation dependent library (CDL) restraints added in 1.1 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: 0.76 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: 2.06 Time building geometry restraints manager: 1.83 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: 1.250 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.660 Find NCS groups from input model: 0.060 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.390 ------------------------------------------------------------------------------- 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 : 0.731 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: 0.2006 time to fit residues: 67.9236 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 : 0.747 ------------------------------------------------------------------------------- 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 = 0.193119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.170502 restraints weight = 8654.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.175190 restraints weight = 4047.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.178073 restraints weight = 2340.205| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 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 : 4.824 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 5.13194 ( 864) metal coordination : bond 0.01355 ( 8) metal coordination : angle 2.72214 ( 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 : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7680 (tttm) cc_final: 0.7146 (mmmt) REVERT: A 173 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7768 (ptt90) REVERT: A 257 MET cc_start: 0.5254 (ppp) cc_final: 0.5053 (ptm) REVERT: A 509 TRP cc_start: 0.7405 (m-10) cc_final: 0.6963 (m-90) REVERT: A 666 MET cc_start: 0.5946 (mmm) cc_final: 0.4876 (mmm) REVERT: A 807 LYS cc_start: 0.7846 (ptpt) cc_final: 0.6974 (tmtt) REVERT: A 913 THR cc_start: 0.7919 (m) cc_final: 0.7650 (t) outliers start: 16 outliers final: 9 residues processed: 181 average time/residue: 0.1831 time to fit residues: 43.8643 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 : 0.695 ------------------------------------------------------------------------------- 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: 0.8980 chunk 45 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** 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 = 0.187186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.165044 restraints weight = 8946.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.169468 restraints weight = 4259.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.172203 restraints weight = 2497.175| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6791 Z= 0.156 Angle : 0.564 6.313 9216 Z= 0.304 Chirality : 0.043 0.153 1026 Planarity : 0.005 0.041 1176 Dihedral : 4.735 31.270 909 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.47 % Allowed : 13.17 % Favored : 84.36 % 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: 0.88 (0.27), residues: 360 sheet: 0.48 (0.57), residues: 73 loop : 0.35 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 154 HIS 0.004 0.001 HIS A 599 PHE 0.028 0.002 PHE A 753 TYR 0.023 0.002 TYR A 530 ARG 0.003 0.000 ARG A 733 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 310) hydrogen bonds : angle 4.92787 ( 864) metal coordination : bond 0.00567 ( 8) metal coordination : angle 1.97678 ( 6) covalent geometry : bond 0.00348 ( 6783) covalent geometry : angle 0.56168 ( 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 168 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7551 (tttm) cc_final: 0.7054 (mmmt) REVERT: A 173 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7762 (ptt90) REVERT: A 324 THR cc_start: 0.8428 (p) cc_final: 0.8055 (t) REVERT: A 343 SER cc_start: 0.8063 (m) cc_final: 0.7645 (m) REVERT: A 509 TRP cc_start: 0.7499 (m-10) cc_final: 0.6891 (m-90) REVERT: A 666 MET cc_start: 0.6007 (mmm) cc_final: 0.4964 (mmm) REVERT: A 668 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7649 (mtp) REVERT: A 714 LYS cc_start: 0.7711 (mmtm) cc_final: 0.6869 (tptp) REVERT: A 794 MET cc_start: 0.6056 (ttp) cc_final: 0.5709 (ptm) outliers start: 18 outliers final: 12 residues processed: 159 average time/residue: 0.1711 time to fit residues: 37.4216 Evaluate side-chains 151 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 662 VAL Chi-restraints excluded: chain A residue 668 MET 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 A residue 838 LEU Chi-restraints excluded: chain A residue 855 MET 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: 0.6980 chunk 49 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.186859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.164403 restraints weight = 9103.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.168906 restraints weight = 4357.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.171588 restraints weight = 2556.738| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6791 Z= 0.122 Angle : 0.512 5.843 9216 Z= 0.275 Chirality : 0.041 0.126 1026 Planarity : 0.004 0.043 1176 Dihedral : 4.477 24.749 907 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.02 % Allowed : 14.13 % Favored : 82.85 % 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: 0.34 (0.57), residues: 66 loop : 0.34 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 917 HIS 0.008 0.001 HIS A 309 PHE 0.026 0.002 PHE A 753 TYR 0.023 0.001 TYR A 530 ARG 0.006 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 310) hydrogen bonds : angle 4.73847 ( 864) metal coordination : bond 0.00506 ( 8) metal coordination : angle 1.65312 ( 6) covalent geometry : bond 0.00278 ( 6783) covalent geometry : angle 0.51001 ( 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 173 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7596 (tttm) cc_final: 0.7106 (mmmt) REVERT: A 288 LYS cc_start: 0.7475 (tttm) cc_final: 0.7073 (ttpt) REVERT: A 324 THR cc_start: 0.8400 (p) cc_final: 0.8078 (t) REVERT: A 343 SER cc_start: 0.8074 (m) cc_final: 0.7619 (m) REVERT: A 509 TRP cc_start: 0.7479 (m-10) cc_final: 0.6791 (m-90) REVERT: A 540 THR cc_start: 0.8036 (t) cc_final: 0.7787 (t) REVERT: A 666 MET cc_start: 0.5903 (mmm) cc_final: 0.4879 (mmm) REVERT: A 714 LYS cc_start: 0.7738 (mmtm) cc_final: 0.6816 (tptp) REVERT: A 794 MET cc_start: 0.6143 (ttp) cc_final: 0.5670 (ptm) REVERT: A 811 GLU cc_start: 0.7424 (tt0) cc_final: 0.7222 (tt0) outliers start: 22 outliers final: 15 residues processed: 161 average time/residue: 0.1630 time to fit residues: 35.8530 Evaluate side-chains 155 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 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 856 ILE 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 153 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.3980 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ** 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 = 0.4095 r_free = 0.4095 target = 0.181441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.158462 restraints weight = 9037.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.162770 restraints weight = 4373.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.165356 restraints weight = 2612.908| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6791 Z= 0.139 Angle : 0.538 5.922 9216 Z= 0.285 Chirality : 0.042 0.136 1026 Planarity : 0.004 0.044 1176 Dihedral : 4.509 25.218 907 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.88 % Allowed : 14.68 % Favored : 82.44 % 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: 0.76 (0.30), residues: 811 helix: 1.00 (0.28), residues: 359 sheet: 0.45 (0.58), residues: 73 loop : 0.18 (0.33), residues: 379 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 0.030 0.002 PHE A 753 TYR 0.012 0.001 TYR A 788 ARG 0.005 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 310) hydrogen bonds : angle 4.69386 ( 864) metal coordination : bond 0.01099 ( 8) metal coordination : angle 2.39491 ( 6) covalent geometry : bond 0.00318 ( 6783) covalent geometry : angle 0.53512 ( 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 173 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7722 (tttm) cc_final: 0.7221 (mmmt) REVERT: A 324 THR cc_start: 0.8469 (p) cc_final: 0.8130 (t) REVERT: A 343 SER cc_start: 0.8106 (m) cc_final: 0.7681 (m) REVERT: A 509 TRP cc_start: 0.7500 (m-90) cc_final: 0.6905 (m-90) REVERT: A 540 THR cc_start: 0.8066 (t) cc_final: 0.7728 (t) REVERT: A 666 MET cc_start: 0.5827 (mmm) cc_final: 0.4815 (mmm) REVERT: A 714 LYS cc_start: 0.7769 (mmtm) cc_final: 0.6770 (tptp) REVERT: A 775 LEU cc_start: 0.8648 (mt) cc_final: 0.8424 (mp) REVERT: A 794 MET cc_start: 0.6283 (ttp) cc_final: 0.5751 (ptm) REVERT: A 811 GLU cc_start: 0.7552 (tt0) cc_final: 0.7301 (tt0) outliers start: 21 outliers final: 17 residues processed: 159 average time/residue: 0.1511 time to fit residues: 34.0362 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 : 0.752 ------------------------------------------------------------------------------- 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 587 VAL Chi-restraints excluded: chain A residue 649 SER 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 795 SER 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 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: 2.9990 chunk 63 optimal weight: 0.2980 chunk 13 optimal weight: 0.1980 chunk 18 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.183063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.160010 restraints weight = 8849.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.164319 restraints weight = 4243.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.166992 restraints weight = 2522.013| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.5309 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= 0.113 Angle : 0.527 8.362 9216 Z= 0.274 Chirality : 0.041 0.211 1026 Planarity : 0.004 0.044 1176 Dihedral : 4.355 24.223 907 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.88 % Allowed : 15.64 % 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: 0.80 (0.30), residues: 811 helix: 0.92 (0.28), residues: 374 sheet: 0.31 (0.57), residues: 73 loop : 0.33 (0.33), residues: 364 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 0.021 0.001 PHE A 753 TYR 0.026 0.001 TYR A 530 ARG 0.008 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 310) hydrogen bonds : angle 4.56613 ( 864) metal coordination : bond 0.00524 ( 8) metal coordination : angle 1.86380 ( 6) covalent geometry : bond 0.00256 ( 6783) covalent geometry : angle 0.52467 ( 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 171 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7687 (tttm) cc_final: 0.7244 (mmmt) REVERT: A 288 LYS cc_start: 0.7255 (tttm) cc_final: 0.7005 (ttpt) REVERT: A 324 THR cc_start: 0.8449 (p) cc_final: 0.8108 (t) REVERT: A 343 SER cc_start: 0.8076 (m) cc_final: 0.7663 (m) REVERT: A 509 TRP cc_start: 0.7500 (m-90) cc_final: 0.6864 (m-90) REVERT: A 540 THR cc_start: 0.8184 (t) cc_final: 0.7903 (t) REVERT: A 666 MET cc_start: 0.5694 (mmm) cc_final: 0.4618 (mmm) REVERT: A 714 LYS cc_start: 0.7816 (mmtm) cc_final: 0.6890 (tptp) REVERT: A 811 GLU cc_start: 0.7492 (tt0) cc_final: 0.7228 (tt0) REVERT: A 825 ASP cc_start: 0.6847 (t70) cc_final: 0.6520 (p0) outliers start: 21 outliers final: 18 residues processed: 160 average time/residue: 0.1620 time to fit residues: 36.4546 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 : 0.812 ------------------------------------------------------------------------------- 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 488 ILE 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 663 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP 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: 0.4980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 80 optimal weight: 0.0070 overall best weight: 0.9004 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.181303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.158472 restraints weight = 8879.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.162746 restraints weight = 4300.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.165479 restraints weight = 2572.304| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6791 Z= 0.137 Angle : 0.560 8.531 9216 Z= 0.290 Chirality : 0.043 0.342 1026 Planarity : 0.004 0.046 1176 Dihedral : 4.375 24.050 907 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.57 % Allowed : 14.68 % Favored : 81.76 % 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: 373 sheet: 0.37 (0.59), residues: 71 loop : 0.20 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.004 0.001 HIS A 309 PHE 0.022 0.002 PHE A 753 TYR 0.029 0.002 TYR A 530 ARG 0.007 0.001 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 310) hydrogen bonds : angle 4.56712 ( 864) metal coordination : bond 0.00676 ( 8) metal coordination : angle 1.82094 ( 6) covalent geometry : bond 0.00320 ( 6783) covalent geometry : angle 0.55787 ( 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 176 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7824 (tttm) cc_final: 0.7300 (mmmt) REVERT: A 343 SER cc_start: 0.8118 (m) cc_final: 0.7714 (m) REVERT: A 509 TRP cc_start: 0.7554 (m-90) cc_final: 0.6998 (m-90) REVERT: A 519 MET cc_start: 0.7818 (mmm) cc_final: 0.7561 (mtp) REVERT: A 540 THR cc_start: 0.8215 (t) cc_final: 0.7985 (t) REVERT: A 666 MET cc_start: 0.5704 (mmm) cc_final: 0.4622 (mmm) REVERT: A 714 LYS cc_start: 0.7746 (mmtm) cc_final: 0.6952 (tptp) REVERT: A 753 PHE cc_start: 0.7680 (t80) cc_final: 0.7457 (t80) REVERT: A 811 GLU cc_start: 0.7516 (tt0) cc_final: 0.7262 (tt0) REVERT: A 825 ASP cc_start: 0.6898 (t70) cc_final: 0.6526 (p0) outliers start: 26 outliers final: 23 residues processed: 161 average time/residue: 0.1505 time to fit residues: 34.1906 Evaluate side-chains 163 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 653 TYR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 663 LEU 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 760 ASP 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 Chi-restraints excluded: chain B residue 164 SER 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: 3.9990 chunk 9 optimal weight: 0.0470 chunk 13 optimal weight: 0.0000 chunk 40 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 0.0050 chunk 49 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 overall best weight: 0.1794 ------------------------------------------------------------------------------- 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** 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 = 0.185542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.162724 restraints weight = 8824.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.167022 restraints weight = 4245.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.169680 restraints weight = 2529.972| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6791 Z= 0.099 Angle : 0.528 9.191 9216 Z= 0.272 Chirality : 0.041 0.286 1026 Planarity : 0.004 0.044 1176 Dihedral : 4.222 22.747 907 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.51 % Allowed : 17.42 % Favored : 81.07 % 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: 0.91 (0.30), residues: 811 helix: 1.10 (0.28), residues: 372 sheet: 0.20 (0.56), residues: 77 loop : 0.33 (0.33), residues: 362 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 0.019 0.001 PHE A 753 TYR 0.025 0.001 TYR A 530 ARG 0.006 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.02983 ( 310) hydrogen bonds : angle 4.42068 ( 864) metal coordination : bond 0.00354 ( 8) metal coordination : angle 1.50961 ( 6) covalent geometry : bond 0.00215 ( 6783) covalent geometry : angle 0.52665 ( 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 157 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7803 (tttm) cc_final: 0.7272 (mmmt) REVERT: A 509 TRP cc_start: 0.7543 (m-90) cc_final: 0.6901 (m-90) REVERT: A 519 MET cc_start: 0.7718 (mmm) cc_final: 0.7261 (mtt) REVERT: A 540 THR cc_start: 0.8247 (t) cc_final: 0.8038 (t) REVERT: A 691 ASN cc_start: 0.8649 (m-40) cc_final: 0.8427 (m110) REVERT: A 714 LYS cc_start: 0.7695 (mmtm) cc_final: 0.6947 (tptp) REVERT: A 811 GLU cc_start: 0.7383 (tt0) cc_final: 0.7113 (tt0) REVERT: A 825 ASP cc_start: 0.6867 (t70) cc_final: 0.6512 (p0) REVERT: B 149 TYR cc_start: 0.7398 (t80) cc_final: 0.7081 (t80) outliers start: 11 outliers final: 10 residues processed: 148 average time/residue: 0.1623 time to fit residues: 33.5254 Evaluate side-chains 151 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 653 TYR Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.4643 > 50: distance: 58 - 150: 17.337 distance: 61 - 147: 10.883 distance: 69 - 134: 18.165 distance: 99 - 104: 5.385 distance: 104 - 105: 4.819 distance: 105 - 106: 3.582 distance: 105 - 108: 4.046 distance: 106 - 107: 6.925 distance: 106 - 111: 3.881 distance: 108 - 110: 6.900 distance: 111 - 112: 6.419 distance: 112 - 115: 4.988 distance: 113 - 114: 11.400 distance: 113 - 118: 3.182 distance: 115 - 116: 7.670 distance: 115 - 117: 4.085 distance: 119 - 120: 4.264 distance: 119 - 122: 3.746 distance: 120 - 121: 3.265 distance: 122 - 123: 3.420 distance: 124 - 125: 7.596 distance: 125 - 128: 6.483 distance: 126 - 127: 7.888 distance: 128 - 129: 14.537 distance: 128 - 130: 8.664 distance: 131 - 132: 5.181 distance: 132 - 133: 10.362 distance: 133 - 134: 4.633 distance: 133 - 135: 3.340 distance: 135 - 136: 4.942 distance: 135 - 210: 16.528 distance: 136 - 137: 3.459 distance: 136 - 139: 3.357 distance: 137 - 138: 4.039 distance: 137 - 147: 3.988 distance: 138 - 207: 9.127 distance: 140 - 141: 3.704 distance: 141 - 143: 4.598 distance: 142 - 144: 5.403 distance: 145 - 146: 4.590 distance: 147 - 148: 5.613 distance: 148 - 149: 5.286 distance: 148 - 151: 3.852 distance: 149 - 150: 8.230 distance: 149 - 157: 3.885 distance: 151 - 152: 5.790 distance: 152 - 154: 6.076 distance: 153 - 155: 3.014 distance: 155 - 156: 5.226 distance: 157 - 199: 7.810 distance: 158 - 159: 4.594 distance: 158 - 161: 5.863 distance: 159 - 160: 9.137 distance: 159 - 168: 7.636 distance: 160 - 196: 7.318 distance: 161 - 162: 9.348 distance: 162 - 163: 4.842 distance: 162 - 164: 7.493 distance: 163 - 165: 5.009 distance: 164 - 166: 9.109 distance: 165 - 167: 13.649 distance: 166 - 167: 12.844 distance: 168 - 169: 17.413 distance: 169 - 170: 15.074 distance: 169 - 172: 6.675 distance: 170 - 171: 8.119 distance: 170 - 179: 16.716 distance: 172 - 173: 16.440 distance: 173 - 174: 4.200 distance: 174 - 175: 5.101 distance: 176 - 178: 13.968 distance: 179 - 180: 16.385 distance: 180 - 181: 5.211 distance: 180 - 183: 25.475 distance: 181 - 182: 5.245 distance: 181 - 188: 7.742 distance: 183 - 184: 11.669 distance: 184 - 185: 22.445 distance: 185 - 186: 22.283 distance: 185 - 187: 7.339