Starting phenix.real_space_refine on Thu Jul 2 17:51:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nhd_49409/07_2026/9nhd_49409.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nhd_49409/07_2026/9nhd_49409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nhd_49409/07_2026/9nhd_49409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nhd_49409/07_2026/9nhd_49409.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nhd_49409/07_2026/9nhd_49409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nhd_49409/07_2026/9nhd_49409.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 1 5.21 5 S 39 5.16 5 C 5712 2.51 5 N 1582 2.21 5 O 1853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9235 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 736, 5941 Classifications: {'peptide': 736} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 700} Chain breaks: 3 Chain: "B" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 518 Classifications: {'RNA': 24} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 14, 'rna3p_pyr': 8} Link IDs: {'rna2p': 2, 'rna3p': 21} Chain: "C" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 501 Classifications: {'RNA': 24} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 12} Link IDs: {'rna2p': 2, 'rna3p': 21} Chain: "E" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 373 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain breaks: 1 Chain: "F" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1901 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain breaks: 4 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.77, per 1000 atoms: 0.19 Number of scatterers: 9235 At special positions: 0 Unit cell: (105.56, 95.55, 108.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 48 15.00 Mg 1 11.99 O 1853 8.00 N 1582 7.00 C 5712 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: 1.01 Conformation dependent library (CDL) restraints added in 188.1 milliseconds 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1930 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 40.0% alpha, 16.6% beta 20 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 181 through 190 removed outlier: 3.564A pdb=" N ARG A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.625A pdb=" N LEU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 262 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 317 through 329 Processing helix chain 'A' and resid 333 through 342 removed outlier: 3.536A pdb=" N VAL A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.966A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 431 through 434 removed outlier: 4.052A pdb=" N ALA A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 431 through 434' Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.654A pdb=" N MET A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 467 Processing helix chain 'A' and resid 467 through 477 removed outlier: 3.502A pdb=" N VAL A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.612A pdb=" N MET A 519 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 520 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A 521 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 522 " --> pdb=" O MET A 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 516 through 522' Processing helix chain 'A' and resid 541 through 560 Processing helix chain 'A' and resid 575 through 590 Processing helix chain 'A' and resid 604 through 616 removed outlier: 4.105A pdb=" N VAL A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 650 removed outlier: 3.505A pdb=" N LEU A 650 " --> pdb=" O ILE A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 729 Processing helix chain 'A' and resid 746 through 752 Processing helix chain 'A' and resid 754 through 767 Processing helix chain 'A' and resid 842 through 855 Processing helix chain 'A' and resid 867 through 880 Processing helix chain 'A' and resid 889 through 893 removed outlier: 3.708A pdb=" N ASN A 893 " --> pdb=" O TYR A 890 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 119 removed outlier: 3.606A pdb=" N LYS E 118 " --> pdb=" O ASP E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 137 through 145 removed outlier: 4.221A pdb=" N LYS E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR E 144 " --> pdb=" O GLU E 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 110 removed outlier: 3.765A pdb=" N GLU F 93 " --> pdb=" O MET F 89 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP F 99 " --> pdb=" O ASN F 95 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 115 Processing helix chain 'F' and resid 166 through 178 Processing helix chain 'F' and resid 190 through 199 Processing helix chain 'F' and resid 218 through 233 removed outlier: 3.740A pdb=" N ASP F 223 " --> pdb=" O PRO F 219 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ALA F 224 " --> pdb=" O GLU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 260 Processing helix chain 'F' and resid 271 through 277 removed outlier: 4.064A pdb=" N THR F 275 " --> pdb=" O SER F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 296 removed outlier: 3.652A pdb=" N GLU F 294 " --> pdb=" O CYS F 290 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 323 removed outlier: 3.784A pdb=" N ARG F 317 " --> pdb=" O THR F 313 " (cutoff:3.500A) Proline residue: F 320 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 267 Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 267 removed outlier: 3.575A pdb=" N THR A 294 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A 296 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 303 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU A 302 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 161 " --> pdb=" O LYS A 480 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS A 480 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 208 removed outlier: 3.663A pdb=" N ASP A 174 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU A 233 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 356 Processing sheet with id=AA6, first strand: chain 'A' and resid 369 through 372 removed outlier: 3.551A pdb=" N GLU A 375 " --> pdb=" O MET A 372 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 399 through 402 Processing sheet with id=AA8, first strand: chain 'A' and resid 491 through 492 removed outlier: 3.570A pdb=" N ARG A 491 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 801 " --> pdb=" O VAL A 818 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 831 " --> pdb=" O SER A 779 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 735 " --> pdb=" O ALA A 774 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE A 776 " --> pdb=" O ILE A 735 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ILE A 737 " --> pdb=" O ILE A 776 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL A 778 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG A 739 " --> pdb=" O VAL A 778 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 497 through 500 removed outlier: 3.553A pdb=" N GLN A 500 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 569 through 571 removed outlier: 7.903A pdb=" N VAL A 569 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 535 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE A 571 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR A 537 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 595 " --> pdb=" O GLN A 623 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL A 625 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N CYS A 597 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 148 through 156 removed outlier: 6.903A pdb=" N GLN F 142 " --> pdb=" O LYS F 150 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER F 152 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL F 140 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N HIS F 154 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N PHE F 138 " --> pdb=" O HIS F 154 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N THR F 156 " --> pdb=" O GLY F 136 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY F 136 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 120 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N PHE F 216 " --> pdb=" O ASP F 117 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N TYR F 119 " --> pdb=" O PHE F 216 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET F 215 " --> pdb=" O TYR F 246 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 921 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2583 1.34 - 1.46: 1957 1.46 - 1.58: 4826 1.58 - 1.70: 94 1.70 - 1.82: 61 Bond restraints: 9521 Sorted by residual: bond pdb=" C4 C C 10 " pdb=" N4 C C 10 " ideal model delta sigma weight residual 1.335 1.298 0.037 9.00e-03 1.23e+04 1.71e+01 bond pdb=" C4 C C 11 " pdb=" N4 C C 11 " ideal model delta sigma weight residual 1.335 1.298 0.037 9.00e-03 1.23e+04 1.69e+01 bond pdb=" C4 C C 17 " pdb=" N4 C C 17 " ideal model delta sigma weight residual 1.335 1.299 0.036 9.00e-03 1.23e+04 1.58e+01 bond pdb=" CZ ARG A 812 " pdb=" NH2 ARG A 812 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.30e-02 5.92e+03 1.35e+01 bond pdb=" CA PRO F 213 " pdb=" C PRO F 213 " ideal model delta sigma weight residual 1.514 1.533 -0.019 5.50e-03 3.31e+04 1.22e+01 ... (remaining 9516 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 12176 2.33 - 4.65: 825 4.65 - 6.98: 92 6.98 - 9.31: 11 9.31 - 11.63: 3 Bond angle restraints: 13107 Sorted by residual: angle pdb=" N6 A C 12 " pdb=" C6 A C 12 " pdb=" N1 A C 12 " ideal model delta sigma weight residual 118.60 113.47 5.13 6.00e-01 2.78e+00 7.30e+01 angle pdb=" C3' G B 5 " pdb=" O3' G B 5 " pdb=" P U B 6 " ideal model delta sigma weight residual 120.20 108.57 11.63 1.50e+00 4.44e-01 6.02e+01 angle pdb=" C5 A C 18 " pdb=" C6 A C 18 " pdb=" N1 A C 18 " ideal model delta sigma weight residual 117.70 121.18 -3.48 5.00e-01 4.00e+00 4.86e+01 angle pdb=" O2 C C 17 " pdb=" C2 C C 17 " pdb=" N3 C C 17 " ideal model delta sigma weight residual 121.90 117.26 4.64 7.00e-01 2.04e+00 4.39e+01 angle pdb=" O2 C C 10 " pdb=" C2 C C 10 " pdb=" N3 C C 10 " ideal model delta sigma weight residual 121.90 117.28 4.62 7.00e-01 2.04e+00 4.35e+01 ... (remaining 13102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.86: 5498 27.86 - 55.73: 256 55.73 - 83.59: 71 83.59 - 111.45: 5 111.45 - 139.32: 1 Dihedral angle restraints: 5831 sinusoidal: 2843 harmonic: 2988 Sorted by residual: dihedral pdb=" CA ILE F 198 " pdb=" C ILE F 198 " pdb=" N ILE F 199 " pdb=" CA ILE F 199 " ideal model delta harmonic sigma weight residual 180.00 152.17 27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" C5' U B 6 " pdb=" C4' U B 6 " pdb=" C3' U B 6 " pdb=" O3' U B 6 " ideal model delta sinusoidal sigma weight residual 147.00 112.03 34.97 1 8.00e+00 1.56e-02 2.71e+01 dihedral pdb=" C3' U B 6 " pdb=" C4' U B 6 " pdb=" O4' U B 6 " pdb=" C1' U B 6 " ideal model delta sinusoidal sigma weight residual -2.00 30.64 -32.64 1 8.00e+00 1.56e-02 2.37e+01 ... (remaining 5828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1359 0.105 - 0.211: 135 0.211 - 0.316: 15 0.316 - 0.422: 4 0.422 - 0.527: 2 Chirality restraints: 1515 Sorted by residual: chirality pdb=" P U B 1 " pdb=" OP1 U B 1 " pdb=" OP2 U B 1 " pdb=" O5' U B 1 " both_signs ideal model delta sigma weight residual True 2.41 2.94 -0.53 2.00e-01 2.50e+01 6.94e+00 chirality pdb=" P G B 3 " pdb=" OP1 G B 3 " pdb=" OP2 G B 3 " pdb=" O5' G B 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" P A B 4 " pdb=" OP1 A B 4 " pdb=" OP2 A B 4 " pdb=" O5' A B 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.80 -0.39 2.00e-01 2.50e+01 3.78e+00 ... (remaining 1512 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 18 " 0.144 2.00e-02 2.50e+03 6.32e-02 1.10e+02 pdb=" N9 A C 18 " -0.020 2.00e-02 2.50e+03 pdb=" C8 A C 18 " -0.091 2.00e-02 2.50e+03 pdb=" N7 A C 18 " -0.036 2.00e-02 2.50e+03 pdb=" C5 A C 18 " 0.006 2.00e-02 2.50e+03 pdb=" C6 A C 18 " 0.032 2.00e-02 2.50e+03 pdb=" N6 A C 18 " 0.085 2.00e-02 2.50e+03 pdb=" N1 A C 18 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A C 18 " -0.045 2.00e-02 2.50e+03 pdb=" N3 A C 18 " -0.048 2.00e-02 2.50e+03 pdb=" C4 A C 18 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 245 " 0.095 2.00e-02 2.50e+03 5.86e-02 6.88e+01 pdb=" CG TYR A 245 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 245 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR A 245 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 245 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A 245 " -0.051 2.00e-02 2.50e+03 pdb=" CZ TYR A 245 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 245 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 199 " 0.094 2.00e-02 2.50e+03 5.56e-02 6.19e+01 pdb=" CG TYR A 199 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 199 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR A 199 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR A 199 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR A 199 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR A 199 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR A 199 " 0.095 2.00e-02 2.50e+03 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 45 2.51 - 3.11: 6753 3.11 - 3.71: 14782 3.71 - 4.30: 19700 4.30 - 4.90: 31547 Nonbonded interactions: 72827 Sorted by model distance: nonbonded pdb=" NZ LYS A 612 " pdb=" OD2 ASP F 283 " model vdw 1.916 3.120 nonbonded pdb=" O3' G C 15 " pdb="MG MG C 101 " model vdw 2.041 2.170 nonbonded pdb=" OP1 U C 16 " pdb="MG MG C 101 " model vdw 2.111 2.170 nonbonded pdb=" OD1 ASP A 740 " pdb="MG MG C 101 " model vdw 2.157 2.170 nonbonded pdb=" OG1 THR A 516 " pdb=" OG SER A 861 " model vdw 2.244 3.040 ... (remaining 72822 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.880 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 0.007 0.048 9521 Z= 0.453 Angle : 1.199 11.634 13107 Z= 0.803 Chirality : 0.068 0.527 1515 Planarity : 0.010 0.108 1490 Dihedral : 16.584 139.317 3901 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.11 % Allowed : 2.73 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.25), residues: 995 helix: -0.27 (0.27), residues: 340 sheet: -0.80 (0.39), residues: 169 loop : -1.11 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 301 TYR 0.096 0.013 TYR A 271 PHE 0.071 0.008 PHE A 898 TRP 0.071 0.006 TRP A 477 HIS 0.010 0.002 HIS A 874 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.45 ( 9521) covalent geometry : angle 1.19885 / 0.80 (13107) hydrogen bonds : bond 0.20048 / 13.21 ( 365) hydrogen bonds : angle 7.07153 / 4.77 ( 1017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.9074 (ttpt) cc_final: 0.8791 (mttp) REVERT: A 265 GLN cc_start: 0.7269 (tm-30) cc_final: 0.6960 (tm-30) REVERT: A 267 MET cc_start: 0.8447 (mmm) cc_final: 0.7828 (mmm) REVERT: A 381 GLU cc_start: 0.8429 (tt0) cc_final: 0.7735 (mt-10) REVERT: A 412 LEU cc_start: 0.8027 (mm) cc_final: 0.7733 (mm) REVERT: A 563 MET cc_start: 0.6960 (mtt) cc_final: 0.6703 (mtt) REVERT: A 641 LYS cc_start: 0.7355 (mtpt) cc_final: 0.7147 (tppt) REVERT: A 871 GLN cc_start: 0.7796 (mm110) cc_final: 0.7516 (mm110) REVERT: A 897 TYR cc_start: 0.7623 (p90) cc_final: 0.7182 (p90) REVERT: F 215 MET cc_start: 0.7039 (mpp) cc_final: 0.5993 (mpp) REVERT: F 303 THR cc_start: 0.8681 (p) cc_final: 0.8406 (p) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.0791 time to fit residues: 21.7552 Evaluate side-chains 149 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 GLN A 297 GLN A 388 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.123694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.103325 restraints weight = 20727.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.106760 restraints weight = 11360.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.107529 restraints weight = 6992.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.107755 restraints weight = 5748.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108067 restraints weight = 5278.032| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9521 Z= 0.166 Angle : 0.649 7.963 13107 Z= 0.353 Chirality : 0.045 0.219 1515 Planarity : 0.005 0.069 1490 Dihedral : 15.321 140.371 1846 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.22 % Allowed : 3.60 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.27), residues: 995 helix: -0.05 (0.27), residues: 357 sheet: -0.70 (0.39), residues: 192 loop : -0.98 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 606 TYR 0.018 0.002 TYR A 872 PHE 0.018 0.002 PHE A 464 TRP 0.011 0.002 TRP A 288 HIS 0.010 0.002 HIS F 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 9521) covalent geometry : angle 0.64915 / 0.35 (13107) hydrogen bonds : bond 0.06093 / 3.98 ( 365) hydrogen bonds : angle 5.46254 / 3.77 ( 1017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.9139 (ttpt) cc_final: 0.8852 (mttp) REVERT: A 265 GLN cc_start: 0.7093 (tm-30) cc_final: 0.6790 (tm-30) REVERT: A 267 MET cc_start: 0.8396 (mmm) cc_final: 0.7945 (mmm) REVERT: A 412 LEU cc_start: 0.7778 (mm) cc_final: 0.7552 (mm) REVERT: A 641 LYS cc_start: 0.7365 (mtpt) cc_final: 0.7159 (tppt) REVERT: A 665 MET cc_start: 0.7380 (ttm) cc_final: 0.7151 (ttm) REVERT: F 101 GLN cc_start: 0.7969 (pm20) cc_final: 0.7584 (pm20) REVERT: F 215 MET cc_start: 0.6851 (mpp) cc_final: 0.5797 (mpp) REVERT: F 303 THR cc_start: 0.8714 (p) cc_final: 0.8396 (p) outliers start: 2 outliers final: 0 residues processed: 180 average time/residue: 0.0735 time to fit residues: 19.3558 Evaluate side-chains 138 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.121534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.101490 restraints weight = 20830.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.104324 restraints weight = 11469.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.105374 restraints weight = 7003.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105714 restraints weight = 5615.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.105975 restraints weight = 5326.642| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9521 Z= 0.188 Angle : 0.637 9.655 13107 Z= 0.343 Chirality : 0.045 0.236 1515 Planarity : 0.005 0.056 1490 Dihedral : 15.287 142.429 1846 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.11 % Allowed : 5.02 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.27), residues: 995 helix: -0.11 (0.27), residues: 358 sheet: -0.85 (0.39), residues: 190 loop : -0.95 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 223 TYR 0.033 0.002 TYR A 697 PHE 0.020 0.002 PHE F 267 TRP 0.025 0.002 TRP A 533 HIS 0.007 0.001 HIS F 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 ( 9521) covalent geometry : angle 0.63707 / 0.34 (13107) hydrogen bonds : bond 0.05424 / 3.53 ( 365) hydrogen bonds : angle 5.23880 / 3.59 ( 1017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLN cc_start: 0.7117 (tm-30) cc_final: 0.6002 (tm-30) REVERT: A 412 LEU cc_start: 0.7822 (mm) cc_final: 0.7536 (mm) REVERT: A 641 LYS cc_start: 0.7327 (mtpt) cc_final: 0.7046 (tppt) REVERT: F 101 GLN cc_start: 0.7905 (pm20) cc_final: 0.7684 (pm20) REVERT: F 215 MET cc_start: 0.6921 (mpp) cc_final: 0.5763 (mpp) REVERT: F 303 THR cc_start: 0.8739 (p) cc_final: 0.8417 (p) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.0840 time to fit residues: 20.3893 Evaluate side-chains 135 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.120760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.100653 restraints weight = 21355.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103351 restraints weight = 11558.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.104278 restraints weight = 7328.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.104370 restraints weight = 5978.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.105819 restraints weight = 5722.936| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9521 Z= 0.185 Angle : 0.630 9.234 13107 Z= 0.336 Chirality : 0.045 0.230 1515 Planarity : 0.005 0.050 1490 Dihedral : 15.266 143.270 1846 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.27), residues: 995 helix: -0.05 (0.27), residues: 358 sheet: -1.10 (0.38), residues: 196 loop : -0.94 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 606 TYR 0.039 0.002 TYR A 697 PHE 0.016 0.002 PHE F 267 TRP 0.019 0.002 TRP A 533 HIS 0.009 0.001 HIS F 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 ( 9521) covalent geometry : angle 0.62955 / 0.34 (13107) hydrogen bonds : bond 0.04954 / 3.24 ( 365) hydrogen bonds : angle 5.13588 / 3.53 ( 1017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLN cc_start: 0.7142 (tm-30) cc_final: 0.6425 (tm-30) REVERT: A 267 MET cc_start: 0.8206 (mmm) cc_final: 0.7571 (mmm) REVERT: A 455 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8022 (mm-30) REVERT: A 541 GLN cc_start: 0.9095 (mp10) cc_final: 0.8631 (mp10) REVERT: A 698 SER cc_start: 0.9069 (p) cc_final: 0.8825 (p) REVERT: A 837 ASP cc_start: 0.8515 (t0) cc_final: 0.8264 (t0) REVERT: F 181 MET cc_start: 0.8018 (mmt) cc_final: 0.7639 (mmm) REVERT: F 215 MET cc_start: 0.6965 (mpp) cc_final: 0.5849 (mpp) REVERT: F 303 THR cc_start: 0.8793 (p) cc_final: 0.8491 (p) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.0814 time to fit residues: 19.5369 Evaluate side-chains 134 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.123316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.103092 restraints weight = 20873.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.106091 restraints weight = 11195.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.106953 restraints weight = 6940.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.107465 restraints weight = 5605.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.107757 restraints weight = 5206.553| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9521 Z= 0.124 Angle : 0.593 7.849 13107 Z= 0.315 Chirality : 0.043 0.239 1515 Planarity : 0.004 0.046 1490 Dihedral : 15.318 143.491 1846 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.27), residues: 995 helix: 0.03 (0.27), residues: 358 sheet: -0.80 (0.38), residues: 196 loop : -0.86 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 865 TYR 0.030 0.002 TYR A 697 PHE 0.015 0.001 PHE F 267 TRP 0.015 0.002 TRP A 533 HIS 0.005 0.001 HIS F 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9521) covalent geometry : angle 0.59299 / 0.31 (13107) hydrogen bonds : bond 0.04475 / 2.97 ( 365) hydrogen bonds : angle 4.93701 / 3.40 ( 1017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LYS cc_start: 0.9221 (ttpt) cc_final: 0.8797 (mttp) REVERT: A 265 GLN cc_start: 0.7190 (tm-30) cc_final: 0.6452 (tm-30) REVERT: A 267 MET cc_start: 0.8204 (mmm) cc_final: 0.7476 (mmm) REVERT: A 603 TYR cc_start: 0.7151 (m-10) cc_final: 0.6728 (m-10) REVERT: A 636 MET cc_start: 0.6363 (ppp) cc_final: 0.5170 (mtt) REVERT: F 101 GLN cc_start: 0.8054 (pm20) cc_final: 0.7720 (pm20) REVERT: F 181 MET cc_start: 0.8059 (mmt) cc_final: 0.7717 (mmm) REVERT: F 215 MET cc_start: 0.6948 (mpp) cc_final: 0.5942 (mpp) REVERT: F 303 THR cc_start: 0.8677 (p) cc_final: 0.8353 (p) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.0814 time to fit residues: 20.2704 Evaluate side-chains 141 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 3 optimal weight: 0.0970 chunk 73 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 445 HIS ** A 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 871 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.118487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.098503 restraints weight = 21621.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.101224 restraints weight = 11780.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.102398 restraints weight = 7533.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.102738 restraints weight = 5904.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.102866 restraints weight = 5449.371| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9521 Z= 0.255 Angle : 0.713 11.561 13107 Z= 0.377 Chirality : 0.047 0.217 1515 Planarity : 0.005 0.047 1490 Dihedral : 15.310 144.492 1846 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.26), residues: 995 helix: -0.25 (0.26), residues: 358 sheet: -1.27 (0.37), residues: 196 loop : -0.99 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 562 TYR 0.038 0.003 TYR A 697 PHE 0.019 0.003 PHE A 337 TRP 0.021 0.002 TRP A 533 HIS 0.007 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.26 ( 9521) covalent geometry : angle 0.71266 / 0.38 (13107) hydrogen bonds : bond 0.05698 / 3.77 ( 365) hydrogen bonds : angle 5.22113 / 3.63 ( 1017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLN cc_start: 0.7243 (tm-30) cc_final: 0.6207 (tm-30) REVERT: A 455 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8082 (mm-30) REVERT: A 837 ASP cc_start: 0.8685 (t0) cc_final: 0.8445 (t0) REVERT: F 101 GLN cc_start: 0.8218 (pm20) cc_final: 0.7854 (pm20) REVERT: F 161 CYS cc_start: 0.8672 (t) cc_final: 0.8101 (m) REVERT: F 215 MET cc_start: 0.7114 (mpp) cc_final: 0.6117 (mpp) REVERT: F 303 THR cc_start: 0.8851 (p) cc_final: 0.8558 (p) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.0898 time to fit residues: 20.1694 Evaluate side-chains 124 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 33 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 34 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 445 HIS ** A 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.122821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.102772 restraints weight = 20848.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.105801 restraints weight = 11146.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.106896 restraints weight = 6881.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.107336 restraints weight = 5404.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.107608 restraints weight = 4960.326| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9521 Z= 0.125 Angle : 0.610 9.408 13107 Z= 0.321 Chirality : 0.044 0.227 1515 Planarity : 0.004 0.046 1490 Dihedral : 15.383 144.158 1846 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.27), residues: 995 helix: -0.08 (0.27), residues: 358 sheet: -0.84 (0.38), residues: 195 loop : -0.88 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 725 TYR 0.033 0.002 TYR A 697 PHE 0.020 0.001 PHE A 337 TRP 0.019 0.002 TRP A 515 HIS 0.013 0.001 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9521) covalent geometry : angle 0.60972 / 0.32 (13107) hydrogen bonds : bond 0.04433 / 2.94 ( 365) hydrogen bonds : angle 4.98556 / 3.47 ( 1017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLN cc_start: 0.7180 (tm-30) cc_final: 0.6188 (tm-30) REVERT: A 267 MET cc_start: 0.8217 (mmm) cc_final: 0.7272 (mmm) REVERT: A 603 TYR cc_start: 0.7050 (m-10) cc_final: 0.6646 (m-10) REVERT: A 636 MET cc_start: 0.6630 (ppp) cc_final: 0.5079 (mtt) REVERT: F 101 GLN cc_start: 0.8259 (pm20) cc_final: 0.8059 (pm20) REVERT: F 161 CYS cc_start: 0.8659 (t) cc_final: 0.8081 (m) REVERT: F 181 MET cc_start: 0.7886 (mmt) cc_final: 0.7602 (mmm) REVERT: F 215 MET cc_start: 0.6967 (mpp) cc_final: 0.5941 (mpp) REVERT: F 303 THR cc_start: 0.8621 (p) cc_final: 0.8340 (p) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.0856 time to fit residues: 20.4656 Evaluate side-chains 133 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 13 optimal weight: 0.0670 chunk 46 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 61 optimal weight: 0.4980 chunk 58 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.122875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.102925 restraints weight = 20757.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.105973 restraints weight = 11035.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.106795 restraints weight = 6742.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.107311 restraints weight = 5491.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.107609 restraints weight = 5080.923| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9521 Z= 0.132 Angle : 0.614 9.923 13107 Z= 0.322 Chirality : 0.044 0.216 1515 Planarity : 0.004 0.046 1490 Dihedral : 15.337 144.371 1846 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.27), residues: 995 helix: -0.03 (0.27), residues: 358 sheet: -0.62 (0.39), residues: 191 loop : -0.88 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 292 TYR 0.033 0.002 TYR A 697 PHE 0.023 0.002 PHE A 337 TRP 0.016 0.002 TRP A 533 HIS 0.002 0.001 HIS A 445 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 9521) covalent geometry : angle 0.61352 / 0.32 (13107) hydrogen bonds : bond 0.04304 / 2.83 ( 365) hydrogen bonds : angle 4.88657 / 3.40 ( 1017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLN cc_start: 0.7169 (tm-30) cc_final: 0.6163 (tm-30) REVERT: A 267 MET cc_start: 0.8128 (mmm) cc_final: 0.7159 (mmm) REVERT: A 381 GLU cc_start: 0.8420 (tt0) cc_final: 0.8218 (tt0) REVERT: A 603 TYR cc_start: 0.7021 (m-10) cc_final: 0.6676 (m-10) REVERT: A 636 MET cc_start: 0.6463 (ppp) cc_final: 0.5189 (mtt) REVERT: A 695 GLN cc_start: 0.7790 (pm20) cc_final: 0.7567 (pm20) REVERT: F 101 GLN cc_start: 0.8312 (pm20) cc_final: 0.8087 (pm20) REVERT: F 161 CYS cc_start: 0.8675 (t) cc_final: 0.8102 (m) REVERT: F 181 MET cc_start: 0.7878 (mmt) cc_final: 0.7581 (mmm) REVERT: F 215 MET cc_start: 0.6968 (mpp) cc_final: 0.5922 (mpp) REVERT: F 303 THR cc_start: 0.8536 (p) cc_final: 0.8202 (p) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0820 time to fit residues: 19.6627 Evaluate side-chains 134 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.123049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.103132 restraints weight = 20573.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.106188 restraints weight = 10973.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.107003 restraints weight = 6720.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.107516 restraints weight = 5486.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107795 restraints weight = 5071.820| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9521 Z= 0.133 Angle : 0.609 10.610 13107 Z= 0.320 Chirality : 0.044 0.216 1515 Planarity : 0.004 0.045 1490 Dihedral : 15.310 144.571 1846 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.27), residues: 995 helix: -0.01 (0.27), residues: 358 sheet: -0.67 (0.39), residues: 191 loop : -0.87 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 606 TYR 0.029 0.002 TYR A 697 PHE 0.022 0.001 PHE A 337 TRP 0.016 0.002 TRP A 533 HIS 0.003 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9521) covalent geometry : angle 0.60915 / 0.32 (13107) hydrogen bonds : bond 0.04271 / 2.83 ( 365) hydrogen bonds : angle 4.86639 / 3.38 ( 1017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLN cc_start: 0.7134 (tm-30) cc_final: 0.6659 (tm-30) REVERT: A 603 TYR cc_start: 0.7094 (m-10) cc_final: 0.6792 (m-10) REVERT: A 636 MET cc_start: 0.6424 (ppp) cc_final: 0.5084 (mtt) REVERT: A 693 MET cc_start: 0.8102 (mmm) cc_final: 0.7852 (mmm) REVERT: A 872 TYR cc_start: 0.8067 (m-10) cc_final: 0.7803 (m-10) REVERT: F 101 GLN cc_start: 0.8282 (pm20) cc_final: 0.7992 (pm20) REVERT: F 161 CYS cc_start: 0.8688 (t) cc_final: 0.8106 (m) REVERT: F 181 MET cc_start: 0.7893 (mmt) cc_final: 0.7628 (mmm) REVERT: F 215 MET cc_start: 0.6992 (mpp) cc_final: 0.5933 (mpp) REVERT: F 303 THR cc_start: 0.8544 (p) cc_final: 0.8228 (p) REVERT: F 342 LEU cc_start: 0.7646 (pp) cc_final: 0.7398 (pp) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.0836 time to fit residues: 20.2858 Evaluate side-chains 135 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 38 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 94 optimal weight: 0.0670 chunk 68 optimal weight: 4.9990 chunk 20 optimal weight: 0.0770 chunk 95 optimal weight: 0.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 712 HIS E 121 HIS F 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.122926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.102866 restraints weight = 20803.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.105957 restraints weight = 11076.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.106730 restraints weight = 6747.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.107369 restraints weight = 5558.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107637 restraints weight = 5066.791| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9521 Z= 0.137 Angle : 0.610 9.119 13107 Z= 0.321 Chirality : 0.044 0.215 1515 Planarity : 0.004 0.045 1490 Dihedral : 15.287 144.896 1846 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.27), residues: 995 helix: -0.06 (0.27), residues: 358 sheet: -0.68 (0.39), residues: 191 loop : -0.85 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 292 TYR 0.029 0.002 TYR A 697 PHE 0.010 0.001 PHE F 267 TRP 0.018 0.002 TRP A 533 HIS 0.003 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 9521) covalent geometry : angle 0.60973 / 0.32 (13107) hydrogen bonds : bond 0.04283 / 2.84 ( 365) hydrogen bonds : angle 4.83936 / 3.36 ( 1017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLN cc_start: 0.7179 (tm-30) cc_final: 0.6285 (tm-30) REVERT: A 267 MET cc_start: 0.8127 (mmm) cc_final: 0.7244 (mmm) REVERT: A 603 TYR cc_start: 0.7200 (m-10) cc_final: 0.6734 (m-10) REVERT: A 636 MET cc_start: 0.6341 (ppp) cc_final: 0.4940 (mtt) REVERT: A 872 TYR cc_start: 0.8152 (m-10) cc_final: 0.7859 (m-10) REVERT: F 101 GLN cc_start: 0.8310 (pm20) cc_final: 0.7996 (pm20) REVERT: F 161 CYS cc_start: 0.8713 (t) cc_final: 0.8125 (m) REVERT: F 181 MET cc_start: 0.7951 (mmt) cc_final: 0.7748 (mmm) REVERT: F 215 MET cc_start: 0.6992 (mpp) cc_final: 0.5919 (mpp) REVERT: F 303 THR cc_start: 0.8535 (p) cc_final: 0.8216 (p) REVERT: F 342 LEU cc_start: 0.7659 (pp) cc_final: 0.7429 (pp) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0752 time to fit residues: 18.0037 Evaluate side-chains 136 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 94 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 41 optimal weight: 0.0270 chunk 78 optimal weight: 0.0020 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 99 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.3646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 121 HIS F 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.124774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.104714 restraints weight = 20417.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.107780 restraints weight = 10834.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.108981 restraints weight = 6689.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.109368 restraints weight = 5193.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.109509 restraints weight = 4795.001| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9521 Z= 0.121 Angle : 0.616 9.137 13107 Z= 0.322 Chirality : 0.044 0.215 1515 Planarity : 0.004 0.044 1490 Dihedral : 15.309 144.910 1846 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.27), residues: 995 helix: -0.06 (0.27), residues: 358 sheet: -0.75 (0.38), residues: 201 loop : -0.81 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 292 TYR 0.030 0.001 TYR A 697 PHE 0.026 0.001 PHE A 337 TRP 0.056 0.003 TRP A 533 HIS 0.004 0.001 HIS A 855 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9521) covalent geometry : angle 0.61625 / 0.32 (13107) hydrogen bonds : bond 0.04163 / 2.77 ( 365) hydrogen bonds : angle 4.79669 / 3.36 ( 1017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1380.83 seconds wall clock time: 24 minutes 53.82 seconds (1493.82 seconds total)