Starting phenix.real_space_refine on Wed Aug 5 04:58:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sap_54693/08_2026/9sap_54693.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sap_54693/08_2026/9sap_54693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sap_54693/08_2026/9sap_54693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sap_54693/08_2026/9sap_54693.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sap_54693/08_2026/9sap_54693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sap_54693/08_2026/9sap_54693.map" } resolution = 2.9 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 28 5.49 5 S 56 5.16 5 C 5431 2.51 5 N 1445 2.21 5 O 1701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8663 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 4} Link IDs: {'rna3p': 9} Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {'F86': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Chain: "T" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 311 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 10} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 6718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6718 Classifications: {'peptide': 833} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 804} Chain breaks: 4 Chain: "B" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 882 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Chain: "C" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 464 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} 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 2417 SG CYS A 301 67.273 41.427 38.804 1.00 34.21 S ATOM 2458 SG CYS A 306 69.990 43.872 37.756 1.00 40.32 S ATOM 2490 SG CYS A 310 66.415 44.101 36.287 1.00 27.84 S ATOM 3898 SG CYS A 487 70.917 35.013 58.532 1.00 28.16 S ATOM 5151 SG CYS A 645 74.175 36.713 57.499 1.00 38.54 S ATOM 5157 SG CYS A 646 71.888 35.100 54.829 1.00 22.28 S Time building chain proxies: 1.46, per 1000 atoms: 0.17 Number of scatterers: 8663 At special positions: 0 Unit cell: (91.8, 93.6, 112.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 56 16.00 P 28 15.00 O 1701 8.00 N 1445 7.00 C 5431 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 174.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 6 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 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: 50 helices and 9 sheets defined 54.1% alpha, 13.0% beta 7 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 83 through 90 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.689A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.580A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 169 through 198 removed outlier: 4.197A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 3.978A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 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 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 322 through 326 removed outlier: 3.770A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.475A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.523A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 478 Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 518 removed outlier: 4.040A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 5.870A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 removed outlier: 3.528A pdb=" N SER A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.597A pdb=" N SER A 709 " --> pdb=" O ASN A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 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 842 Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 855 through 867 removed outlier: 3.631A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 896 removed outlier: 3.984A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.494A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 79 through 97 Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.589A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.040A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.520A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 42 Processing helix chain 'C' and resid 44 through 61 removed outlier: 3.683A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.535A pdb=" N ILE A 223 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 202 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.777A pdb=" N VAL A 335 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL A 341 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE A 333 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER A 343 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG A 331 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.777A pdb=" N VAL A 335 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL A 341 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE A 333 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER A 343 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG A 331 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 387 through 390 removed outlier: 6.140A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 400 removed outlier: 6.542A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG A 555 " --> pdb=" O LYS A 545 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 758 removed outlier: 4.172A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 400 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1349 1.28 - 1.42: 2506 1.42 - 1.55: 4920 1.55 - 1.69: 52 1.69 - 1.82: 84 Bond restraints: 8911 Sorted by residual: bond pdb=" C12 F86 P 25 " pdb=" N2 F86 P 25 " ideal model delta sigma weight residual 1.293 1.354 -0.061 1.00e-02 1.00e+04 3.76e+01 bond pdb=" C12 F86 P 23 " pdb=" N2 F86 P 23 " ideal model delta sigma weight residual 1.293 1.354 -0.061 1.00e-02 1.00e+04 3.71e+01 bond pdb=" C12 F86 P 24 " pdb=" N2 F86 P 24 " ideal model delta sigma weight residual 1.293 1.352 -0.059 1.00e-02 1.00e+04 3.45e+01 bond pdb=" CA SER A 501 " pdb=" CB SER A 501 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.66e-02 3.63e+03 9.85e+00 bond pdb=" N VAL A 202 " pdb=" CA VAL A 202 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.25e+00 ... (remaining 8906 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 11916 2.51 - 5.02: 280 5.02 - 7.52: 16 7.52 - 10.03: 1 10.03 - 12.54: 3 Bond angle restraints: 12216 Sorted by residual: angle pdb=" N ASP A 454 " pdb=" CA ASP A 454 " pdb=" C ASP A 454 " ideal model delta sigma weight residual 110.68 99.38 11.30 1.39e+00 5.18e-01 6.61e+01 angle pdb=" N TYR A 122 " pdb=" CA TYR A 122 " pdb=" CB TYR A 122 " ideal model delta sigma weight residual 110.23 97.69 12.54 1.62e+00 3.81e-01 5.99e+01 angle pdb=" N VAL A 234 " pdb=" CA VAL A 234 " pdb=" CB VAL A 234 " ideal model delta sigma weight residual 111.23 100.08 11.15 1.65e+00 3.67e-01 4.57e+01 angle pdb=" N TYR A 217 " pdb=" CA TYR A 217 " pdb=" CB TYR A 217 " ideal model delta sigma weight residual 111.66 101.87 9.79 1.56e+00 4.11e-01 3.94e+01 angle pdb=" CA GLY A 503 " pdb=" C GLY A 503 " pdb=" O GLY A 503 " ideal model delta sigma weight residual 122.78 117.27 5.51 1.20e+00 6.94e-01 2.11e+01 ... (remaining 12211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4532 17.78 - 35.57: 569 35.57 - 53.35: 117 53.35 - 71.14: 41 71.14 - 88.92: 10 Dihedral angle restraints: 5269 sinusoidal: 2281 harmonic: 2988 Sorted by residual: dihedral pdb=" N TYR A 122 " pdb=" C TYR A 122 " pdb=" CA TYR A 122 " pdb=" CB TYR A 122 " ideal model delta harmonic sigma weight residual 122.80 109.52 13.28 0 2.50e+00 1.60e-01 2.82e+01 dihedral pdb=" N VAL A 234 " pdb=" C VAL A 234 " pdb=" CA VAL A 234 " pdb=" CB VAL A 234 " ideal model delta harmonic sigma weight residual 123.40 112.11 11.29 0 2.50e+00 1.60e-01 2.04e+01 dihedral pdb=" CA ASP A 454 " pdb=" C ASP A 454 " pdb=" N TYR A 455 " pdb=" CA TYR A 455 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 5266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1295 0.106 - 0.212: 89 0.212 - 0.318: 7 0.318 - 0.425: 2 0.425 - 0.531: 1 Chirality restraints: 1394 Sorted by residual: chirality pdb=" P G P 14 " pdb=" OP1 G P 14 " pdb=" OP2 G P 14 " pdb=" O5' G P 14 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CA ASP A 454 " pdb=" N ASP A 454 " pdb=" C ASP A 454 " pdb=" CB ASP A 454 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA VAL A 202 " pdb=" N VAL A 202 " pdb=" C VAL A 202 " pdb=" CB VAL A 202 " both_signs ideal model delta sigma weight residual False 2.44 2.78 -0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 1391 not shown) Planarity restraints: 1451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 889 " 0.547 9.50e-02 1.11e+02 2.45e-01 3.68e+01 pdb=" NE ARG A 889 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 889 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 889 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 889 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 33 " 0.485 9.50e-02 1.11e+02 2.17e-01 2.89e+01 pdb=" NE ARG A 33 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 33 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 33 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 33 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 118 " -0.371 9.50e-02 1.11e+02 1.66e-01 1.70e+01 pdb=" NE ARG A 118 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 118 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 118 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 118 " -0.014 2.00e-02 2.50e+03 ... (remaining 1448 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1177 2.75 - 3.29: 7947 3.29 - 3.83: 14477 3.83 - 4.36: 17675 4.36 - 4.90: 29424 Nonbonded interactions: 70700 Sorted by model distance: nonbonded pdb=" OE1 GLN A 210 " pdb=" OH TYR A 237 " model vdw 2.216 3.040 nonbonded pdb=" OG SER A 433 " pdb=" OE1 GLU A 876 " model vdw 2.219 3.040 nonbonded pdb=" OG SER A 239 " pdb=" OD1 ASP A 465 " model vdw 2.257 3.040 nonbonded pdb=" OD1 ASP A 194 " pdb=" OH TYR A 289 " model vdw 2.272 3.040 nonbonded pdb=" OH TYR A 294 " pdb=" OD1 ASN A 314 " model vdw 2.278 3.040 ... (remaining 70695 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 individual isotropic 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: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.220 Find NCS groups from input model: 0.030 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.006 0.061 8922 Z= 0.351 Angle : 0.813 12.540 12222 Z= 0.540 Chirality : 0.057 0.531 1394 Planarity : 0.011 0.245 1451 Dihedral : 16.663 88.921 3339 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.13 % Allowed : 16.07 % Favored : 81.80 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 6.25 % 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: -0.11 (0.26), residues: 993 helix: 0.47 (0.24), residues: 463 sheet: -0.06 (0.50), residues: 100 loop : -0.56 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 735 TYR 0.018 0.002 TYR A 515 PHE 0.015 0.002 PHE C 49 TRP 0.030 0.002 TRP A 916 HIS 0.013 0.002 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.34 ( 8911) covalent geometry : angle 0.81270 / 0.54 (12216) hydrogen bonds : bond 0.14074 / 14.55 ( 410) hydrogen bonds : angle 6.20219 / 7.23 ( 1133) metal coordination : bond 0.01527 / 0.84 ( 8) metal coordination : angle 1.65381 / 3.14 ( 6) Misc. bond : bond 0.04063 / 2.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.187 Fit side-chains REVERT: A 438 LYS cc_start: 0.7220 (mmtm) cc_final: 0.6746 (mmmt) REVERT: A 883 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6772 (tp) REVERT: B 89 THR cc_start: 0.7387 (m) cc_final: 0.7159 (p) REVERT: B 111 ARG cc_start: 0.5009 (OUTLIER) cc_final: 0.3242 (pmm150) outliers start: 19 outliers final: 9 residues processed: 117 average time/residue: 0.3539 time to fit residues: 44.9037 Evaluate side-chains 110 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain C residue 59 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 GLN A 381 HIS A 444 GLN A 790 ASN A 822 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.172297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.139154 restraints weight = 9589.057| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.46 r_work: 0.3475 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.0549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8922 Z= 0.167 Angle : 0.542 5.144 12222 Z= 0.296 Chirality : 0.041 0.138 1394 Planarity : 0.004 0.038 1451 Dihedral : 11.078 73.458 1493 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.60 % Allowed : 15.84 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.21 (0.26), residues: 993 helix: 0.83 (0.24), residues: 470 sheet: -0.11 (0.50), residues: 100 loop : -0.48 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 33 TYR 0.016 0.002 TYR A 515 PHE 0.014 0.002 PHE A 741 TRP 0.017 0.001 TRP A 916 HIS 0.009 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 ( 8911) covalent geometry : angle 0.54064 / 0.30 (12216) hydrogen bonds : bond 0.05948 / 6.36 ( 410) hydrogen bonds : angle 4.85794 / 5.49 ( 1133) metal coordination : bond 0.01485 / 0.82 ( 8) metal coordination : angle 1.93282 / 3.79 ( 6) Misc. bond : bond 0.00150 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.302 Fit side-chains REVERT: A 438 LYS cc_start: 0.7278 (mmtm) cc_final: 0.7004 (mptm) REVERT: A 804 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6984 (m-30) REVERT: B 89 THR cc_start: 0.7266 (m) cc_final: 0.6988 (p) REVERT: B 111 ARG cc_start: 0.5374 (OUTLIER) cc_final: 0.5156 (mtt180) REVERT: C 13 LEU cc_start: 0.5552 (OUTLIER) cc_final: 0.5216 (tm) REVERT: C 45 THR cc_start: 0.5915 (OUTLIER) cc_final: 0.5699 (m) outliers start: 32 outliers final: 17 residues processed: 128 average time/residue: 0.3699 time to fit residues: 51.3325 Evaluate side-chains 120 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 45 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 HIS A 790 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.177780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.145607 restraints weight = 9569.754| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.45 r_work: 0.3509 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8922 Z= 0.099 Angle : 0.442 4.857 12222 Z= 0.242 Chirality : 0.038 0.137 1394 Planarity : 0.003 0.035 1451 Dihedral : 10.796 73.489 1486 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.70 % Allowed : 16.85 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.71 (0.27), residues: 993 helix: 1.25 (0.25), residues: 465 sheet: -0.04 (0.51), residues: 99 loop : -0.16 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 21 TYR 0.022 0.001 TYR A 530 PHE 0.009 0.001 PHE A 753 TRP 0.014 0.001 TRP A 916 HIS 0.005 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.10 ( 8911) covalent geometry : angle 0.44116 / 0.24 (12216) hydrogen bonds : bond 0.04215 / 4.54 ( 410) hydrogen bonds : angle 4.45207 / 5.02 ( 1133) metal coordination : bond 0.00650 / 0.38 ( 8) metal coordination : angle 1.26069 / 2.43 ( 6) Misc. bond : bond 0.00068 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 438 LYS cc_start: 0.7236 (mmtm) cc_final: 0.6898 (mptm) REVERT: A 883 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6943 (tp) REVERT: B 89 THR cc_start: 0.7222 (m) cc_final: 0.6992 (p) REVERT: B 111 ARG cc_start: 0.5350 (OUTLIER) cc_final: 0.5063 (mtt90) REVERT: C 45 THR cc_start: 0.5724 (OUTLIER) cc_final: 0.5501 (m) outliers start: 24 outliers final: 8 residues processed: 129 average time/residue: 0.3230 time to fit residues: 45.3265 Evaluate side-chains 114 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain C residue 45 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 734 ASN A 790 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.172403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.139260 restraints weight = 9720.531| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.49 r_work: 0.3455 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8922 Z= 0.151 Angle : 0.508 4.974 12222 Z= 0.274 Chirality : 0.040 0.136 1394 Planarity : 0.004 0.037 1451 Dihedral : 10.878 73.495 1485 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.04 % Allowed : 16.40 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.26), residues: 993 helix: 1.10 (0.24), residues: 469 sheet: -0.02 (0.51), residues: 99 loop : -0.35 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.015 0.002 TYR A 515 PHE 0.014 0.002 PHE A 741 TRP 0.012 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 8911) covalent geometry : angle 0.50637 / 0.27 (12216) hydrogen bonds : bond 0.05170 / 5.53 ( 410) hydrogen bonds : angle 4.51746 / 5.10 ( 1133) metal coordination : bond 0.01253 / 0.68 ( 8) metal coordination : angle 1.84233 / 3.56 ( 6) Misc. bond : bond 0.00093 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.255 Fit side-chains REVERT: A 438 LYS cc_start: 0.7280 (mmtm) cc_final: 0.6903 (mptm) REVERT: A 804 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6956 (m-30) REVERT: A 883 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6955 (tp) REVERT: B 89 THR cc_start: 0.7373 (m) cc_final: 0.7117 (p) REVERT: B 111 ARG cc_start: 0.5299 (OUTLIER) cc_final: 0.5086 (mtt180) REVERT: C 13 LEU cc_start: 0.5583 (OUTLIER) cc_final: 0.5263 (tm) outliers start: 36 outliers final: 20 residues processed: 125 average time/residue: 0.3382 time to fit residues: 46.3545 Evaluate side-chains 123 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 59 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 80 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN A 416 ASN A 790 ASN B 157 GLN C 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.172515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139542 restraints weight = 9640.469| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.46 r_work: 0.3461 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8922 Z= 0.172 Angle : 0.533 5.011 12222 Z= 0.288 Chirality : 0.041 0.140 1394 Planarity : 0.004 0.072 1451 Dihedral : 10.963 73.581 1485 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.72 % Allowed : 16.85 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.34 (0.26), residues: 993 helix: 0.95 (0.24), residues: 470 sheet: -0.05 (0.50), residues: 100 loop : -0.42 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.017 0.002 TYR A 788 PHE 0.015 0.002 PHE A 741 TRP 0.012 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 8911) covalent geometry : angle 0.53090 / 0.29 (12216) hydrogen bonds : bond 0.05504 / 5.85 ( 410) hydrogen bonds : angle 4.58719 / 5.18 ( 1133) metal coordination : bond 0.01496 / 0.82 ( 8) metal coordination : angle 1.97161 / 3.83 ( 6) Misc. bond : bond 0.00108 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 0.186 Fit side-chains REVERT: A 438 LYS cc_start: 0.7290 (mmtm) cc_final: 0.6953 (mptm) REVERT: A 804 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6955 (m-30) REVERT: A 883 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7020 (tp) REVERT: B 89 THR cc_start: 0.7388 (m) cc_final: 0.7154 (p) REVERT: C 13 LEU cc_start: 0.5569 (OUTLIER) cc_final: 0.5230 (tm) outliers start: 42 outliers final: 26 residues processed: 131 average time/residue: 0.3197 time to fit residues: 45.7938 Evaluate side-chains 125 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 59 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 54 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN A 403 ASN A 416 ASN A 790 ASN B 157 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.171409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138511 restraints weight = 9617.392| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.46 r_work: 0.3458 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8922 Z= 0.181 Angle : 0.543 5.014 12222 Z= 0.293 Chirality : 0.042 0.143 1394 Planarity : 0.004 0.062 1451 Dihedral : 10.880 73.631 1481 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.49 % Allowed : 18.43 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.26 (0.26), residues: 993 helix: 0.89 (0.24), residues: 470 sheet: -0.12 (0.50), residues: 100 loop : -0.48 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.016 0.002 TYR A 515 PHE 0.014 0.002 PHE A 753 TRP 0.012 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 8911) covalent geometry : angle 0.54133 / 0.29 (12216) hydrogen bonds : bond 0.05636 / 5.98 ( 410) hydrogen bonds : angle 4.61152 / 5.22 ( 1133) metal coordination : bond 0.01624 / 0.89 ( 8) metal coordination : angle 2.02917 / 3.94 ( 6) Misc. bond : bond 0.00121 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.344 Fit side-chains REVERT: A 438 LYS cc_start: 0.7121 (mmtm) cc_final: 0.6887 (mptm) REVERT: A 804 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6960 (m-30) REVERT: A 883 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6974 (tp) REVERT: B 89 THR cc_start: 0.7409 (m) cc_final: 0.7183 (p) outliers start: 40 outliers final: 28 residues processed: 126 average time/residue: 0.3170 time to fit residues: 43.9695 Evaluate side-chains 126 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 59 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 80 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN A 416 ASN A 790 ASN B 88 GLN B 157 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.173081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140335 restraints weight = 9657.874| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.46 r_work: 0.3464 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8922 Z= 0.134 Angle : 0.491 4.888 12222 Z= 0.267 Chirality : 0.040 0.134 1394 Planarity : 0.004 0.057 1451 Dihedral : 10.806 73.495 1481 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.27 % Allowed : 18.88 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.26), residues: 993 helix: 1.03 (0.24), residues: 470 sheet: -0.07 (0.50), residues: 100 loop : -0.41 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.014 0.001 TYR A 788 PHE 0.013 0.001 PHE A 741 TRP 0.012 0.001 TRP A 916 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 8911) covalent geometry : angle 0.48944 / 0.27 (12216) hydrogen bonds : bond 0.04985 / 5.31 ( 410) hydrogen bonds : angle 4.50280 / 5.10 ( 1133) metal coordination : bond 0.01284 / 0.72 ( 8) metal coordination : angle 1.55449 / 3.03 ( 6) Misc. bond : bond 0.00085 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.206 Fit side-chains REVERT: A 438 LYS cc_start: 0.7179 (mmtm) cc_final: 0.6924 (mptm) REVERT: A 804 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6932 (m-30) REVERT: A 883 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6980 (tp) REVERT: B 89 THR cc_start: 0.7358 (m) cc_final: 0.7056 (p) REVERT: C 13 LEU cc_start: 0.5567 (OUTLIER) cc_final: 0.5242 (tm) outliers start: 38 outliers final: 25 residues processed: 129 average time/residue: 0.2986 time to fit residues: 42.2290 Evaluate side-chains 124 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 59 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 54 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 1 optimal weight: 30.0000 chunk 46 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 65 optimal weight: 0.0970 chunk 13 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN A 416 ASN A 613 HIS A 790 ASN B 157 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.174130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141610 restraints weight = 9549.638| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.45 r_work: 0.3486 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8922 Z= 0.131 Angle : 0.487 5.189 12222 Z= 0.264 Chirality : 0.040 0.133 1394 Planarity : 0.004 0.054 1451 Dihedral : 10.769 73.488 1481 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.04 % Allowed : 19.33 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.48 (0.26), residues: 993 helix: 1.08 (0.24), residues: 470 sheet: -0.05 (0.51), residues: 100 loop : -0.36 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.014 0.001 TYR A 867 PHE 0.013 0.001 PHE A 741 TRP 0.012 0.001 TRP A 916 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 8911) covalent geometry : angle 0.48612 / 0.26 (12216) hydrogen bonds : bond 0.04854 / 5.17 ( 410) hydrogen bonds : angle 4.45258 / 5.05 ( 1133) metal coordination : bond 0.01176 / 0.66 ( 8) metal coordination : angle 1.52394 / 2.97 ( 6) Misc. bond : bond 0.00075 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.188 Fit side-chains REVERT: A 438 LYS cc_start: 0.7179 (mmtm) cc_final: 0.6838 (mptm) REVERT: A 804 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6943 (m-30) REVERT: A 883 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6976 (tp) REVERT: B 89 THR cc_start: 0.7346 (m) cc_final: 0.7048 (p) REVERT: C 13 LEU cc_start: 0.5554 (OUTLIER) cc_final: 0.5227 (tm) outliers start: 36 outliers final: 26 residues processed: 125 average time/residue: 0.3153 time to fit residues: 43.1933 Evaluate side-chains 128 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 59 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 55 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN A 416 ASN A 790 ASN B 157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.172931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.140238 restraints weight = 9575.169| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.46 r_work: 0.3465 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8922 Z= 0.151 Angle : 0.513 5.964 12222 Z= 0.276 Chirality : 0.041 0.136 1394 Planarity : 0.004 0.052 1451 Dihedral : 10.798 73.543 1481 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.16 % Allowed : 19.44 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.42 (0.26), residues: 993 helix: 1.04 (0.24), residues: 470 sheet: -0.10 (0.50), residues: 100 loop : -0.41 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 33 TYR 0.017 0.002 TYR A 289 PHE 0.014 0.002 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 8911) covalent geometry : angle 0.51176 / 0.28 (12216) hydrogen bonds : bond 0.05147 / 5.49 ( 410) hydrogen bonds : angle 4.49228 / 5.10 ( 1133) metal coordination : bond 0.01348 / 0.74 ( 8) metal coordination : angle 1.78086 / 3.46 ( 6) Misc. bond : bond 0.00088 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.318 Fit side-chains REVERT: A 438 LYS cc_start: 0.7224 (mmtm) cc_final: 0.6880 (mptm) REVERT: A 804 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6954 (m-30) REVERT: A 883 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6960 (tp) REVERT: B 89 THR cc_start: 0.7354 (m) cc_final: 0.7055 (p) REVERT: C 13 LEU cc_start: 0.5603 (OUTLIER) cc_final: 0.5283 (tm) outliers start: 37 outliers final: 26 residues processed: 124 average time/residue: 0.2996 time to fit residues: 40.8734 Evaluate side-chains 125 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 91 optimal weight: 0.0670 chunk 89 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN A 416 ASN A 790 ASN B 157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.176365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144047 restraints weight = 9662.199| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.47 r_work: 0.3499 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8922 Z= 0.095 Angle : 0.442 6.336 12222 Z= 0.240 Chirality : 0.037 0.129 1394 Planarity : 0.003 0.051 1451 Dihedral : 10.655 73.534 1481 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.81 % Allowed : 20.67 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.76 (0.27), residues: 993 helix: 1.27 (0.25), residues: 473 sheet: 0.08 (0.51), residues: 100 loop : -0.17 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.013 0.001 TYR A 788 PHE 0.010 0.001 PHE A 741 TRP 0.013 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 ( 8911) covalent geometry : angle 0.44102 / 0.24 (12216) hydrogen bonds : bond 0.03964 / 4.26 ( 410) hydrogen bonds : angle 4.29491 / 4.87 ( 1133) metal coordination : bond 0.00739 / 0.42 ( 8) metal coordination : angle 1.34617 / 2.59 ( 6) Misc. bond : bond 0.00025 / 0.02 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 438 LYS cc_start: 0.7192 (mmtm) cc_final: 0.6857 (mptm) REVERT: A 883 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7032 (tp) REVERT: B 89 THR cc_start: 0.7285 (m) cc_final: 0.6970 (p) REVERT: C 13 LEU cc_start: 0.5519 (OUTLIER) cc_final: 0.5199 (tm) outliers start: 25 outliers final: 17 residues processed: 119 average time/residue: 0.3325 time to fit residues: 43.5128 Evaluate side-chains 119 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 0.0270 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 56 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN A 416 ASN A 790 ASN B 157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.175147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.142631 restraints weight = 9590.023| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.46 r_work: 0.3514 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8922 Z= 0.109 Angle : 0.455 6.205 12222 Z= 0.245 Chirality : 0.038 0.129 1394 Planarity : 0.003 0.049 1451 Dihedral : 10.645 73.419 1481 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.81 % Allowed : 20.45 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.78 (0.27), residues: 993 helix: 1.33 (0.25), residues: 471 sheet: 0.02 (0.51), residues: 99 loop : -0.19 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 33 TYR 0.015 0.001 TYR A 289 PHE 0.012 0.001 PHE A 741 TRP 0.012 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 8911) covalent geometry : angle 0.45404 / 0.25 (12216) hydrogen bonds : bond 0.04236 / 4.56 ( 410) hydrogen bonds : angle 4.28771 / 4.86 ( 1133) metal coordination : bond 0.00854 / 0.51 ( 8) metal coordination : angle 1.35512 / 2.64 ( 6) Misc. bond : bond 0.00044 / 0.04 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2223.24 seconds wall clock time: 38 minutes 32.13 seconds (2312.13 seconds total)