Starting phenix.real_space_refine on Thu Jul 2 12:14:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sap_54693/07_2026/9sap_54693.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sap_54693/07_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_54693/07_2026/9sap_54693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sap_54693/07_2026/9sap_54693.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sap_54693/07_2026/9sap_54693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sap_54693/07_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): 0.01s 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: 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: 2.11, per 1000 atoms: 0.24 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: 1.02 Conformation dependent library (CDL) restraints added in 279.9 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: 1.13 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: 1.72 Time building geometry restraints manager: 1.22 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: 11948 2.51 - 5.02: 248 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: 1318 0.106 - 0.212: 66 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.060 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.170 ------------------------------------------------------------------------------- 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= 0.348 Angle : 0.792 12.540 12222 Z= 0.521 Chirality : 0.055 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 0.00550 / 0.34 ( 8911) covalent geometry : angle 0.79107 / 0.52 (12216) hydrogen bonds : bond 0.14074 / 13.63 ( 410) hydrogen bonds : angle 6.20219 / 6.86 ( 1133) metal coordination : bond 0.01527 / 0.78 ( 8) metal coordination : angle 1.65381 / 3.14 ( 6) Misc. bond : bond 0.04063 / 2.25 ( 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 : 0.346 Fit side-chains REVERT: A 438 LYS cc_start: 0.7220 (mmtm) cc_final: 0.6747 (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: 0.7158 (p) REVERT: B 111 ARG cc_start: 0.5009 (OUTLIER) cc_final: 0.3243 (pmm150) outliers start: 19 outliers final: 9 residues processed: 117 average time/residue: 0.4819 time to fit residues: 61.1195 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 : 0.287 ------------------------------------------------------------------------------- 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: 0.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.173112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139992 restraints weight = 9560.102| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.47 r_work: 0.3481 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0573 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= 0.166 Angle : 0.539 5.073 12222 Z= 0.295 Chirality : 0.041 0.139 1394 Planarity : 0.004 0.038 1451 Dihedral : 11.139 73.548 1493 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.82 % Allowed : 15.39 % Favored : 80.79 % 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: 0.84 (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 0.003 0.001 ARG A 836 TYR 0.016 0.002 TYR A 289 PHE 0.014 0.002 PHE A 741 TRP 0.019 0.002 TRP A 916 HIS 0.008 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 8911) covalent geometry : angle 0.53786 / 0.29 (12216) hydrogen bonds : bond 0.05874 / 5.92 ( 410) hydrogen bonds : angle 4.86813 / 5.19 ( 1133) metal coordination : bond 0.01493 / 0.76 ( 8) metal coordination : angle 1.96476 / 3.86 ( 6) Misc. bond : bond 0.00186 / 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 142 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.327 Fit side-chains REVERT: A 438 LYS cc_start: 0.7291 (mmtm) cc_final: 0.7011 (mptm) REVERT: A 804 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6970 (m-30) REVERT: B 89 THR cc_start: 0.7304 (m) cc_final: 0.7027 (p) REVERT: B 111 ARG cc_start: 0.5384 (OUTLIER) cc_final: 0.5179 (mtt180) REVERT: C 13 LEU cc_start: 0.5551 (OUTLIER) cc_final: 0.5213 (tm) REVERT: C 45 THR cc_start: 0.5945 (OUTLIER) cc_final: 0.5730 (m) outliers start: 34 outliers final: 18 residues processed: 130 average time/residue: 0.4703 time to fit residues: 66.3848 Evaluate side-chains 122 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 501 SER 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: 0.6980 chunk 43 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 16 optimal weight: 0.0770 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.177858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.145549 restraints weight = 9561.977| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.46 r_work: 0.3513 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8922 Z= 0.100 Angle : 0.440 4.865 12222 Z= 0.242 Chirality : 0.038 0.136 1394 Planarity : 0.003 0.035 1451 Dihedral : 10.860 73.386 1486 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.03 % Allowed : 16.29 % Favored : 80.67 % 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: 0.73 (0.27), residues: 993 helix: 1.26 (0.25), residues: 465 sheet: -0.02 (0.51), residues: 99 loop : -0.15 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 21 TYR 0.023 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 0.00200 / 0.10 ( 8911) covalent geometry : angle 0.43904 / 0.24 (12216) hydrogen bonds : bond 0.04160 / 4.25 ( 410) hydrogen bonds : angle 4.45125 / 4.71 ( 1133) metal coordination : bond 0.00580 / 0.31 ( 8) metal coordination : angle 1.25543 / 2.41 ( 6) Misc. bond : bond 0.00022 / 0.01 ( 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: 27 poor density : 113 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 438 LYS cc_start: 0.7246 (mmtm) cc_final: 0.6904 (mptm) REVERT: A 883 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6970 (tp) REVERT: B 89 THR cc_start: 0.7221 (m) cc_final: 0.7005 (p) outliers start: 27 outliers final: 11 residues processed: 127 average time/residue: 0.4433 time to fit residues: 61.4267 Evaluate side-chains 115 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 501 SER Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 799 CYS 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 174 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN A 734 ASN A 790 ASN A 892 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.172936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139771 restraints weight = 9728.346| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.50 r_work: 0.3462 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1020 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= 0.140 Angle : 0.494 4.911 12222 Z= 0.268 Chirality : 0.040 0.133 1394 Planarity : 0.004 0.037 1451 Dihedral : 10.814 73.456 1481 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.04 % Allowed : 16.29 % Favored : 79.66 % 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: 0.56 (0.26), residues: 993 helix: 1.15 (0.24), residues: 469 sheet: 0.03 (0.52), residues: 99 loop : -0.32 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 33 TYR 0.015 0.002 TYR A 788 PHE 0.015 0.001 PHE C 49 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 0.00314 / 0.14 ( 8911) covalent geometry : angle 0.49308 / 0.27 (12216) hydrogen bonds : bond 0.04978 / 5.03 ( 410) hydrogen bonds : angle 4.47444 / 4.75 ( 1133) metal coordination : bond 0.01134 / 0.57 ( 8) metal coordination : angle 1.67962 / 3.23 ( 6) Misc. bond : bond 0.00079 / 0.04 ( 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 137 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.324 Fit side-chains REVERT: A 438 LYS cc_start: 0.7289 (mmtm) cc_final: 0.6911 (mptm) REVERT: A 804 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6948 (m-30) REVERT: A 883 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6980 (tp) REVERT: B 89 THR cc_start: 0.7367 (m) cc_final: 0.7102 (p) REVERT: C 13 LEU cc_start: 0.5584 (OUTLIER) cc_final: 0.5263 (tm) outliers start: 36 outliers final: 22 residues processed: 125 average time/residue: 0.4023 time to fit residues: 55.3506 Evaluate side-chains 123 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 380 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 501 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 ASN A 790 ASN C 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.172289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139279 restraints weight = 9631.709| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.46 r_work: 0.3467 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8922 Z= 0.179 Angle : 0.540 5.034 12222 Z= 0.292 Chirality : 0.042 0.144 1394 Planarity : 0.004 0.074 1451 Dihedral : 10.929 73.577 1481 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.49 % Allowed : 16.74 % Favored : 78.76 % 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: 0.93 (0.24), residues: 470 sheet: -0.01 (0.51), 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 0.011 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 8911) covalent geometry : angle 0.53797 / 0.29 (12216) hydrogen bonds : bond 0.05615 / 5.62 ( 410) hydrogen bonds : angle 4.59611 / 4.90 ( 1133) metal coordination : bond 0.01575 / 0.80 ( 8) metal coordination : angle 2.09773 / 4.06 ( 6) Misc. bond : bond 0.00089 / 0.05 ( 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 144 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 0.323 Fit side-chains REVERT: A 438 LYS cc_start: 0.7200 (mmtm) cc_final: 0.6883 (mptm) REVERT: A 804 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.6956 (m-30) REVERT: A 883 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7000 (tp) REVERT: B 89 THR cc_start: 0.7378 (m) cc_final: 0.7146 (p) REVERT: C 13 LEU cc_start: 0.5578 (OUTLIER) cc_final: 0.5233 (tm) outliers start: 40 outliers final: 26 residues processed: 135 average time/residue: 0.3906 time to fit residues: 57.9402 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 : 0.309 ------------------------------------------------------------------------------- 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 405 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 501 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 54 optimal weight: 6.9990 chunk 83 optimal weight: 0.0970 chunk 92 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.172982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.140052 restraints weight = 9603.954| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.47 r_work: 0.3466 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8922 Z= 0.152 Angle : 0.507 5.033 12222 Z= 0.275 Chirality : 0.040 0.136 1394 Planarity : 0.004 0.061 1451 Dihedral : 10.886 73.517 1481 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.27 % Allowed : 17.98 % Favored : 77.75 % 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: 0.37 (0.26), residues: 993 helix: 0.98 (0.24), residues: 470 sheet: -0.03 (0.51), 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 0.016 0.002 TYR A 788 PHE 0.014 0.002 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 0.00344 / 0.15 ( 8911) covalent geometry : angle 0.50519 / 0.27 (12216) hydrogen bonds : bond 0.05203 / 5.22 ( 410) hydrogen bonds : angle 4.53998 / 4.84 ( 1133) metal coordination : bond 0.01433 / 0.73 ( 8) metal coordination : angle 1.72396 / 3.35 ( 6) Misc. bond : bond 0.00087 / 0.05 ( 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 140 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.316 Fit side-chains REVERT: A 438 LYS cc_start: 0.7203 (mmtm) cc_final: 0.6976 (mptm) REVERT: A 804 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6940 (m-30) REVERT: A 883 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6973 (tp) REVERT: B 89 THR cc_start: 0.7360 (m) cc_final: 0.7140 (p) REVERT: C 13 LEU cc_start: 0.5591 (OUTLIER) cc_final: 0.5250 (tm) outliers start: 38 outliers final: 26 residues processed: 129 average time/residue: 0.3683 time to fit residues: 52.2187 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 : 0.198 ------------------------------------------------------------------------------- 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 497 ASN Chi-restraints excluded: chain A residue 501 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 59 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 80 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 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 157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.173197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140409 restraints weight = 9660.632| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.46 r_work: 0.3463 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1144 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= 0.135 Angle : 0.491 5.359 12222 Z= 0.266 Chirality : 0.040 0.134 1394 Planarity : 0.004 0.057 1451 Dihedral : 10.836 73.467 1481 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.93 % Allowed : 18.65 % Favored : 77.42 % 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: 0.45 (0.26), residues: 993 helix: 1.06 (0.24), residues: 470 sheet: -0.04 (0.51), residues: 100 loop : -0.39 (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 0.00300 / 0.13 ( 8911) covalent geometry : angle 0.49035 / 0.27 (12216) hydrogen bonds : bond 0.04927 / 4.97 ( 410) hydrogen bonds : angle 4.48369 / 4.77 ( 1133) metal coordination : bond 0.01234 / 0.62 ( 8) metal coordination : angle 1.56816 / 3.05 ( 6) Misc. bond : bond 0.00074 / 0.04 ( 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 142 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.316 Fit side-chains REVERT: A 438 LYS cc_start: 0.7144 (mmtm) cc_final: 0.6924 (mptm) REVERT: A 804 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6938 (m-30) REVERT: A 883 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6988 (tp) REVERT: B 89 THR cc_start: 0.7332 (m) cc_final: 0.7038 (p) REVERT: C 13 LEU cc_start: 0.5570 (OUTLIER) cc_final: 0.5240 (tm) outliers start: 35 outliers final: 26 residues processed: 132 average time/residue: 0.3618 time to fit residues: 52.5002 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 : 0.244 ------------------------------------------------------------------------------- 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 468 GLN Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 501 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 59 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 65 optimal weight: 0.0670 chunk 13 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN A 403 ASN A 416 ASN A 613 HIS A 790 ASN B 157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.173209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140448 restraints weight = 9583.759| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.46 r_work: 0.3477 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8922 Z= 0.136 Angle : 0.491 5.232 12222 Z= 0.266 Chirality : 0.040 0.134 1394 Planarity : 0.004 0.054 1451 Dihedral : 10.812 73.468 1481 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.93 % Allowed : 19.21 % 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: 0.48 (0.26), residues: 993 helix: 1.08 (0.24), residues: 470 sheet: -0.03 (0.50), residues: 100 loop : -0.37 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.015 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 0.00303 / 0.14 ( 8911) covalent geometry : angle 0.48995 / 0.27 (12216) hydrogen bonds : bond 0.04889 / 4.92 ( 410) hydrogen bonds : angle 4.46292 / 4.75 ( 1133) metal coordination : bond 0.01193 / 0.60 ( 8) metal coordination : angle 1.62016 / 3.16 ( 6) Misc. bond : bond 0.00070 / 0.04 ( 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 134 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.233 Fit side-chains REVERT: A 438 LYS cc_start: 0.7181 (mmtm) cc_final: 0.6842 (mptm) REVERT: A 804 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6945 (m-30) REVERT: A 883 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6983 (tp) REVERT: B 89 THR cc_start: 0.7359 (m) cc_final: 0.7052 (p) REVERT: C 13 LEU cc_start: 0.5566 (OUTLIER) cc_final: 0.5238 (tm) outliers start: 35 outliers final: 27 residues processed: 124 average time/residue: 0.3415 time to fit residues: 46.5416 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 : 0.185 ------------------------------------------------------------------------------- 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 501 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 55 optimal weight: 0.0570 chunk 61 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.7704 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.174901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.142216 restraints weight = 9612.379| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.47 r_work: 0.3488 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8922 Z= 0.106 Angle : 0.456 5.993 12222 Z= 0.247 Chirality : 0.038 0.129 1394 Planarity : 0.003 0.051 1451 Dihedral : 10.717 73.345 1481 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.48 % Allowed : 19.78 % 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: 0.66 (0.27), residues: 993 helix: 1.22 (0.25), residues: 471 sheet: 0.08 (0.51), residues: 100 loop : -0.27 (0.29), residues: 422 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 0.011 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 0.00223 / 0.11 ( 8911) covalent geometry : angle 0.45558 / 0.25 (12216) hydrogen bonds : bond 0.04257 / 4.31 ( 410) hydrogen bonds : angle 4.35740 / 4.62 ( 1133) metal coordination : bond 0.00911 / 0.47 ( 8) metal coordination : angle 1.34391 / 2.63 ( 6) Misc. bond : bond 0.00042 / 0.03 ( 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: 31 poor density : 104 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 438 LYS cc_start: 0.7151 (mmtm) cc_final: 0.6801 (mptm) REVERT: A 883 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6988 (tp) REVERT: B 89 THR cc_start: 0.7307 (m) cc_final: 0.6989 (p) REVERT: C 13 LEU cc_start: 0.5530 (OUTLIER) cc_final: 0.5211 (tm) outliers start: 31 outliers final: 19 residues processed: 125 average time/residue: 0.3867 time to fit residues: 53.1269 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 : 0.259 ------------------------------------------------------------------------------- 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 497 ASN Chi-restraints excluded: chain A residue 501 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 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 7 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.173711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.140938 restraints weight = 9610.213| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.47 r_work: 0.3486 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8922 Z= 0.141 Angle : 0.498 5.879 12222 Z= 0.268 Chirality : 0.040 0.133 1394 Planarity : 0.004 0.050 1451 Dihedral : 10.753 73.447 1481 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.92 % Allowed : 20.11 % Favored : 76.97 % 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: 0.57 (0.26), residues: 993 helix: 1.14 (0.24), residues: 471 sheet: 0.01 (0.51), residues: 100 loop : -0.32 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.015 0.002 TYR A 788 PHE 0.014 0.002 PHE A 741 TRP 0.010 0.001 TRP A 916 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8911) covalent geometry : angle 0.49677 / 0.27 (12216) hydrogen bonds : bond 0.04864 / 4.90 ( 410) hydrogen bonds : angle 4.41670 / 4.69 ( 1133) metal coordination : bond 0.01215 / 0.61 ( 8) metal coordination : angle 1.68772 / 3.25 ( 6) Misc. bond : bond 0.00075 / 0.04 ( 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 125 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.316 Fit side-chains REVERT: A 438 LYS cc_start: 0.7180 (mmtm) cc_final: 0.6881 (mmtt) REVERT: A 883 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7029 (tp) REVERT: B 89 THR cc_start: 0.7363 (m) cc_final: 0.7070 (p) REVERT: C 13 LEU cc_start: 0.5540 (OUTLIER) cc_final: 0.5223 (tm) outliers start: 26 outliers final: 22 residues processed: 116 average time/residue: 0.3488 time to fit residues: 44.4643 Evaluate side-chains 122 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 501 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 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 41 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: 0.0980 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.174141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141514 restraints weight = 9589.373| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.46 r_work: 0.3493 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8922 Z= 0.113 Angle : 0.465 6.080 12222 Z= 0.252 Chirality : 0.039 0.131 1394 Planarity : 0.003 0.051 1451 Dihedral : 10.698 73.363 1481 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.37 % Allowed : 19.55 % 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: 0.70 (0.27), residues: 993 helix: 1.24 (0.24), residues: 471 sheet: 0.09 (0.51), residues: 100 loop : -0.24 (0.29), residues: 422 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 0.012 0.001 PHE A 741 TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 8911) covalent geometry : angle 0.46427 / 0.25 (12216) hydrogen bonds : bond 0.04385 / 4.45 ( 410) hydrogen bonds : angle 4.34677 / 4.61 ( 1133) metal coordination : bond 0.01009 / 0.51 ( 8) metal coordination : angle 1.43049 / 2.81 ( 6) Misc. bond : bond 0.00054 / 0.03 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2746.28 seconds wall clock time: 47 minutes 37.86 seconds (2857.86 seconds total)