Starting phenix.real_space_refine on Thu Jul 2 16:09:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ctt_30469/07_2026/7ctt_30469.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ctt_30469/07_2026/7ctt_30469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ctt_30469/07_2026/7ctt_30469.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ctt_30469/07_2026/7ctt_30469.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ctt_30469/07_2026/7ctt_30469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ctt_30469/07_2026/7ctt_30469.map" model { file = "/net/cci-nas-00/data/ceres_data/7ctt_30469/07_2026/7ctt_30469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ctt_30469/07_2026/7ctt_30469.cif" } resolution = 3.2 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= 0.002 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 37 5.49 5 Mg 1 5.21 5 S 61 5.16 5 C 5548 2.51 5 N 1492 2.21 5 O 1770 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 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: 8912 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 826, 6610 Classifications: {'peptide': 826} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 28, 'TRANS': 797} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 856 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 221 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "Q" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 336 Classifications: {'RNA': 16} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna3p': 15} Chain: "T" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 384 Classifications: {'RNA': 18} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 8} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 1, ' ZN': 2, 'GE6': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1801 SG CYS A 301 70.372 57.844 32.268 1.00 49.99 S ATOM 1842 SG CYS A 306 70.771 56.913 28.427 1.00 47.23 S ATOM 1874 SG CYS A 310 73.351 56.249 31.282 1.00 45.07 S ATOM 3267 SG CYS A 487 51.270 58.877 37.590 1.00 56.43 S ATOM 4520 SG CYS A 645 50.345 58.349 33.598 1.00 59.56 S ATOM 4526 SG CYS A 646 53.921 59.698 35.506 1.00 56.53 S Time building chain proxies: 1.48, per 1000 atoms: 0.17 Number of scatterers: 8912 At special positions: 0 Unit cell: (112, 90, 104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 61 16.00 P 37 15.00 Mg 1 11.99 F 1 9.00 O 1770 8.00 N 1492 7.00 C 5548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 237.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " 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 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 8 sheets defined 51.6% alpha, 11.6% beta 16 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.618A pdb=" N ASN A 88 " --> pdb=" O THR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 147 Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 170 through 199 removed outlier: 4.376A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.772A 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: 3.905A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.471A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.805A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 383 removed outlier: 4.148A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.899A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.926A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.809A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 573 removed outlier: 3.665A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 580 Processing helix chain 'A' and resid 596 through 607 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 Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.512A pdb=" N ILE A 715 " --> pdb=" O GLY A 712 " (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 789 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 852 through 867 removed outlier: 4.050A pdb=" N ILE A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 890 removed outlier: 4.253A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 110 through 114 removed outlier: 3.769A pdb=" N GLY B 113 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS B 114 " --> pdb=" O ARG B 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 114' Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.972A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 25 through 40 removed outlier: 3.912A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 removed outlier: 3.829A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 99 Processing helix chain 'D' and resid 100 through 111 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: 6.822A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.144A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.173A 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: 6.144A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 559 removed outlier: 3.538A pdb=" N THR A 540 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 removed outlier: 4.031A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 819 through 821 392 hydrogen bonds defined for protein. 1092 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1387 1.32 - 1.44: 2752 1.44 - 1.56: 4869 1.56 - 1.69: 74 1.69 - 1.81: 94 Bond restraints: 9176 Sorted by residual: bond pdb=" C10 GE6 A1004 " pdb=" O05 GE6 A1004 " ideal model delta sigma weight residual 1.229 1.491 -0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C03 GE6 A1004 " pdb=" O01 GE6 A1004 " ideal model delta sigma weight residual 1.383 1.608 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C02 GE6 A1004 " pdb=" C03 GE6 A1004 " ideal model delta sigma weight residual 1.539 1.344 0.195 2.00e-02 2.50e+03 9.49e+01 bond pdb=" C09 GE6 A1004 " pdb=" N01 GE6 A1004 " ideal model delta sigma weight residual 1.336 1.517 -0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" C04 GE6 A1004 " pdb=" O01 GE6 A1004 " ideal model delta sigma weight residual 1.436 1.287 0.149 2.00e-02 2.50e+03 5.59e+01 ... (remaining 9171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 12506 2.33 - 4.66: 99 4.66 - 7.00: 16 7.00 - 9.33: 5 9.33 - 11.66: 2 Bond angle restraints: 12628 Sorted by residual: angle pdb=" O08 GE6 A1004 " pdb=" P01 GE6 A1004 " pdb=" O09 GE6 A1004 " ideal model delta sigma weight residual 121.07 109.41 11.66 3.00e+00 1.11e-01 1.51e+01 angle pdb=" P02 GE6 A1004 " pdb=" O10 GE6 A1004 " pdb=" P03 GE6 A1004 " ideal model delta sigma weight residual 132.81 122.63 10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" O10 GE6 A1004 " pdb=" P03 GE6 A1004 " pdb=" O12 GE6 A1004 " ideal model delta sigma weight residual 100.75 109.60 -8.85 3.00e+00 1.11e-01 8.70e+00 angle pdb=" N SER A 682 " pdb=" CA SER A 682 " pdb=" C SER A 682 " ideal model delta sigma weight residual 113.28 109.71 3.57 1.22e+00 6.72e-01 8.56e+00 angle pdb=" O06 GE6 A1004 " pdb=" P01 GE6 A1004 " pdb=" O07 GE6 A1004 " ideal model delta sigma weight residual 101.35 109.85 -8.50 3.00e+00 1.11e-01 8.03e+00 ... (remaining 12623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4868 17.31 - 34.62: 435 34.62 - 51.92: 84 51.92 - 69.23: 12 69.23 - 86.54: 4 Dihedral angle restraints: 5403 sinusoidal: 2346 harmonic: 3057 Sorted by residual: dihedral pdb=" CA SER A 759 " pdb=" C SER A 759 " pdb=" N ASP A 760 " pdb=" CA ASP A 760 " ideal model delta harmonic sigma weight residual 180.00 153.97 26.03 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA LEU A 758 " pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta harmonic sigma weight residual 180.00 155.38 24.62 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CB GLU A 254 " pdb=" CG GLU A 254 " pdb=" CD GLU A 254 " pdb=" OE1 GLU A 254 " ideal model delta sinusoidal sigma weight residual 0.00 -86.54 86.54 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 5400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1325 0.066 - 0.132: 128 0.132 - 0.198: 4 0.198 - 0.264: 0 0.264 - 0.330: 1 Chirality restraints: 1458 Sorted by residual: chirality pdb=" C02 GE6 A1004 " pdb=" C01 GE6 A1004 " pdb=" C03 GE6 A1004 " pdb=" O02 GE6 A1004 " both_signs ideal model delta sigma weight residual False 2.75 2.42 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C01 GE6 A1004 " pdb=" C02 GE6 A1004 " pdb=" C04 GE6 A1004 " pdb=" O03 GE6 A1004 " both_signs ideal model delta sigma weight residual False -2.44 -2.61 0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CB ILE A 494 " pdb=" CA ILE A 494 " pdb=" CG1 ILE A 494 " pdb=" CG2 ILE A 494 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.21e-01 ... (remaining 1455 not shown) Planarity restraints: 1481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 758 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.77e+00 pdb=" C LEU A 758 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 758 " -0.011 2.00e-02 2.50e+03 pdb=" N SER A 759 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 242 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A 243 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 607 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C SER A 607 " -0.022 2.00e-02 2.50e+03 pdb=" O SER A 607 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP A 608 " 0.008 2.00e-02 2.50e+03 ... (remaining 1478 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 215 2.67 - 3.23: 8870 3.23 - 3.79: 14833 3.79 - 4.34: 20526 4.34 - 4.90: 32481 Nonbonded interactions: 76925 Sorted by model distance: nonbonded pdb=" OD1 ASP A 761 " pdb="MG MG A1003 " model vdw 2.114 2.170 nonbonded pdb=" O ILE A 837 " pdb=" OH TYR A 884 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR A 122 " pdb=" OE1 GLU A 144 " model vdw 2.235 3.040 nonbonded pdb=" OG1 THR A 226 " pdb=" OG SER A 229 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASP A 623 " pdb=" OG SER A 682 " model vdw 2.266 3.040 ... (remaining 76920 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: 1.430 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: 0.020 Process input model: 9.620 Find NCS groups from input model: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 : 0.008 0.277 9184 Z= 0.336 Angle : 0.640 17.315 12634 Z= 0.309 Chirality : 0.040 0.330 1458 Planarity : 0.003 0.033 1481 Dihedral : 13.125 86.538 3427 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.01 % Allowed : 12.05 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.22), residues: 1017 helix: -1.62 (0.20), residues: 461 sheet: -2.54 (0.52), residues: 63 loop : -2.41 (0.24), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 750 TYR 0.013 0.001 TYR A 788 PHE 0.011 0.001 PHE A 741 TRP 0.007 0.001 TRP A 617 HIS 0.005 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00671 / 0.33 ( 9176) covalent geometry : angle 0.59294 / 0.30 (12628) hydrogen bonds : bond 0.13867 / 8.54 ( 423) hydrogen bonds : angle 6.28328 / 4.29 ( 1168) metal coordination : bond 0.11555 / 5.83 ( 8) metal coordination : angle 11.07078 / 5.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7103 (tp30) REVERT: A 411 LYS cc_start: 0.7436 (mppt) cc_final: 0.7091 (mttm) REVERT: A 624 ARG cc_start: 0.8129 (mmt180) cc_final: 0.7838 (mmt180) REVERT: A 626 MET cc_start: 0.8004 (ttt) cc_final: 0.7803 (ttt) REVERT: A 826 TYR cc_start: 0.7331 (m-10) cc_final: 0.7115 (m-80) REVERT: A 924 MET cc_start: 0.7535 (mmt) cc_final: 0.7236 (mmt) REVERT: A 928 HIS cc_start: 0.6340 (OUTLIER) cc_final: 0.5755 (t70) REVERT: C 31 GLN cc_start: 0.6623 (tp-100) cc_final: 0.6421 (tp-100) REVERT: C 34 GLN cc_start: 0.8519 (tp40) cc_final: 0.8055 (tp40) outliers start: 9 outliers final: 6 residues processed: 222 average time/residue: 0.0769 time to fit residues: 23.9048 Evaluate side-chains 186 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 179 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.1980 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN A 492 GLN A 611 ASN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS B 157 GLN D 100 ASN D 108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.173935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134794 restraints weight = 10732.968| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.50 r_work: 0.3707 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9184 Z= 0.129 Angle : 0.537 8.397 12634 Z= 0.275 Chirality : 0.040 0.251 1458 Planarity : 0.003 0.025 1481 Dihedral : 6.912 56.048 1591 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.15 % Allowed : 15.54 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.25), residues: 1017 helix: -0.41 (0.23), residues: 468 sheet: -2.20 (0.49), residues: 77 loop : -1.55 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.014 0.001 TYR A 788 PHE 0.010 0.001 PHE A 741 TRP 0.007 0.001 TRP A 617 HIS 0.009 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9176) covalent geometry : angle 0.53344 / 0.27 (12628) hydrogen bonds : bond 0.03316 / 2.00 ( 423) hydrogen bonds : angle 4.77359 / 3.22 ( 1168) metal coordination : bond 0.01088 / 0.55 ( 8) metal coordination : angle 2.69706 / 1.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8039 (p) cc_final: 0.7692 (t) REVERT: A 180 GLU cc_start: 0.7967 (mm-30) cc_final: 0.5667 (tp30) REVERT: A 331 ARG cc_start: 0.7021 (mtp180) cc_final: 0.6812 (mtp85) REVERT: A 411 LYS cc_start: 0.7261 (mppt) cc_final: 0.6857 (mttm) REVERT: A 455 TYR cc_start: 0.7738 (m-80) cc_final: 0.7493 (m-80) REVERT: A 463 MET cc_start: 0.7813 (ttt) cc_final: 0.7490 (ttt) REVERT: A 666 MET cc_start: 0.8058 (ptp) cc_final: 0.7838 (ptp) REVERT: A 789 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: A 826 TYR cc_start: 0.7895 (m-10) cc_final: 0.7689 (m-80) REVERT: A 858 ARG cc_start: 0.7229 (ttt90) cc_final: 0.6841 (ttt-90) REVERT: A 889 ARG cc_start: 0.6606 (mmt90) cc_final: 0.5933 (mmm-85) REVERT: A 924 MET cc_start: 0.7810 (mmt) cc_final: 0.7546 (mmt) REVERT: A 928 HIS cc_start: 0.7049 (OUTLIER) cc_final: 0.6548 (t70) REVERT: C 31 GLN cc_start: 0.6801 (tp-100) cc_final: 0.6483 (tp-100) REVERT: C 34 GLN cc_start: 0.8684 (tp40) cc_final: 0.8260 (tp40) REVERT: C 55 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8291 (tt) outliers start: 28 outliers final: 15 residues processed: 220 average time/residue: 0.0732 time to fit residues: 23.0081 Evaluate side-chains 198 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 55 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 59 optimal weight: 0.0020 chunk 39 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.173487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.134294 restraints weight = 10754.520| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.49 r_work: 0.3704 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9184 Z= 0.136 Angle : 0.536 6.737 12634 Z= 0.274 Chirality : 0.040 0.301 1458 Planarity : 0.003 0.025 1481 Dihedral : 6.664 55.665 1584 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.15 % Allowed : 17.57 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.25), residues: 1017 helix: -0.06 (0.23), residues: 469 sheet: -2.20 (0.48), residues: 87 loop : -1.36 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 889 TYR 0.025 0.002 TYR A 606 PHE 0.020 0.001 PHE A 157 TRP 0.007 0.001 TRP A 617 HIS 0.009 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9176) covalent geometry : angle 0.53374 / 0.27 (12628) hydrogen bonds : bond 0.03234 / 1.94 ( 423) hydrogen bonds : angle 4.63699 / 3.12 ( 1168) metal coordination : bond 0.00850 / 0.41 ( 8) metal coordination : angle 2.42424 / 1.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8085 (p) cc_final: 0.7685 (t) REVERT: A 180 GLU cc_start: 0.7984 (mm-30) cc_final: 0.5763 (tp30) REVERT: A 206 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7674 (m) REVERT: A 331 ARG cc_start: 0.6939 (mtp180) cc_final: 0.6693 (mtp85) REVERT: A 411 LYS cc_start: 0.7223 (mppt) cc_final: 0.6800 (mttm) REVERT: A 426 LYS cc_start: 0.8405 (mttp) cc_final: 0.7970 (mtpp) REVERT: A 483 TYR cc_start: 0.8615 (m-80) cc_final: 0.8339 (m-80) REVERT: A 545 LYS cc_start: 0.6785 (ptmt) cc_final: 0.6432 (pttt) REVERT: A 624 ARG cc_start: 0.8121 (mmt180) cc_final: 0.7524 (mmt180) REVERT: A 666 MET cc_start: 0.8069 (ptp) cc_final: 0.7865 (ptp) REVERT: A 789 GLN cc_start: 0.7804 (tt0) cc_final: 0.7392 (tt0) REVERT: A 889 ARG cc_start: 0.6633 (mmt90) cc_final: 0.5972 (mmm-85) REVERT: A 922 GLU cc_start: 0.8427 (tp30) cc_final: 0.8097 (tp30) REVERT: A 924 MET cc_start: 0.7801 (mmt) cc_final: 0.7555 (mmt) REVERT: C 31 GLN cc_start: 0.6817 (tp-100) cc_final: 0.6532 (tp-100) REVERT: C 34 GLN cc_start: 0.8698 (tp40) cc_final: 0.8290 (tp40) REVERT: C 55 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8354 (tt) outliers start: 28 outliers final: 16 residues processed: 209 average time/residue: 0.0706 time to fit residues: 21.1368 Evaluate side-chains 203 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 55 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 3 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 HIS B 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.171112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.132742 restraints weight = 10977.761| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.42 r_work: 0.3681 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9184 Z= 0.173 Angle : 0.547 6.489 12634 Z= 0.281 Chirality : 0.040 0.210 1458 Planarity : 0.003 0.026 1481 Dihedral : 6.638 56.498 1582 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.49 % Allowed : 18.81 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.25), residues: 1017 helix: 0.10 (0.24), residues: 469 sheet: -1.91 (0.51), residues: 77 loop : -1.36 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 750 TYR 0.018 0.002 TYR A 788 PHE 0.017 0.002 PHE A 694 TRP 0.007 0.001 TRP A 617 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 9176) covalent geometry : angle 0.54436 / 0.28 (12628) hydrogen bonds : bond 0.03285 / 1.96 ( 423) hydrogen bonds : angle 4.62825 / 3.11 ( 1168) metal coordination : bond 0.01186 / 0.53 ( 8) metal coordination : angle 2.36354 / 1.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8205 (p) cc_final: 0.7803 (t) REVERT: A 131 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8812 (tt) REVERT: A 180 GLU cc_start: 0.8004 (mm-30) cc_final: 0.5660 (tp30) REVERT: A 411 LYS cc_start: 0.7252 (mppt) cc_final: 0.6806 (mttm) REVERT: A 426 LYS cc_start: 0.8411 (mttp) cc_final: 0.7980 (mtpp) REVERT: A 463 MET cc_start: 0.7856 (ttt) cc_final: 0.7405 (tmt) REVERT: A 483 TYR cc_start: 0.8606 (m-80) cc_final: 0.8369 (m-80) REVERT: A 624 ARG cc_start: 0.8213 (mmt180) cc_final: 0.7669 (mmt180) REVERT: A 811 GLU cc_start: 0.7262 (tt0) cc_final: 0.6999 (tt0) REVERT: A 889 ARG cc_start: 0.6596 (mmt90) cc_final: 0.5961 (mmm-85) REVERT: A 924 MET cc_start: 0.7870 (mmt) cc_final: 0.7589 (mmt) REVERT: A 928 HIS cc_start: 0.6983 (OUTLIER) cc_final: 0.6531 (t70) REVERT: C 31 GLN cc_start: 0.6783 (tp-100) cc_final: 0.6503 (tp-100) REVERT: C 34 GLN cc_start: 0.8769 (tp40) cc_final: 0.8368 (tp40) REVERT: C 55 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8454 (tt) outliers start: 31 outliers final: 22 residues processed: 211 average time/residue: 0.0705 time to fit residues: 21.0705 Evaluate side-chains 210 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 55 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.171589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.132223 restraints weight = 10826.405| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.50 r_work: 0.3678 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9184 Z= 0.161 Angle : 0.547 6.366 12634 Z= 0.282 Chirality : 0.041 0.305 1458 Planarity : 0.003 0.025 1481 Dihedral : 6.662 56.233 1582 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.94 % Allowed : 19.48 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.25), residues: 1017 helix: 0.09 (0.24), residues: 469 sheet: -1.79 (0.52), residues: 77 loop : -1.30 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 836 TYR 0.017 0.002 TYR A 217 PHE 0.014 0.002 PHE A 694 TRP 0.007 0.001 TRP A 617 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 9176) covalent geometry : angle 0.54483 / 0.28 (12628) hydrogen bonds : bond 0.03250 / 1.94 ( 423) hydrogen bonds : angle 4.62581 / 3.11 ( 1168) metal coordination : bond 0.01113 / 0.49 ( 8) metal coordination : angle 2.28064 / 1.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8156 (p) cc_final: 0.7747 (t) REVERT: A 131 LEU cc_start: 0.9096 (tp) cc_final: 0.8833 (tt) REVERT: A 180 GLU cc_start: 0.8039 (mm-30) cc_final: 0.5832 (tp30) REVERT: A 411 LYS cc_start: 0.7312 (mppt) cc_final: 0.6924 (mmtm) REVERT: A 426 LYS cc_start: 0.8414 (mttp) cc_final: 0.7982 (mtpp) REVERT: A 463 MET cc_start: 0.8032 (ttt) cc_final: 0.7613 (tmt) REVERT: A 566 MET cc_start: 0.7542 (mtp) cc_final: 0.7336 (mtm) REVERT: A 624 ARG cc_start: 0.8186 (mmt180) cc_final: 0.7678 (mmt180) REVERT: A 811 GLU cc_start: 0.7323 (tt0) cc_final: 0.7054 (tt0) REVERT: A 889 ARG cc_start: 0.6615 (mmt90) cc_final: 0.5955 (mmm-85) REVERT: A 924 MET cc_start: 0.7896 (mmt) cc_final: 0.7641 (mmt) REVERT: A 928 HIS cc_start: 0.6968 (OUTLIER) cc_final: 0.6505 (t70) REVERT: B 155 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6832 (pp20) REVERT: C 29 TRP cc_start: 0.8210 (t-100) cc_final: 0.7926 (t-100) REVERT: C 31 GLN cc_start: 0.6767 (tp-100) cc_final: 0.6562 (tp-100) REVERT: C 34 GLN cc_start: 0.8777 (tp40) cc_final: 0.8372 (tp40) REVERT: C 55 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8369 (tt) outliers start: 35 outliers final: 26 residues processed: 209 average time/residue: 0.0702 time to fit residues: 21.3750 Evaluate side-chains 212 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 55 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.169393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.131064 restraints weight = 10856.863| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.38 r_work: 0.3661 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9184 Z= 0.200 Angle : 0.581 6.213 12634 Z= 0.299 Chirality : 0.042 0.272 1458 Planarity : 0.003 0.029 1481 Dihedral : 6.795 58.059 1582 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.28 % Allowed : 20.72 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.25), residues: 1017 helix: 0.08 (0.24), residues: 469 sheet: -1.76 (0.52), residues: 77 loop : -1.34 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.020 0.002 TYR A 788 PHE 0.017 0.002 PHE A 694 TRP 0.008 0.001 TRP A 617 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 9176) covalent geometry : angle 0.57901 / 0.30 (12628) hydrogen bonds : bond 0.03469 / 2.08 ( 423) hydrogen bonds : angle 4.69459 / 3.16 ( 1168) metal coordination : bond 0.01454 / 0.60 ( 8) metal coordination : angle 2.20674 / 0.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8277 (p) cc_final: 0.7858 (t) REVERT: A 131 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8880 (tt) REVERT: A 180 GLU cc_start: 0.8110 (mm-30) cc_final: 0.5928 (tp30) REVERT: A 411 LYS cc_start: 0.7260 (mppt) cc_final: 0.6862 (mttm) REVERT: A 426 LYS cc_start: 0.8429 (mttp) cc_final: 0.7997 (mtpp) REVERT: A 463 MET cc_start: 0.8135 (ttt) cc_final: 0.7779 (tmt) REVERT: A 525 ASP cc_start: 0.8601 (t0) cc_final: 0.8263 (t0) REVERT: A 811 GLU cc_start: 0.7351 (tt0) cc_final: 0.7075 (tt0) REVERT: A 889 ARG cc_start: 0.6591 (mmt90) cc_final: 0.5956 (mmm-85) REVERT: A 924 MET cc_start: 0.8001 (mmt) cc_final: 0.7686 (mmt) REVERT: A 928 HIS cc_start: 0.7049 (OUTLIER) cc_final: 0.6563 (t70) REVERT: B 155 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6930 (pp20) REVERT: C 34 GLN cc_start: 0.8776 (tp40) cc_final: 0.8321 (tp40) REVERT: C 55 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8498 (tt) outliers start: 38 outliers final: 30 residues processed: 207 average time/residue: 0.0671 time to fit residues: 20.1747 Evaluate side-chains 220 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 55 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 99 optimal weight: 0.0770 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 68 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 0.0040 chunk 53 optimal weight: 0.7980 overall best weight: 0.3550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.178417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.141300 restraints weight = 10612.683| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.22 r_work: 0.3748 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9184 Z= 0.119 Angle : 0.539 9.346 12634 Z= 0.275 Chirality : 0.040 0.245 1458 Planarity : 0.003 0.025 1481 Dihedral : 6.750 55.323 1582 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.83 % Allowed : 22.18 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.26), residues: 1017 helix: 0.25 (0.24), residues: 476 sheet: -1.41 (0.56), residues: 67 loop : -1.14 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 733 TYR 0.019 0.001 TYR A 787 PHE 0.014 0.001 PHE A 504 TRP 0.011 0.001 TRP A 617 HIS 0.013 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9176) covalent geometry : angle 0.53761 / 0.27 (12628) hydrogen bonds : bond 0.03097 / 1.85 ( 423) hydrogen bonds : angle 4.54013 / 3.05 ( 1168) metal coordination : bond 0.00776 / 0.33 ( 8) metal coordination : angle 1.98038 / 0.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8227 (p) cc_final: 0.7839 (t) REVERT: A 180 GLU cc_start: 0.8093 (mm-30) cc_final: 0.6117 (tp30) REVERT: A 240 LEU cc_start: 0.8705 (mt) cc_final: 0.8445 (mt) REVERT: A 411 LYS cc_start: 0.7361 (mppt) cc_final: 0.6968 (mttm) REVERT: A 426 LYS cc_start: 0.8405 (mttp) cc_final: 0.7996 (mtpp) REVERT: A 525 ASP cc_start: 0.8728 (t0) cc_final: 0.8315 (t0) REVERT: A 624 ARG cc_start: 0.8296 (mmt180) cc_final: 0.8005 (mmt180) REVERT: A 633 MET cc_start: 0.8391 (ttp) cc_final: 0.7374 (ttp) REVERT: A 811 GLU cc_start: 0.7335 (tt0) cc_final: 0.7050 (tt0) REVERT: A 889 ARG cc_start: 0.6683 (mmt90) cc_final: 0.6033 (mmm-85) REVERT: B 155 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6853 (pp20) REVERT: C 29 TRP cc_start: 0.8354 (t-100) cc_final: 0.8041 (t-100) REVERT: C 34 GLN cc_start: 0.8703 (tp40) cc_final: 0.8123 (tp40) REVERT: C 59 LEU cc_start: 0.7665 (tp) cc_final: 0.7449 (tp) outliers start: 34 outliers final: 23 residues processed: 213 average time/residue: 0.0714 time to fit residues: 21.8228 Evaluate side-chains 209 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 4 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 57 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 0.0010 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.174116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.134860 restraints weight = 10735.219| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.50 r_work: 0.3715 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9184 Z= 0.131 Angle : 0.559 10.824 12634 Z= 0.285 Chirality : 0.041 0.241 1458 Planarity : 0.003 0.025 1481 Dihedral : 6.664 55.216 1582 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.49 % Allowed : 22.86 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.26), residues: 1017 helix: 0.29 (0.24), residues: 474 sheet: -1.25 (0.58), residues: 67 loop : -1.03 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.021 0.001 TYR A 787 PHE 0.011 0.001 PHE A 165 TRP 0.008 0.001 TRP A 617 HIS 0.010 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 9176) covalent geometry : angle 0.55780 / 0.29 (12628) hydrogen bonds : bond 0.03138 / 1.88 ( 423) hydrogen bonds : angle 4.51938 / 3.04 ( 1168) metal coordination : bond 0.00889 / 0.39 ( 8) metal coordination : angle 1.97170 / 0.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8172 (p) cc_final: 0.7777 (t) REVERT: A 131 LEU cc_start: 0.8590 (tt) cc_final: 0.8362 (tp) REVERT: A 180 GLU cc_start: 0.7915 (mm-30) cc_final: 0.5918 (tp30) REVERT: A 411 LYS cc_start: 0.7322 (mppt) cc_final: 0.6907 (mttm) REVERT: A 426 LYS cc_start: 0.8377 (mttp) cc_final: 0.7958 (mtpp) REVERT: A 494 ILE cc_start: 0.8585 (mt) cc_final: 0.8355 (mm) REVERT: A 525 ASP cc_start: 0.8669 (t0) cc_final: 0.8303 (t0) REVERT: A 624 ARG cc_start: 0.8066 (mmt180) cc_final: 0.7780 (mmt180) REVERT: A 633 MET cc_start: 0.8310 (ttp) cc_final: 0.7456 (ttp) REVERT: A 682 SER cc_start: 0.7466 (OUTLIER) cc_final: 0.7091 (m) REVERT: A 811 GLU cc_start: 0.7270 (tt0) cc_final: 0.6946 (tt0) REVERT: A 889 ARG cc_start: 0.6655 (mmt90) cc_final: 0.5987 (mmm-85) REVERT: A 928 HIS cc_start: 0.6862 (OUTLIER) cc_final: 0.6388 (t70) REVERT: B 155 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6687 (pp20) REVERT: C 29 TRP cc_start: 0.8225 (t-100) cc_final: 0.7887 (t-100) REVERT: C 34 GLN cc_start: 0.8584 (tp40) cc_final: 0.7982 (tp40) outliers start: 31 outliers final: 24 residues processed: 213 average time/residue: 0.0786 time to fit residues: 24.1417 Evaluate side-chains 213 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 171 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 56 optimal weight: 0.0570 chunk 57 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.173863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.135865 restraints weight = 10765.398| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.39 r_work: 0.3714 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9184 Z= 0.146 Angle : 0.580 10.467 12634 Z= 0.295 Chirality : 0.042 0.350 1458 Planarity : 0.003 0.026 1481 Dihedral : 6.691 55.383 1582 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.28 % Allowed : 22.64 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.26), residues: 1017 helix: 0.32 (0.24), residues: 474 sheet: -1.29 (0.58), residues: 67 loop : -1.09 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.018 0.001 TYR A 787 PHE 0.014 0.002 PHE A 753 TRP 0.009 0.001 TRP A 617 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 9176) covalent geometry : angle 0.57812 / 0.29 (12628) hydrogen bonds : bond 0.03248 / 1.94 ( 423) hydrogen bonds : angle 4.53981 / 3.05 ( 1168) metal coordination : bond 0.00980 / 0.42 ( 8) metal coordination : angle 2.04443 / 0.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8227 (p) cc_final: 0.7830 (t) REVERT: A 180 GLU cc_start: 0.7922 (mm-30) cc_final: 0.5959 (tp30) REVERT: A 411 LYS cc_start: 0.7405 (mppt) cc_final: 0.6986 (mttm) REVERT: A 426 LYS cc_start: 0.8368 (mttp) cc_final: 0.7958 (mtpp) REVERT: A 525 ASP cc_start: 0.8628 (t0) cc_final: 0.8280 (t0) REVERT: A 624 ARG cc_start: 0.8076 (mmt180) cc_final: 0.7844 (mmt180) REVERT: A 633 MET cc_start: 0.8268 (ttp) cc_final: 0.7416 (ttp) REVERT: A 681 SER cc_start: 0.7955 (t) cc_final: 0.7682 (m) REVERT: A 682 SER cc_start: 0.7456 (OUTLIER) cc_final: 0.7141 (m) REVERT: A 811 GLU cc_start: 0.7198 (tt0) cc_final: 0.6879 (tt0) REVERT: A 889 ARG cc_start: 0.6673 (mmt90) cc_final: 0.6014 (mmm-85) REVERT: A 928 HIS cc_start: 0.6908 (OUTLIER) cc_final: 0.6415 (t70) REVERT: B 94 MET cc_start: 0.6160 (ptm) cc_final: 0.5219 (ptp) REVERT: B 155 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6758 (pp20) REVERT: C 29 TRP cc_start: 0.8296 (t-100) cc_final: 0.7979 (t-100) REVERT: C 34 GLN cc_start: 0.8521 (tp40) cc_final: 0.7938 (tp40) outliers start: 38 outliers final: 30 residues processed: 214 average time/residue: 0.0645 time to fit residues: 19.9894 Evaluate side-chains 221 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 4 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.177042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.140046 restraints weight = 10524.345| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.21 r_work: 0.3733 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9184 Z= 0.143 Angle : 0.587 10.184 12634 Z= 0.299 Chirality : 0.041 0.323 1458 Planarity : 0.003 0.028 1481 Dihedral : 6.702 55.009 1582 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.94 % Allowed : 22.86 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.26), residues: 1017 helix: 0.34 (0.24), residues: 477 sheet: -1.26 (0.58), residues: 67 loop : -1.01 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.024 0.001 TYR A 787 PHE 0.016 0.001 PHE A 165 TRP 0.007 0.001 TRP A 617 HIS 0.009 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 9176) covalent geometry : angle 0.58600 / 0.30 (12628) hydrogen bonds : bond 0.03196 / 1.90 ( 423) hydrogen bonds : angle 4.54080 / 3.04 ( 1168) metal coordination : bond 0.00915 / 0.40 ( 8) metal coordination : angle 2.00680 / 0.86 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8244 (p) cc_final: 0.7855 (t) REVERT: A 180 GLU cc_start: 0.8101 (mm-30) cc_final: 0.6172 (tp30) REVERT: A 411 LYS cc_start: 0.7502 (mppt) cc_final: 0.7080 (mttm) REVERT: A 426 LYS cc_start: 0.8410 (mttp) cc_final: 0.8007 (mtpp) REVERT: A 525 ASP cc_start: 0.8720 (t0) cc_final: 0.8379 (t0) REVERT: A 545 LYS cc_start: 0.6231 (ptpt) cc_final: 0.6008 (pttt) REVERT: A 633 MET cc_start: 0.8299 (ttp) cc_final: 0.7462 (ttp) REVERT: A 681 SER cc_start: 0.7950 (t) cc_final: 0.7719 (m) REVERT: A 682 SER cc_start: 0.7482 (OUTLIER) cc_final: 0.7214 (m) REVERT: A 811 GLU cc_start: 0.7364 (tt0) cc_final: 0.7075 (tt0) REVERT: A 889 ARG cc_start: 0.6725 (mmt90) cc_final: 0.6063 (mmm-85) REVERT: A 928 HIS cc_start: 0.7253 (OUTLIER) cc_final: 0.6724 (t70) REVERT: B 94 MET cc_start: 0.6203 (ptm) cc_final: 0.5224 (ptp) REVERT: B 155 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6867 (pp20) REVERT: C 29 TRP cc_start: 0.8366 (t-100) cc_final: 0.8071 (t-100) REVERT: C 34 GLN cc_start: 0.8630 (tp40) cc_final: 0.8083 (tp40) REVERT: C 55 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8424 (tt) outliers start: 35 outliers final: 29 residues processed: 210 average time/residue: 0.0716 time to fit residues: 21.6138 Evaluate side-chains 219 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 74 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 54 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.173742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.135435 restraints weight = 10639.847| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.40 r_work: 0.3708 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9184 Z= 0.151 Angle : 0.594 10.091 12634 Z= 0.302 Chirality : 0.041 0.304 1458 Planarity : 0.003 0.028 1481 Dihedral : 6.710 55.324 1582 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.94 % Allowed : 23.31 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.26), residues: 1017 helix: 0.33 (0.24), residues: 477 sheet: -1.31 (0.58), residues: 67 loop : -1.02 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 183 TYR 0.021 0.001 TYR A 787 PHE 0.014 0.001 PHE A 165 TRP 0.007 0.001 TRP A 617 HIS 0.009 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 9176) covalent geometry : angle 0.59221 / 0.30 (12628) hydrogen bonds : bond 0.03242 / 1.93 ( 423) hydrogen bonds : angle 4.55216 / 3.05 ( 1168) metal coordination : bond 0.01010 / 0.44 ( 8) metal coordination : angle 2.03848 / 0.89 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1952.20 seconds wall clock time: 34 minutes 8.36 seconds (2048.36 seconds total)