Starting phenix.real_space_refine on Fri Sep 11 11:54:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ctt_30469/09_2026/7ctt_30469.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ctt_30469/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ctt_30469/09_2026/7ctt_30469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ctt_30469/09_2026/7ctt_30469.map" model { file = "/net/cci-nas-00/data/ceres_data/7ctt_30469/09_2026/7ctt_30469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ctt_30469/09_2026/7ctt_30469.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ctt_30469/09_2026/7ctt_30469.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ctt_30469/09_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-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 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: 2.00, per 1000 atoms: 0.22 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: 0.86 Conformation dependent library (CDL) restraints added in 338.6 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: 1.75 Time building geometry restraints manager: 1.16 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: 12442 2.33 - 4.66: 163 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: 4834 17.31 - 34.62: 436 34.62 - 51.92: 112 51.92 - 69.23: 17 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=" O5' U T 19 " pdb=" C5' U T 19 " pdb=" C4' U T 19 " pdb=" C3' U T 19 " ideal model delta sinusoidal sigma weight residual 180.00 152.26 27.74 3 6.40e+00 2.44e-02 2.30e+01 ... (remaining 5400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1291 0.066 - 0.132: 128 0.132 - 0.198: 5 0.198 - 0.264: 33 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=" P U T 11 " pdb=" OP1 U T 11 " pdb=" OP2 U T 11 " pdb=" O5' U T 11 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" P A T 9 " pdb=" OP1 A T 9 " pdb=" OP2 A T 9 " pdb=" O5' A T 9 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (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: 1.870 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.720 Find NCS groups from input model: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.090 ------------------------------------------------------------------------------- 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= 0.337 Angle : 0.675 17.315 12634 Z= 0.315 Chirality : 0.053 0.330 1458 Planarity : 0.003 0.033 1481 Dihedral : 13.930 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 0.00673 / 0.33 ( 9176) covalent geometry : angle 0.63024 / 0.31 (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 : 0.338 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: 0.0885 time to fit residues: 27.7930 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 : 0.378 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.174076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.134677 restraints weight = 10753.322| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.51 r_work: 0.3707 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9184 Z= 0.132 Angle : 0.584 8.590 12634 Z= 0.285 Chirality : 0.043 0.246 1458 Planarity : 0.003 0.026 1481 Dihedral : 9.025 64.656 1591 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.04 % Allowed : 15.77 % Favored : 81.19 % 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: -1.64 (0.25), residues: 1017 helix: -0.40 (0.23), residues: 468 sheet: -2.19 (0.50), residues: 77 loop : -1.54 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 889 TYR 0.013 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 0.00296 / 0.13 ( 9176) covalent geometry : angle 0.58130 / 0.28 (12628) hydrogen bonds : bond 0.03255 / 1.96 ( 423) hydrogen bonds : angle 4.75762 / 3.21 ( 1168) metal coordination : bond 0.01001 / 0.50 ( 8) metal coordination : angle 2.48626 / 1.12 ( 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 233 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8056 (p) cc_final: 0.7702 (t) REVERT: A 180 GLU cc_start: 0.7970 (mm-30) cc_final: 0.5674 (tp30) REVERT: A 331 ARG cc_start: 0.7039 (mtp180) cc_final: 0.6835 (mtp85) REVERT: A 411 LYS cc_start: 0.7262 (mppt) cc_final: 0.6862 (mttm) REVERT: A 455 TYR cc_start: 0.7749 (m-80) cc_final: 0.7509 (m-80) REVERT: A 463 MET cc_start: 0.7806 (ttt) cc_final: 0.7502 (ttt) REVERT: A 666 MET cc_start: 0.8058 (ptp) cc_final: 0.7856 (ptp) REVERT: A 789 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7309 (tt0) REVERT: A 826 TYR cc_start: 0.7882 (m-10) cc_final: 0.7676 (m-80) REVERT: A 858 ARG cc_start: 0.7246 (ttt90) cc_final: 0.6847 (ttt-90) REVERT: A 889 ARG cc_start: 0.6599 (mmt90) cc_final: 0.5929 (mmm-85) REVERT: A 924 MET cc_start: 0.7727 (mmt) cc_final: 0.7414 (mmt) REVERT: A 928 HIS cc_start: 0.7022 (OUTLIER) cc_final: 0.6525 (t70) REVERT: C 31 GLN cc_start: 0.6896 (tp-100) cc_final: 0.6566 (tp-100) REVERT: C 34 GLN cc_start: 0.8688 (tp40) cc_final: 0.8267 (tp40) REVERT: C 55 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8294 (tt) outliers start: 27 outliers final: 14 residues processed: 219 average time/residue: 0.0825 time to fit residues: 25.8062 Evaluate side-chains 198 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 HIS ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 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 = 0.4200 r_free = 0.4200 target = 0.171194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132160 restraints weight = 10811.847| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.42 r_work: 0.3676 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9184 Z= 0.175 Angle : 0.599 6.446 12634 Z= 0.294 Chirality : 0.044 0.295 1458 Planarity : 0.003 0.026 1481 Dihedral : 8.649 63.327 1584 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.15 % Allowed : 18.02 % Favored : 78.83 % 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: -1.40 (0.25), residues: 1017 helix: -0.16 (0.23), residues: 473 sheet: -2.04 (0.51), residues: 77 loop : -1.48 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 750 TYR 0.020 0.002 TYR A 606 PHE 0.020 0.002 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 0.00406 / 0.18 ( 9176) covalent geometry : angle 0.59638 / 0.29 (12628) hydrogen bonds : bond 0.03416 / 2.04 ( 423) hydrogen bonds : angle 4.69627 / 3.16 ( 1168) metal coordination : bond 0.01141 / 0.51 ( 8) metal coordination : angle 2.49274 / 1.14 ( 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 219 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8172 (p) cc_final: 0.7764 (t) REVERT: A 131 LEU cc_start: 0.9083 (tp) cc_final: 0.8808 (tt) REVERT: A 180 GLU cc_start: 0.8027 (mm-30) cc_final: 0.5860 (tp30) REVERT: A 331 ARG cc_start: 0.7048 (mtp180) cc_final: 0.6816 (mtp85) REVERT: A 411 LYS cc_start: 0.7294 (mppt) cc_final: 0.6862 (mttm) REVERT: A 426 LYS cc_start: 0.8426 (mttp) cc_final: 0.7996 (mtpp) REVERT: A 483 TYR cc_start: 0.8628 (m-80) cc_final: 0.8335 (m-80) REVERT: A 545 LYS cc_start: 0.6853 (ptmt) cc_final: 0.6635 (pttt) REVERT: A 889 ARG cc_start: 0.6631 (mmt90) cc_final: 0.5955 (mmm-85) REVERT: A 924 MET cc_start: 0.7783 (mmt) cc_final: 0.7465 (mmt) REVERT: A 928 HIS cc_start: 0.6983 (OUTLIER) cc_final: 0.6542 (t70) REVERT: C 21 ARG cc_start: 0.7218 (mpt180) cc_final: 0.6981 (mmt180) REVERT: C 31 GLN cc_start: 0.6861 (tp-100) cc_final: 0.6576 (tp-100) REVERT: C 34 GLN cc_start: 0.8718 (tp40) cc_final: 0.8299 (tp40) REVERT: C 55 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8450 (tt) outliers start: 28 outliers final: 19 residues processed: 208 average time/residue: 0.0819 time to fit residues: 24.4964 Evaluate side-chains 205 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 315 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 THR 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 675 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 C residue 4 SER 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: 0.3980 chunk 99 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 51 optimal weight: 0.0470 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.178350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.141569 restraints weight = 10660.487| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.18 r_work: 0.3770 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1712 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= 0.120 Angle : 0.558 6.821 12634 Z= 0.273 Chirality : 0.043 0.221 1458 Planarity : 0.003 0.025 1481 Dihedral : 8.508 62.467 1584 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.27 % Allowed : 18.58 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.25), residues: 1017 helix: 0.17 (0.24), residues: 470 sheet: -1.84 (0.51), residues: 77 loop : -1.30 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 889 TYR 0.017 0.001 TYR A 217 PHE 0.015 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 0.00272 / 0.12 ( 9176) covalent geometry : angle 0.55561 / 0.27 (12628) hydrogen bonds : bond 0.03051 / 1.83 ( 423) hydrogen bonds : angle 4.53770 / 3.05 ( 1168) metal coordination : bond 0.00687 / 0.33 ( 8) metal coordination : angle 2.19467 / 0.97 ( 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 227 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8215 (p) cc_final: 0.7820 (t) REVERT: A 131 LEU cc_start: 0.9061 (tp) cc_final: 0.8794 (tt) REVERT: A 180 GLU cc_start: 0.8045 (mm-30) cc_final: 0.5907 (tp30) REVERT: A 411 LYS cc_start: 0.7303 (mppt) cc_final: 0.6855 (mttm) REVERT: A 426 LYS cc_start: 0.8407 (mttp) cc_final: 0.8173 (mtpp) REVERT: A 483 TYR cc_start: 0.8597 (m-80) cc_final: 0.8384 (m-80) REVERT: A 525 ASP cc_start: 0.8482 (t0) cc_final: 0.8204 (t0) REVERT: A 542 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.8011 (tpt) REVERT: A 562 ILE cc_start: 0.8617 (tp) cc_final: 0.8186 (tt) REVERT: A 624 ARG cc_start: 0.8266 (mmt180) cc_final: 0.7712 (mmt180) REVERT: A 889 ARG cc_start: 0.6637 (mmt90) cc_final: 0.5998 (mmm-85) REVERT: A 924 MET cc_start: 0.7982 (mmt) cc_final: 0.7775 (mmt) REVERT: C 21 ARG cc_start: 0.7293 (mpt180) cc_final: 0.7014 (mmt180) REVERT: C 31 GLN cc_start: 0.6856 (tp-100) cc_final: 0.6567 (tp-100) REVERT: C 34 GLN cc_start: 0.8813 (tp40) cc_final: 0.8451 (tp40) REVERT: C 55 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8509 (tt) outliers start: 29 outliers final: 19 residues processed: 215 average time/residue: 0.0865 time to fit residues: 26.8514 Evaluate side-chains 209 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 542 MET 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 833 ASP Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain B residue 103 LEU 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: 3.9990 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.170815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133441 restraints weight = 10877.059| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.30 r_work: 0.3669 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9184 Z= 0.207 Angle : 0.626 6.109 12634 Z= 0.309 Chirality : 0.046 0.296 1458 Planarity : 0.003 0.029 1481 Dihedral : 8.469 61.569 1582 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.05 % Allowed : 19.59 % Favored : 76.35 % 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: 0.11 (0.24), residues: 468 sheet: -2.00 (0.49), residues: 87 loop : -1.29 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.022 0.002 TYR A 788 PHE 0.018 0.002 PHE A 694 TRP 0.023 0.002 TRP C 29 HIS 0.007 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 ( 9176) covalent geometry : angle 0.62435 / 0.31 (12628) hydrogen bonds : bond 0.03512 / 2.10 ( 423) hydrogen bonds : angle 4.65926 / 3.15 ( 1168) metal coordination : bond 0.01456 / 0.61 ( 8) metal coordination : angle 2.29456 / 1.05 ( 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: 36 poor density : 190 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8280 (p) cc_final: 0.7860 (t) REVERT: A 131 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8873 (tt) REVERT: A 180 GLU cc_start: 0.8070 (mm-30) cc_final: 0.5814 (tp30) REVERT: A 411 LYS cc_start: 0.7362 (mppt) cc_final: 0.6945 (mttm) REVERT: A 426 LYS cc_start: 0.8417 (mttp) cc_final: 0.8011 (mtpp) REVERT: A 889 ARG cc_start: 0.6566 (mmt90) cc_final: 0.5970 (mmm-85) REVERT: A 924 MET cc_start: 0.7834 (mmt) cc_final: 0.7510 (mmt) REVERT: B 155 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.6910 (pp20) REVERT: C 34 GLN cc_start: 0.8796 (tp40) cc_final: 0.8449 (tp40) REVERT: C 55 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8522 (tt) outliers start: 36 outliers final: 26 residues processed: 212 average time/residue: 0.0805 time to fit residues: 24.7477 Evaluate side-chains 215 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 246 THR 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 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP 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 B residue 155 GLU 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: 0.7980 chunk 57 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 chunk 66 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 = 0.4217 r_free = 0.4217 target = 0.172536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.134229 restraints weight = 10798.708| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.40 r_work: 0.3699 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1910 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= 0.150 Angle : 0.594 6.654 12634 Z= 0.291 Chirality : 0.044 0.259 1458 Planarity : 0.003 0.028 1481 Dihedral : 8.444 61.313 1582 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.49 % Allowed : 21.06 % Favored : 75.45 % 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: -0.93 (0.25), residues: 1017 helix: 0.23 (0.24), residues: 468 sheet: -1.80 (0.53), residues: 77 loop : -1.22 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 733 TYR 0.018 0.002 TYR A 217 PHE 0.014 0.001 PHE A 165 TRP 0.038 0.002 TRP C 29 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 9176) covalent geometry : angle 0.59191 / 0.29 (12628) hydrogen bonds : bond 0.03213 / 1.91 ( 423) hydrogen bonds : angle 4.57938 / 3.08 ( 1168) metal coordination : bond 0.01091 / 0.47 ( 8) metal coordination : angle 2.19915 / 0.95 ( 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 219 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8255 (p) cc_final: 0.7843 (t) REVERT: A 131 LEU cc_start: 0.9089 (tp) cc_final: 0.8885 (tt) REVERT: A 180 GLU cc_start: 0.8038 (mm-30) cc_final: 0.5871 (tp30) REVERT: A 390 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8246 (m-30) REVERT: A 411 LYS cc_start: 0.7316 (mppt) cc_final: 0.6890 (mttm) REVERT: A 426 LYS cc_start: 0.8408 (mttp) cc_final: 0.7998 (mtpp) REVERT: A 515 TYR cc_start: 0.7398 (m-80) cc_final: 0.7090 (m-80) REVERT: A 525 ASP cc_start: 0.8650 (t0) cc_final: 0.8269 (t0) REVERT: A 542 MET cc_start: 0.8108 (tpt) cc_final: 0.7908 (tpp) REVERT: A 889 ARG cc_start: 0.6605 (mmt90) cc_final: 0.5941 (mmm-85) REVERT: A 924 MET cc_start: 0.7902 (mmt) cc_final: 0.7640 (mmt) REVERT: B 155 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6815 (pp20) REVERT: C 29 TRP cc_start: 0.8040 (t-100) cc_final: 0.7823 (t60) REVERT: C 34 GLN cc_start: 0.8710 (tp40) cc_final: 0.8391 (tp40) REVERT: C 55 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8459 (tt) outliers start: 31 outliers final: 24 residues processed: 205 average time/residue: 0.0864 time to fit residues: 25.7299 Evaluate side-chains 211 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 265 TYR 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 390 ASP 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 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 833 ASP 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 55 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.172466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.134046 restraints weight = 10942.321| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.41 r_work: 0.3689 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1974 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= 0.159 Angle : 0.601 10.678 12634 Z= 0.294 Chirality : 0.044 0.232 1458 Planarity : 0.003 0.027 1481 Dihedral : 8.390 60.897 1582 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.05 % Allowed : 20.83 % Favored : 75.11 % 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: -0.84 (0.26), residues: 1017 helix: 0.30 (0.24), residues: 468 sheet: -1.75 (0.53), residues: 77 loop : -1.16 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 733 TYR 0.016 0.001 TYR A 788 PHE 0.013 0.001 PHE A 694 TRP 0.020 0.002 TRP C 29 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 9176) covalent geometry : angle 0.59955 / 0.29 (12628) hydrogen bonds : bond 0.03266 / 1.95 ( 423) hydrogen bonds : angle 4.55535 / 3.06 ( 1168) metal coordination : bond 0.01172 / 0.49 ( 8) metal coordination : angle 2.10268 / 0.92 ( 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 228 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8290 (p) cc_final: 0.7872 (t) REVERT: A 131 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8893 (tt) REVERT: A 180 GLU cc_start: 0.8039 (mm-30) cc_final: 0.5905 (tp30) REVERT: A 411 LYS cc_start: 0.7324 (mppt) cc_final: 0.6888 (mttm) REVERT: A 426 LYS cc_start: 0.8405 (mttp) cc_final: 0.7991 (mtpp) REVERT: A 525 ASP cc_start: 0.8663 (t0) cc_final: 0.8283 (t0) REVERT: A 553 ARG cc_start: 0.8250 (ptm160) cc_final: 0.7983 (ptm160) REVERT: A 633 MET cc_start: 0.8315 (ttp) cc_final: 0.7345 (ttp) REVERT: A 889 ARG cc_start: 0.6596 (mmt90) cc_final: 0.5951 (mmm-85) REVERT: A 924 MET cc_start: 0.7926 (mmt) cc_final: 0.7672 (mmt) REVERT: B 155 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6821 (pp20) REVERT: C 34 GLN cc_start: 0.8716 (tp40) cc_final: 0.8407 (tp40) REVERT: C 55 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8406 (tt) REVERT: C 59 LEU cc_start: 0.7645 (tp) cc_final: 0.7397 (tp) outliers start: 36 outliers final: 29 residues processed: 215 average time/residue: 0.0831 time to fit residues: 25.9694 Evaluate side-chains 223 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 338 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 57 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4211 r_free = 0.4211 target = 0.172167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133600 restraints weight = 10846.303| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.41 r_work: 0.3685 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9184 Z= 0.169 Angle : 0.625 10.466 12634 Z= 0.306 Chirality : 0.045 0.221 1458 Planarity : 0.003 0.027 1481 Dihedral : 8.402 60.626 1582 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.50 % Allowed : 21.17 % Favored : 74.32 % 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: -0.87 (0.25), residues: 1017 helix: 0.23 (0.24), residues: 474 sheet: -1.70 (0.54), residues: 77 loop : -1.16 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 721 TYR 0.018 0.001 TYR A 217 PHE 0.015 0.002 PHE A 165 TRP 0.044 0.002 TRP C 29 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 9176) covalent geometry : angle 0.62373 / 0.31 (12628) hydrogen bonds : bond 0.03308 / 1.97 ( 423) hydrogen bonds : angle 4.55617 / 3.06 ( 1168) metal coordination : bond 0.01188 / 0.49 ( 8) metal coordination : angle 2.02805 / 0.87 ( 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 233 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8250 (p) cc_final: 0.7869 (t) REVERT: A 131 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8894 (tt) REVERT: A 180 GLU cc_start: 0.8060 (mm-30) cc_final: 0.5922 (tp30) REVERT: A 411 LYS cc_start: 0.7358 (mppt) cc_final: 0.6905 (mttm) REVERT: A 426 LYS cc_start: 0.8401 (mttp) cc_final: 0.7971 (mtpp) REVERT: A 463 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7236 (ttm) REVERT: A 525 ASP cc_start: 0.8684 (t0) cc_final: 0.8297 (t0) REVERT: A 545 LYS cc_start: 0.6233 (OUTLIER) cc_final: 0.6030 (pttt) REVERT: A 562 ILE cc_start: 0.8511 (tp) cc_final: 0.8241 (tt) REVERT: A 633 MET cc_start: 0.8294 (ttp) cc_final: 0.7452 (ttp) REVERT: A 811 GLU cc_start: 0.7309 (tt0) cc_final: 0.7053 (tt0) REVERT: A 889 ARG cc_start: 0.6575 (mmt90) cc_final: 0.5941 (mmm-85) REVERT: A 924 MET cc_start: 0.7897 (mmt) cc_final: 0.7607 (mmt) REVERT: B 155 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6835 (pp20) REVERT: C 34 GLN cc_start: 0.8696 (tp40) cc_final: 0.8395 (tp40) REVERT: C 55 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8400 (tt) outliers start: 40 outliers final: 31 residues processed: 218 average time/residue: 0.0814 time to fit residues: 25.8407 Evaluate side-chains 220 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 338 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 463 MET Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 545 LYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 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 = 0.4164 r_free = 0.4164 target = 0.168352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.130070 restraints weight = 10880.991| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.32 r_work: 0.3636 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 9184 Z= 0.263 Angle : 0.707 10.911 12634 Z= 0.348 Chirality : 0.049 0.302 1458 Planarity : 0.004 0.029 1481 Dihedral : 8.537 60.319 1582 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.50 % Allowed : 21.17 % Favored : 74.32 % 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: -1.17 (0.25), residues: 1017 helix: -0.00 (0.23), residues: 473 sheet: -1.47 (0.55), residues: 67 loop : -1.42 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 305 TYR 0.026 0.002 TYR A 788 PHE 0.017 0.002 PHE A 165 TRP 0.050 0.002 TRP C 29 HIS 0.007 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.26 ( 9176) covalent geometry : angle 0.70541 / 0.35 (12628) hydrogen bonds : bond 0.03831 / 2.26 ( 423) hydrogen bonds : angle 4.77912 / 3.21 ( 1168) metal coordination : bond 0.01820 / 0.73 ( 8) metal coordination : angle 2.29935 / 0.97 ( 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 232 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8401 (p) cc_final: 0.7974 (t) REVERT: A 180 GLU cc_start: 0.8189 (mm-30) cc_final: 0.5896 (tp30) REVERT: A 411 LYS cc_start: 0.7421 (mppt) cc_final: 0.7004 (mttm) REVERT: A 463 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7276 (tmm) REVERT: A 499 ASP cc_start: 0.8036 (t0) cc_final: 0.7622 (t0) REVERT: A 525 ASP cc_start: 0.8654 (t0) cc_final: 0.8314 (t0) REVERT: A 545 LYS cc_start: 0.6418 (ptpt) cc_final: 0.6141 (pttt) REVERT: A 551 LYS cc_start: 0.8283 (mmmt) cc_final: 0.7585 (ptmt) REVERT: A 626 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7982 (tpt) REVERT: A 633 MET cc_start: 0.8315 (ttp) cc_final: 0.7358 (ttp) REVERT: A 811 GLU cc_start: 0.7435 (tt0) cc_final: 0.7156 (tt0) REVERT: B 94 MET cc_start: 0.6205 (ptm) cc_final: 0.5531 (ptp) REVERT: B 143 ASP cc_start: 0.7686 (t70) cc_final: 0.7447 (t0) REVERT: B 155 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7128 (pp20) REVERT: C 34 GLN cc_start: 0.8705 (tp40) cc_final: 0.8389 (tp40) REVERT: C 55 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8464 (tt) outliers start: 40 outliers final: 30 residues processed: 213 average time/residue: 0.0842 time to fit residues: 25.9126 Evaluate side-chains 224 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 265 TYR 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 338 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 626 MET 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 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 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 6 VAL Chi-restraints excluded: chain C residue 54 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 22 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.171726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132866 restraints weight = 10819.035| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.42 r_work: 0.3678 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9184 Z= 0.170 Angle : 0.650 9.956 12634 Z= 0.318 Chirality : 0.046 0.301 1458 Planarity : 0.003 0.026 1481 Dihedral : 8.515 60.415 1582 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.05 % Allowed : 21.40 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.25), residues: 1017 helix: 0.15 (0.24), residues: 473 sheet: -1.68 (0.53), residues: 77 loop : -1.23 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 889 TYR 0.018 0.002 TYR A 217 PHE 0.015 0.002 PHE A 165 TRP 0.044 0.002 TRP C 29 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 0.64839 / 0.32 (12628) hydrogen bonds : bond 0.03435 / 2.04 ( 423) hydrogen bonds : angle 4.65121 / 3.12 ( 1168) metal coordination : bond 0.01242 / 0.51 ( 8) metal coordination : angle 2.05813 / 0.85 ( 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 227 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8363 (p) cc_final: 0.7937 (t) REVERT: A 180 GLU cc_start: 0.8088 (mm-30) cc_final: 0.5928 (tp30) REVERT: A 411 LYS cc_start: 0.7370 (mppt) cc_final: 0.7041 (mmtm) REVERT: A 426 LYS cc_start: 0.8397 (mttp) cc_final: 0.8164 (mtpp) REVERT: A 463 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7154 (tmm) REVERT: A 525 ASP cc_start: 0.8664 (t0) cc_final: 0.8296 (t0) REVERT: A 545 LYS cc_start: 0.6342 (ptpt) cc_final: 0.6058 (pttt) REVERT: A 551 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7479 (ptmt) REVERT: A 562 ILE cc_start: 0.8526 (tp) cc_final: 0.8261 (tt) REVERT: A 626 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7867 (tpt) REVERT: A 633 MET cc_start: 0.8270 (ttp) cc_final: 0.7428 (ttp) REVERT: A 717 ASP cc_start: 0.7457 (t0) cc_final: 0.6996 (m-30) REVERT: A 758 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7587 (tp) REVERT: A 889 ARG cc_start: 0.6536 (mmt90) cc_final: 0.5913 (mmm-85) REVERT: B 94 MET cc_start: 0.6246 (ptm) cc_final: 0.5314 (ptp) REVERT: B 143 ASP cc_start: 0.7591 (t70) cc_final: 0.7344 (t0) REVERT: B 155 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6919 (pp20) REVERT: C 34 GLN cc_start: 0.8685 (tp40) cc_final: 0.8380 (tp40) REVERT: C 55 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8351 (tt) outliers start: 36 outliers final: 28 residues processed: 212 average time/residue: 0.0850 time to fit residues: 26.1601 Evaluate side-chains 220 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 265 TYR 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 462 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 667 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 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 6 VAL 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: 1.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 76 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 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 = 0.4233 r_free = 0.4233 target = 0.174093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.135525 restraints weight = 10629.056| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.40 r_work: 0.3711 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9184 Z= 0.146 Angle : 0.630 10.112 12634 Z= 0.309 Chirality : 0.045 0.284 1458 Planarity : 0.003 0.024 1481 Dihedral : 8.414 60.169 1582 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.60 % Allowed : 22.18 % Favored : 74.21 % 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: -0.78 (0.26), residues: 1017 helix: 0.25 (0.24), residues: 480 sheet: -1.65 (0.54), residues: 77 loop : -1.07 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 889 TYR 0.018 0.001 TYR A 217 PHE 0.013 0.001 PHE A 165 TRP 0.043 0.002 TRP C 29 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 9176) covalent geometry : angle 0.62843 / 0.31 (12628) hydrogen bonds : bond 0.03284 / 1.95 ( 423) hydrogen bonds : angle 4.53267 / 3.04 ( 1168) metal coordination : bond 0.00955 / 0.41 ( 8) metal coordination : angle 1.99329 / 0.86 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2172.74 seconds wall clock time: 38 minutes 17.39 seconds (2297.39 seconds total)