Starting phenix.real_space_refine on Sat Sep 12 00:42:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uo7_26641/09_2026/7uo7_26641_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uo7_26641/09_2026/7uo7_26641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uo7_26641/09_2026/7uo7_26641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uo7_26641/09_2026/7uo7_26641.map" model { file = "/net/cci-nas-00/data/ceres_data/7uo7_26641/09_2026/7uo7_26641_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uo7_26641/09_2026/7uo7_26641_neut.cif" } resolution = 3.09 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= -0.001 sd= 0.032 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 69 5.49 5 Mg 1 5.21 5 S 82 5.16 5 C 7517 2.51 5 N 2071 2.21 5 O 2520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 12262 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7462 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Chain: "B" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1390 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 559 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "P" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 676 Classifications: {'RNA': 32} Modifications used: {'rna3p_pur': 14, 'rna3p_pyr': 17} Link IDs: {'rna3p': 31} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 722 Classifications: {'RNA': 34} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 16} Link IDs: {'rna2p': 1, 'rna3p': 32} Chain: "D" Number of atoms: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1419 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 53.440 29.475 112.645 1.00 48.49 S ATOM 2487 SG CYS A 306 51.427 26.240 112.674 1.00 49.42 S ATOM 2519 SG CYS A 310 51.496 29.227 114.986 1.00 46.57 S ATOM 3927 SG CYS A 487 55.042 32.825 92.691 1.00 55.11 S ATOM 5180 SG CYS A 645 54.189 29.318 92.380 1.00 57.31 S ATOM 5186 SG CYS A 646 56.390 31.133 95.014 1.00 53.98 S Time building chain proxies: 2.57, per 1000 atoms: 0.21 Number of scatterers: 12262 At special positions: 0 Unit cell: (91.46, 130.196, 165.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 82 16.00 P 69 15.00 Mg 1 11.99 O 2520 8.00 N 2071 7.00 C 7517 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 644.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 301 " pdb=" ZN A1004 " pdb="ZN ZN A1004 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 645 " Number of angles added : 6 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 11 sheets defined 54.3% alpha, 9.5% beta 30 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 Processing helix chain 'A' and resid 76 through 89 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 148 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 169 through 199 removed outlier: 4.062A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ARG A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 249 through 253 removed outlier: 4.148A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.617A pdb=" N ASN A 300 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.641A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 removed outlier: 3.568A pdb=" N ASP A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.084A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.644A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 518 removed outlier: 3.670A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 4.006A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 639 through 643 removed outlier: 3.951A pdb=" N THR A 643 " --> pdb=" O ARG A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 717 through 733 removed outlier: 3.617A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 753 removed outlier: 3.971A pdb=" N GLU A 744 " --> pdb=" O ASP A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 774 Processing helix chain 'A' and resid 778 through 790 removed outlier: 3.599A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 846 through 851 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 3.610A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 915 removed outlier: 3.715A pdb=" N SER A 913 " --> pdb=" O ASP A 910 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 9 through 29 removed outlier: 4.239A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 97 removed outlier: 3.669A pdb=" N LYS B 40 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.968A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 removed outlier: 3.700A pdb=" N TYR B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 2 through 20 removed outlier: 4.037A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.521A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 45 through 62 removed outlier: 3.943A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.583A pdb=" N ALA D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 82 Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.687A pdb=" N ALA D 86 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 142 Processing helix chain 'D' and resid 168 through 172 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 removed outlier: 3.837A pdb=" N GLN A 57 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 58 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 105 removed outlier: 4.038A pdb=" N PHE A 104 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 111 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 224 removed outlier: 7.773A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.256A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 672 through 674 removed outlier: 3.527A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 556 through 559 removed outlier: 3.669A pdb=" N GLN A 541 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A 542 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 755 through 758 removed outlier: 3.619A pdb=" N TRP A 800 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.592A pdb=" N GLN A 822 " --> pdb=" O ASP A 825 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.905A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1554 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3624 1.34 - 1.45: 2362 1.45 - 1.57: 6407 1.57 - 1.69: 132 1.69 - 1.81: 128 Bond restraints: 12653 Sorted by residual: bond pdb=" C TRP A 617 " pdb=" N ASP A 618 " ideal model delta sigma weight residual 1.331 1.571 -0.239 1.29e-02 6.01e+03 3.43e+02 bond pdb=" C ASP A 618 " pdb=" N TYR A 619 " ideal model delta sigma weight residual 1.328 1.582 -0.254 1.44e-02 4.82e+03 3.12e+02 bond pdb=" C4 ATP A1001 " pdb=" N9 ATP A1001 " ideal model delta sigma weight residual 1.374 1.232 0.142 1.00e-02 1.00e+04 2.03e+02 bond pdb=" C3' ATP A1001 " pdb=" C4' ATP A1001 " ideal model delta sigma weight residual 1.526 1.412 0.114 1.10e-02 8.26e+03 1.07e+02 bond pdb=" C5 ATP A1001 " pdb=" N7 ATP A1001 " ideal model delta sigma weight residual 1.387 1.301 0.086 1.00e-02 1.00e+04 7.35e+01 ... (remaining 12648 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 17437 3.82 - 7.64: 27 7.64 - 11.45: 13 11.45 - 15.27: 2 15.27 - 19.09: 2 Bond angle restraints: 17481 Sorted by residual: angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 124.89 14.98 1.00e+00 1.00e+00 2.24e+02 angle pdb=" C3' ATP A1001 " pdb=" C4' ATP A1001 " pdb=" C5' ATP A1001 " ideal model delta sigma weight residual 115.19 96.10 19.09 1.76e+00 3.23e-01 1.18e+02 angle pdb=" O TRP A 617 " pdb=" C TRP A 617 " pdb=" N ASP A 618 " ideal model delta sigma weight residual 123.46 133.34 -9.88 9.90e-01 1.02e+00 9.96e+01 angle pdb=" PA ATP A1001 " pdb=" O3A ATP A1001 " pdb=" PB ATP A1001 " ideal model delta sigma weight residual 136.83 128.28 8.55 1.00e+00 1.00e+00 7.31e+01 angle pdb=" CA TRP A 617 " pdb=" C TRP A 617 " pdb=" N ASP A 618 " ideal model delta sigma weight residual 115.38 104.51 10.87 1.40e+00 5.10e-01 6.03e+01 ... (remaining 17476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.21: 7380 31.21 - 62.41: 236 62.41 - 93.62: 63 93.62 - 124.83: 1 124.83 - 156.04: 2 Dihedral angle restraints: 7682 sinusoidal: 3607 harmonic: 4075 Sorted by residual: dihedral pdb=" CA HIS A 613 " pdb=" C HIS A 613 " pdb=" N LEU A 614 " pdb=" CA LEU A 614 " ideal model delta harmonic sigma weight residual -180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA PRO A 612 " pdb=" C PRO A 612 " pdb=" N HIS A 613 " pdb=" CA HIS A 613 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" C4' C T 19 " pdb=" C3' C T 19 " pdb=" O3' C T 19 " pdb=" P U T 20 " ideal model delta sinusoidal sigma weight residual -110.00 46.04 -156.04 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 7679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1857 0.082 - 0.164: 168 0.164 - 0.247: 1 0.247 - 0.329: 1 0.329 - 0.411: 1 Chirality restraints: 2028 Sorted by residual: chirality pdb=" C3' ATP A1001 " pdb=" C2' ATP A1001 " pdb=" C4' ATP A1001 " pdb=" O3' ATP A1001 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C2' ATP A1001 " pdb=" C1' ATP A1001 " pdb=" C3' ATP A1001 " pdb=" O2' ATP A1001 " both_signs ideal model delta sigma weight residual False -2.68 -2.43 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C3' C T 19 " pdb=" C4' C T 19 " pdb=" O3' C T 19 " pdb=" C2' C T 19 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 2025 not shown) Planarity restraints: 1989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 618 " -0.044 2.00e-02 2.50e+03 8.51e-02 7.24e+01 pdb=" C ASP A 618 " 0.147 2.00e-02 2.50e+03 pdb=" O ASP A 618 " -0.060 2.00e-02 2.50e+03 pdb=" N TYR A 619 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 177 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO B 178 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 42 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C LEU D 42 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU D 42 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN D 43 " 0.009 2.00e-02 2.50e+03 ... (remaining 1986 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 149 2.59 - 3.17: 11242 3.17 - 3.74: 20065 3.74 - 4.32: 28348 4.32 - 4.90: 45546 Nonbonded interactions: 105350 Sorted by model distance: nonbonded pdb=" OD2 ASP A 833 " pdb=" OG SER A 835 " model vdw 2.012 3.040 nonbonded pdb=" OG SER A 433 " pdb=" OE2 GLU A 436 " model vdw 2.027 3.040 nonbonded pdb=" OD2 ASP A 452 " pdb=" OG1 THR A 556 " model vdw 2.028 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG SER B 164 " model vdw 2.058 3.040 nonbonded pdb=" OG1 THR A 409 " pdb=" OE2 GLU C 23 " model vdw 2.077 3.040 ... (remaining 105345 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 6 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 25 or (resid 26 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 50 or (resid 51 and (name N or name CA or \ name C or name O or name CB )) or resid 52 through 191)) } 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: 4.800 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.310 Find NCS groups from input model: 0.090 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.005 0.254 12661 Z= 0.375 Angle : 0.742 29.649 17487 Z= 0.479 Chirality : 0.042 0.411 2028 Planarity : 0.004 0.085 1989 Dihedral : 15.461 156.036 5044 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.76 % Allowed : 6.94 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.61 (0.22), residues: 1363 helix: -0.32 (0.21), residues: 676 sheet: -2.06 (0.45), residues: 130 loop : -1.65 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 624 TYR 0.014 0.001 TYR A 788 PHE 0.013 0.001 PHE D 49 TRP 0.009 0.001 TRP A 916 HIS 0.006 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.37 (12653) covalent geometry : angle 0.67581 / 0.47 (17481) hydrogen bonds : bond 0.16248 / 10.94 ( 629) hydrogen bonds : angle 7.47502 / 5.28 ( 1700) metal coordination : bond 0.04823 / 3.94 ( 8) metal coordination : angle 16.56591 / 10.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 139 LYS cc_start: 0.8468 (tptt) cc_final: 0.8233 (mmtt) outliers start: 9 outliers final: 4 residues processed: 113 average time/residue: 0.1040 time to fit residues: 17.5838 Evaluate side-chains 80 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN A 459 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.069854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.050363 restraints weight = 47481.646| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.44 r_work: 0.3144 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12661 Z= 0.166 Angle : 0.612 8.538 17487 Z= 0.321 Chirality : 0.042 0.426 2028 Planarity : 0.004 0.052 1989 Dihedral : 15.793 160.573 2544 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 1.02 % Allowed : 9.23 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.53 (0.23), residues: 1363 helix: 0.75 (0.20), residues: 667 sheet: -2.10 (0.46), residues: 117 loop : -1.22 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 721 TYR 0.010 0.001 TYR A 788 PHE 0.022 0.002 PHE D 15 TRP 0.009 0.001 TRP B 182 HIS 0.008 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (12653) covalent geometry : angle 0.60870 / 0.32 (17481) hydrogen bonds : bond 0.04552 / 3.03 ( 629) hydrogen bonds : angle 4.82805 / 3.37 ( 1700) metal coordination : bond 0.01126 / 0.70 ( 8) metal coordination : angle 3.69816 / 2.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.7331 (ttm) cc_final: 0.6911 (ttm) REVERT: A 902 MET cc_start: 0.8990 (mtt) cc_final: 0.8605 (mpp) REVERT: B 70 MET cc_start: 0.8537 (tmm) cc_final: 0.8274 (tmm) REVERT: B 171 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6859 (mp0) REVERT: C 34 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8229 (tm-30) REVERT: D 67 MET cc_start: 0.8180 (tpp) cc_final: 0.7763 (tpt) REVERT: D 70 MET cc_start: 0.8747 (tmm) cc_final: 0.8526 (tmm) REVERT: D 155 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8443 (tp30) outliers start: 12 outliers final: 4 residues processed: 93 average time/residue: 0.1029 time to fit residues: 14.4766 Evaluate side-chains 81 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 128 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 25 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 122 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 459 ASN A 543 ASN A 909 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.069547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.050215 restraints weight = 47838.478| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.43 r_work: 0.3142 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12661 Z= 0.139 Angle : 0.537 8.504 17487 Z= 0.283 Chirality : 0.040 0.397 2028 Planarity : 0.003 0.043 1989 Dihedral : 15.744 161.495 2541 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 1.52 % Allowed : 9.91 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.23), residues: 1363 helix: 1.04 (0.21), residues: 677 sheet: -1.98 (0.46), residues: 116 loop : -1.13 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 190 TYR 0.012 0.001 TYR A 788 PHE 0.018 0.001 PHE C 49 TRP 0.008 0.001 TRP B 182 HIS 0.007 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (12653) covalent geometry : angle 0.53357 / 0.28 (17481) hydrogen bonds : bond 0.03817 / 2.56 ( 629) hydrogen bonds : angle 4.46509 / 3.11 ( 1700) metal coordination : bond 0.00576 / 0.39 ( 8) metal coordination : angle 3.17003 / 2.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 242 MET cc_start: 0.7156 (ttm) cc_final: 0.6803 (ttm) REVERT: A 909 ASN cc_start: 0.7615 (OUTLIER) cc_final: 0.7125 (p0) REVERT: B 70 MET cc_start: 0.8615 (tmm) cc_final: 0.8331 (tmm) REVERT: B 129 MET cc_start: 0.8706 (ttm) cc_final: 0.8336 (mtm) REVERT: B 174 MET cc_start: 0.8777 (tpt) cc_final: 0.8558 (tpt) REVERT: C 34 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8182 (tm-30) REVERT: D 67 MET cc_start: 0.8211 (tpp) cc_final: 0.7730 (tpt) REVERT: D 155 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8425 (tp30) REVERT: D 166 ILE cc_start: 0.8540 (mm) cc_final: 0.7660 (mm) outliers start: 18 outliers final: 4 residues processed: 98 average time/residue: 0.0907 time to fit residues: 13.6245 Evaluate side-chains 82 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 909 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 123 optimal weight: 0.0030 chunk 55 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 0.0020 chunk 125 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 ASN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.068804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.049450 restraints weight = 47942.583| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.45 r_work: 0.3127 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12661 Z= 0.160 Angle : 0.555 11.766 17487 Z= 0.287 Chirality : 0.041 0.407 2028 Planarity : 0.003 0.042 1989 Dihedral : 15.758 161.139 2541 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.23 % Rotamer: Outliers : 1.95 % Allowed : 10.58 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.16 (0.23), residues: 1363 helix: 1.03 (0.21), residues: 677 sheet: -1.82 (0.46), residues: 120 loop : -1.05 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 57 TYR 0.026 0.001 TYR D 135 PHE 0.013 0.001 PHE A 471 TRP 0.008 0.001 TRP B 182 HIS 0.007 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (12653) covalent geometry : angle 0.55310 / 0.29 (17481) hydrogen bonds : bond 0.03627 / 2.42 ( 629) hydrogen bonds : angle 4.33807 / 3.02 ( 1700) metal coordination : bond 0.00730 / 0.54 ( 8) metal coordination : angle 2.75853 / 1.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 242 MET cc_start: 0.7176 (ttm) cc_final: 0.6952 (ttm) REVERT: A 909 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7290 (p0) REVERT: B 70 MET cc_start: 0.8635 (tmm) cc_final: 0.8368 (tmm) REVERT: B 129 MET cc_start: 0.8731 (ttm) cc_final: 0.8216 (mtm) REVERT: C 34 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8185 (tm-30) REVERT: D 67 MET cc_start: 0.8216 (tpp) cc_final: 0.7723 (tpt) REVERT: D 135 TYR cc_start: 0.7155 (t80) cc_final: 0.6586 (t80) REVERT: D 155 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8429 (tp30) REVERT: D 158 GLN cc_start: 0.7237 (tp40) cc_final: 0.6698 (tm-30) outliers start: 23 outliers final: 10 residues processed: 99 average time/residue: 0.0921 time to fit residues: 14.5328 Evaluate side-chains 87 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 142 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 chunk 32 optimal weight: 0.8980 chunk 73 optimal weight: 0.0670 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 GLN ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.068563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.049308 restraints weight = 48075.136| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.43 r_work: 0.3125 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12661 Z= 0.163 Angle : 0.550 11.210 17487 Z= 0.283 Chirality : 0.041 0.408 2028 Planarity : 0.003 0.041 1989 Dihedral : 15.777 161.402 2541 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.30 % Rotamer: Outliers : 1.69 % Allowed : 11.94 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.23), residues: 1363 helix: 1.05 (0.21), residues: 674 sheet: -1.79 (0.45), residues: 121 loop : -1.00 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 57 TYR 0.011 0.001 TYR A 788 PHE 0.013 0.001 PHE A 471 TRP 0.008 0.001 TRP B 182 HIS 0.007 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (12653) covalent geometry : angle 0.54733 / 0.28 (17481) hydrogen bonds : bond 0.03512 / 2.35 ( 629) hydrogen bonds : angle 4.27337 / 2.98 ( 1700) metal coordination : bond 0.00762 / 0.56 ( 8) metal coordination : angle 2.79480 / 1.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 242 MET cc_start: 0.7341 (ttm) cc_final: 0.7126 (ttm) REVERT: A 909 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.7329 (p0) REVERT: B 70 MET cc_start: 0.8633 (tmm) cc_final: 0.8373 (tmm) REVERT: B 129 MET cc_start: 0.8737 (ttm) cc_final: 0.8257 (mtm) REVERT: B 171 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: C 34 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8159 (tm-30) REVERT: D 67 MET cc_start: 0.8221 (tpp) cc_final: 0.7689 (tpp) REVERT: D 135 TYR cc_start: 0.7183 (t80) cc_final: 0.6967 (t80) REVERT: D 155 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8376 (tp30) outliers start: 20 outliers final: 13 residues processed: 93 average time/residue: 0.0947 time to fit residues: 13.8862 Evaluate side-chains 89 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 142 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 91 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 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 = 0.3826 r_free = 0.3826 target = 0.068535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.049387 restraints weight = 47881.847| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.41 r_work: 0.3125 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12661 Z= 0.147 Angle : 0.535 9.260 17487 Z= 0.277 Chirality : 0.040 0.408 2028 Planarity : 0.003 0.042 1989 Dihedral : 15.791 161.476 2541 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.62 % Favored : 95.23 % Rotamer: Outliers : 2.03 % Allowed : 12.19 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.23), residues: 1363 helix: 1.09 (0.21), residues: 675 sheet: -1.95 (0.43), residues: 133 loop : -0.98 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 57 TYR 0.013 0.001 TYR A 903 PHE 0.012 0.001 PHE A 471 TRP 0.008 0.001 TRP A 916 HIS 0.007 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (12653) covalent geometry : angle 0.53253 / 0.28 (17481) hydrogen bonds : bond 0.03384 / 2.26 ( 629) hydrogen bonds : angle 4.19695 / 2.92 ( 1700) metal coordination : bond 0.00681 / 0.50 ( 8) metal coordination : angle 2.57723 / 1.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.9290 (mttt) cc_final: 0.9045 (mmtt) REVERT: A 909 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7367 (p0) REVERT: B 70 MET cc_start: 0.8648 (tmm) cc_final: 0.8379 (tmm) REVERT: B 129 MET cc_start: 0.8721 (ttm) cc_final: 0.8286 (mtm) REVERT: B 171 GLU cc_start: 0.7640 (mt-10) cc_final: 0.6981 (mp0) REVERT: C 19 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8601 (mt0) REVERT: C 34 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8147 (tm-30) REVERT: D 135 TYR cc_start: 0.7241 (t80) cc_final: 0.7004 (t80) REVERT: D 155 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8361 (tp30) outliers start: 24 outliers final: 15 residues processed: 99 average time/residue: 0.0937 time to fit residues: 14.6839 Evaluate side-chains 93 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.068282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.049192 restraints weight = 48001.171| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.43 r_work: 0.3117 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12661 Z= 0.160 Angle : 0.543 9.004 17487 Z= 0.281 Chirality : 0.040 0.407 2028 Planarity : 0.003 0.041 1989 Dihedral : 15.792 161.083 2541 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.55 % Favored : 95.30 % Rotamer: Outliers : 2.29 % Allowed : 13.04 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.10 (0.23), residues: 1363 helix: 1.06 (0.21), residues: 681 sheet: -1.92 (0.43), residues: 132 loop : -0.95 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 57 TYR 0.011 0.001 TYR A 788 PHE 0.013 0.001 PHE A 471 TRP 0.008 0.001 TRP D 154 HIS 0.007 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (12653) covalent geometry : angle 0.54098 / 0.28 (17481) hydrogen bonds : bond 0.03376 / 2.25 ( 629) hydrogen bonds : angle 4.17856 / 2.91 ( 1700) metal coordination : bond 0.00814 / 0.60 ( 8) metal coordination : angle 2.67167 / 1.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.438 Fit side-chains REVERT: A 103 LYS cc_start: 0.9292 (mttt) cc_final: 0.9066 (mmtt) REVERT: A 909 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7336 (p0) REVERT: B 70 MET cc_start: 0.8653 (tmm) cc_final: 0.8385 (tmm) REVERT: B 129 MET cc_start: 0.8707 (ttm) cc_final: 0.8298 (mtm) REVERT: B 171 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7186 (mp0) REVERT: C 19 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8605 (mt0) REVERT: C 34 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8160 (tm-30) REVERT: D 155 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8415 (tp30) outliers start: 27 outliers final: 17 residues processed: 102 average time/residue: 0.0970 time to fit residues: 15.4175 Evaluate side-chains 98 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 160 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 140 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 121 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** 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 = 0.3810 r_free = 0.3810 target = 0.067783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.048717 restraints weight = 48245.334| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.40 r_work: 0.3110 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12661 Z= 0.191 Angle : 0.574 10.541 17487 Z= 0.296 Chirality : 0.041 0.408 2028 Planarity : 0.003 0.041 1989 Dihedral : 15.805 160.514 2541 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.21 % Favored : 94.64 % Rotamer: Outliers : 2.29 % Allowed : 13.55 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.23), residues: 1363 helix: 1.05 (0.21), residues: 680 sheet: -2.07 (0.43), residues: 123 loop : -0.95 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 57 TYR 0.022 0.001 TYR D 135 PHE 0.013 0.001 PHE A 471 TRP 0.010 0.001 TRP D 154 HIS 0.007 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (12653) covalent geometry : angle 0.57176 / 0.30 (17481) hydrogen bonds : bond 0.03521 / 2.34 ( 629) hydrogen bonds : angle 4.20904 / 2.94 ( 1700) metal coordination : bond 0.01036 / 0.78 ( 8) metal coordination : angle 2.88430 / 1.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.9309 (mttt) cc_final: 0.9091 (mmtt) REVERT: A 909 ASN cc_start: 0.7590 (OUTLIER) cc_final: 0.7308 (p0) REVERT: B 129 MET cc_start: 0.8727 (ttm) cc_final: 0.8289 (mtm) REVERT: B 171 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7174 (mp0) REVERT: C 19 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8573 (mt0) REVERT: C 23 GLU cc_start: 0.8629 (tt0) cc_final: 0.8408 (tt0) REVERT: C 34 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8192 (tm-30) REVERT: D 67 MET cc_start: 0.8239 (tpp) cc_final: 0.8011 (tpp) REVERT: D 155 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8412 (tp30) outliers start: 27 outliers final: 20 residues processed: 101 average time/residue: 0.0909 time to fit residues: 14.5325 Evaluate side-chains 98 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 160 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 137 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.068207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.049161 restraints weight = 48142.532| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.42 r_work: 0.3124 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12661 Z= 0.152 Angle : 0.573 10.225 17487 Z= 0.293 Chirality : 0.040 0.409 2028 Planarity : 0.003 0.041 1989 Dihedral : 15.820 160.910 2541 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.48 % Favored : 95.38 % Rotamer: Outliers : 2.20 % Allowed : 13.89 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.02 (0.23), residues: 1363 helix: 1.07 (0.21), residues: 682 sheet: -2.03 (0.45), residues: 116 loop : -0.83 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 858 TYR 0.011 0.001 TYR A 921 PHE 0.019 0.001 PHE A 102 TRP 0.008 0.001 TRP A 916 HIS 0.007 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (12653) covalent geometry : angle 0.57088 / 0.29 (17481) hydrogen bonds : bond 0.03368 / 2.23 ( 629) hydrogen bonds : angle 4.17558 / 2.91 ( 1700) metal coordination : bond 0.00741 / 0.54 ( 8) metal coordination : angle 2.53278 / 1.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.9301 (mttt) cc_final: 0.9049 (mmtt) REVERT: A 909 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7359 (p0) REVERT: B 129 MET cc_start: 0.8680 (ttm) cc_final: 0.8246 (mtm) REVERT: B 171 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7183 (mp0) REVERT: C 19 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8572 (mt0) REVERT: C 23 GLU cc_start: 0.8654 (tt0) cc_final: 0.8402 (tt0) REVERT: C 34 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8180 (tm-30) REVERT: D 67 MET cc_start: 0.8249 (tpp) cc_final: 0.8014 (tpp) REVERT: D 155 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8428 (tp30) outliers start: 26 outliers final: 19 residues processed: 101 average time/residue: 0.0844 time to fit residues: 13.3902 Evaluate side-chains 98 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 160 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 4 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 123 optimal weight: 40.0000 chunk 1 optimal weight: 0.2980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 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 = 0.3773 r_free = 0.3773 target = 0.067311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.048112 restraints weight = 48635.250| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.48 r_work: 0.3063 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12661 Z= 0.151 Angle : 0.564 11.180 17487 Z= 0.289 Chirality : 0.040 0.405 2028 Planarity : 0.003 0.041 1989 Dihedral : 15.812 160.354 2541 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.62 % Favored : 95.23 % Rotamer: Outliers : 2.20 % Allowed : 13.55 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.07 (0.23), residues: 1363 helix: 1.16 (0.21), residues: 681 sheet: -1.97 (0.45), residues: 116 loop : -0.81 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 190 TYR 0.015 0.001 TYR D 138 PHE 0.014 0.001 PHE A 102 TRP 0.008 0.001 TRP A 916 HIS 0.007 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (12653) covalent geometry : angle 0.56190 / 0.29 (17481) hydrogen bonds : bond 0.03302 / 2.19 ( 629) hydrogen bonds : angle 4.13207 / 2.88 ( 1700) metal coordination : bond 0.00753 / 0.55 ( 8) metal coordination : angle 2.41496 / 1.54 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 484 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8028 (p0) REVERT: A 909 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.7298 (p0) REVERT: B 129 MET cc_start: 0.8667 (ttm) cc_final: 0.8241 (mtm) REVERT: B 171 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7166 (mp0) REVERT: C 19 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8586 (mt0) REVERT: C 34 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8202 (tm-30) REVERT: D 67 MET cc_start: 0.8253 (tpp) cc_final: 0.8013 (tpp) REVERT: D 155 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8380 (tp30) outliers start: 26 outliers final: 21 residues processed: 98 average time/residue: 0.0866 time to fit residues: 13.3835 Evaluate side-chains 98 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 903 TYR Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 3 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 140 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 123 optimal weight: 40.0000 chunk 125 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.067749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.048769 restraints weight = 48175.002| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.45 r_work: 0.3087 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12661 Z= 0.122 Angle : 0.545 11.008 17487 Z= 0.279 Chirality : 0.040 0.407 2028 Planarity : 0.003 0.042 1989 Dihedral : 15.805 160.730 2541 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.67 % Favored : 96.18 % Rotamer: Outliers : 1.69 % Allowed : 14.14 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.18 (0.23), residues: 1363 helix: 1.25 (0.21), residues: 681 sheet: -1.92 (0.45), residues: 116 loop : -0.76 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 190 TYR 0.011 0.001 TYR A 515 PHE 0.016 0.001 PHE A 102 TRP 0.009 0.001 TRP A 916 HIS 0.006 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (12653) covalent geometry : angle 0.54410 / 0.28 (17481) hydrogen bonds : bond 0.03135 / 2.09 ( 629) hydrogen bonds : angle 4.06164 / 2.83 ( 1700) metal coordination : bond 0.00547 / 0.39 ( 8) metal coordination : angle 2.09252 / 1.32 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3011.11 seconds wall clock time: 52 minutes 28.65 seconds (3148.65 seconds total)