Starting phenix.real_space_refine on Fri Feb 16 00:48:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s7c_24883/02_2024/7s7c_24883.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s7c_24883/02_2024/7s7c_24883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s7c_24883/02_2024/7s7c_24883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s7c_24883/02_2024/7s7c_24883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s7c_24883/02_2024/7s7c_24883.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s7c_24883/02_2024/7s7c_24883.pdb" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 1.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 34 5.49 5 S 73 5.16 5 C 8696 2.51 5 N 2374 2.21 5 O 2672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13850 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7376 Classifications: {'peptide': 924} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 882} Chain breaks: 2 Chain: "B" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2666 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 22, 'TRANS': 307} Chain breaks: 4 Chain: "C" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 644 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 574 Inner-chain residues flagged as termini: ['pdbres=" A D 23 "'] Classifications: {'RNA': 27} Modifications used: {'5*END': 2, 'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 13, 'rna3p_pyr': 5} Link IDs: {'rna2p': 8, 'rna3p': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Classifications: {'RNA': 10} Modifications used: {'5*END': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1166 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 12, 'TRANS': 134} Chain breaks: 2 Chain: "F" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1211 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 7, 'TRANS': 141} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8616 SG CYS B 229 55.471 71.347 93.313 1.00150.17 S ATOM 8641 SG CYS B 232 58.103 69.641 91.184 1.00149.28 S ATOM 8719 SG CYS B 242 58.999 72.151 93.729 1.00145.26 S Time building chain proxies: 7.73, per 1000 atoms: 0.56 Number of scatterers: 13850 At special positions: 0 Unit cell: (129.8, 135.3, 154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 73 16.00 P 34 15.00 O 2672 8.00 N 2374 7.00 C 8696 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 - 3.50 Amino acid : False - 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: 6.42 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 900 " pdb="ZN ZN B 900 " - pdb=" NE2 HIS B 237 " pdb="ZN ZN B 900 " - pdb=" SG CYS B 242 " pdb="ZN ZN B 900 " - pdb=" SG CYS B 232 " pdb="ZN ZN B 900 " - pdb=" SG CYS B 229 " Number of angles added : 3 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3090 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 12 sheets defined 46.2% alpha, 11.0% beta 8 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'A' and resid 141 through 153 removed outlier: 3.550A pdb=" N ASN A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 166 removed outlier: 3.749A pdb=" N GLY A 166 " --> pdb=" O THR A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 166' Processing helix chain 'A' and resid 167 through 181 removed outlier: 3.975A pdb=" N ALA A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 Processing helix chain 'A' and resid 229 through 238 Processing helix chain 'A' and resid 240 through 245 removed outlier: 3.752A pdb=" N MET A 243 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A 245 " --> pdb=" O VAL A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.706A pdb=" N ARG A 258 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP A 259 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.856A pdb=" N PHE A 292 " --> pdb=" O ASN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 356 removed outlier: 3.540A pdb=" N PHE A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.778A pdb=" N MET A 406 " --> pdb=" O TYR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 429 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.550A pdb=" N ARG A 450 " --> pdb=" O PRO A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 474 Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.910A pdb=" N MET A 487 " --> pdb=" O THR A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 544 through 553 removed outlier: 4.347A pdb=" N GLN A 550 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 Processing helix chain 'A' and resid 580 through 587 removed outlier: 3.745A pdb=" N MET A 584 " --> pdb=" O ASN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 597 through 615 removed outlier: 3.659A pdb=" N ILE A 615 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 645 Processing helix chain 'A' and resid 646 through 651 removed outlier: 3.898A pdb=" N LEU A 651 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 Processing helix chain 'A' and resid 709 through 713 removed outlier: 3.896A pdb=" N GLU A 713 " --> pdb=" O SER A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 769 removed outlier: 3.710A pdb=" N ARG A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 807 removed outlier: 3.787A pdb=" N LYS A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 removed outlier: 3.740A pdb=" N ASP A 812 " --> pdb=" O PRO A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 842 removed outlier: 3.524A pdb=" N TYR A 819 " --> pdb=" O LEU A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'A' and resid 871 through 880 removed outlier: 4.123A pdb=" N GLU A 879 " --> pdb=" O ARG A 875 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 895 removed outlier: 3.539A pdb=" N LEU A 888 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 910 Processing helix chain 'A' and resid 928 through 948 removed outlier: 3.959A pdb=" N LEU A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 960 Processing helix chain 'A' and resid 966 through 974 Processing helix chain 'A' and resid 978 through 984 removed outlier: 3.908A pdb=" N ILE A 982 " --> pdb=" O THR A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1015 removed outlier: 3.606A pdb=" N ILE A 993 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1030 Processing helix chain 'A' and resid 1033 through 1037 Processing helix chain 'B' and resid 67 through 75 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 108 through 128 Processing helix chain 'B' and resid 156 through 166 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 277 through 281 removed outlier: 3.851A pdb=" N GLU B 280 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 removed outlier: 3.628A pdb=" N GLY B 300 " --> pdb=" O GLN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 317 removed outlier: 4.247A pdb=" N ARG B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 326 removed outlier: 4.225A pdb=" N GLU B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA B 326 " --> pdb=" O TRP B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.505A pdb=" N TYR B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 667 removed outlier: 3.680A pdb=" N PHE B 666 " --> pdb=" O ASP B 662 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 667 " --> pdb=" O MET B 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 662 through 667' Processing helix chain 'B' and resid 683 through 692 Processing helix chain 'B' and resid 695 through 702 Processing helix chain 'C' and resid 22 through 32 removed outlier: 4.030A pdb=" N GLN C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 Processing helix chain 'E' and resid 633 through 645 Processing helix chain 'E' and resid 646 through 651 Processing helix chain 'E' and resid 652 through 654 No H-bonds generated for 'chain 'E' and resid 652 through 654' Processing helix chain 'E' and resid 752 through 770 removed outlier: 3.626A pdb=" N ARG E 756 " --> pdb=" O PRO E 752 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 799 Processing helix chain 'F' and resid 57 through 72 Processing helix chain 'F' and resid 102 through 127 removed outlier: 5.742A pdb=" N GLN F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU F 111 " --> pdb=" O GLN F 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 103 removed outlier: 6.487A pdb=" N VAL A 249 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU A 282 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE A 251 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 186 " --> pdb=" O TRP A 248 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 185 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N MET A 227 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N PHE A 187 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 455 removed outlier: 6.669A pdb=" N GLY A 453 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 496 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N MET A 538 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE A 498 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU A 328 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 502 through 504 Processing sheet with id=AA4, first strand: chain 'A' and resid 667 through 673 removed outlier: 6.591A pdb=" N VAL A 662 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TRP A 671 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 660 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL A 673 " --> pdb=" O ARG A 658 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ARG A 658 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU A 659 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE A 739 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS A 661 " --> pdb=" O SER A 737 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 676 through 680 Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.615A pdb=" N PHE B 99 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL F 169 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.615A pdb=" N PHE B 99 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL F 169 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 40 removed outlier: 6.897A pdb=" N ASN C 56 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL C 39 " --> pdb=" O PHE C 54 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE C 54 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AB2, first strand: chain 'E' and resid 727 through 732 removed outlier: 3.562A pdb=" N LEU E 693 " --> pdb=" O LYS E 680 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN E 676 " --> pdb=" O GLU E 697 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU E 699 " --> pdb=" O VAL E 674 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL E 674 " --> pdb=" O LEU E 699 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP E 668 " --> pdb=" O ASN E 664 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASN E 664 " --> pdb=" O ASP E 668 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY E 670 " --> pdb=" O VAL E 662 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL E 662 " --> pdb=" O GLY E 670 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS E 663 " --> pdb=" O LEU E 736 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU E 736 " --> pdb=" O LYS E 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 78 through 79 removed outlier: 3.546A pdb=" N ARG F 79 " --> pdb=" O GLU F 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 544 hydrogen bonds defined for protein. 1557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 4.74 Time building geometry restraints manager: 6.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4229 1.33 - 1.45: 1916 1.45 - 1.57: 7867 1.57 - 1.69: 68 1.69 - 1.81: 118 Bond restraints: 14198 Sorted by residual: bond pdb=" C5 G D 8 " pdb=" C6 G D 8 " ideal model delta sigma weight residual 1.419 1.403 0.016 2.00e-02 2.50e+03 6.07e-01 bond pdb=" N7 G D 6 " pdb=" C5 G D 6 " ideal model delta sigma weight residual 1.388 1.374 0.014 2.00e-02 2.50e+03 4.83e-01 bond pdb=" C6 G D 8 " pdb=" O6 G D 8 " ideal model delta sigma weight residual 1.237 1.223 0.014 2.00e-02 2.50e+03 4.68e-01 bond pdb=" C ILE B 660 " pdb=" O ILE B 660 " ideal model delta sigma weight residual 1.247 1.239 0.008 1.23e-02 6.61e+03 4.51e-01 bond pdb=" C1' A D 23 " pdb=" N9 A D 23 " ideal model delta sigma weight residual 1.478 1.465 0.013 2.00e-02 2.50e+03 4.51e-01 ... (remaining 14193 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.41: 646 106.41 - 113.30: 7739 113.30 - 120.20: 5136 120.20 - 127.09: 5577 127.09 - 133.99: 232 Bond angle restraints: 19330 Sorted by residual: angle pdb=" C LYS F 160 " pdb=" N ASN F 161 " pdb=" CA ASN F 161 " ideal model delta sigma weight residual 121.54 126.73 -5.19 1.91e+00 2.74e-01 7.38e+00 angle pdb=" C3' A D 23 " pdb=" C2' A D 23 " pdb=" O2' A D 23 " ideal model delta sigma weight residual 109.80 114.71 -4.91 2.00e+00 2.50e-01 6.03e+00 angle pdb=" C3' U D 18 " pdb=" O3' U D 18 " pdb=" P U D 19 " ideal model delta sigma weight residual 120.20 123.16 -2.96 1.50e+00 4.44e-01 3.88e+00 angle pdb=" O3' A D 23 " pdb=" C3' A D 23 " pdb=" C2' A D 23 " ideal model delta sigma weight residual 113.80 109.98 3.82 2.00e+00 2.50e-01 3.65e+00 angle pdb=" O2' A D 23 " pdb=" C2' A D 23 " pdb=" C1' A D 23 " ideal model delta sigma weight residual 108.20 111.84 -3.64 2.00e+00 2.50e-01 3.32e+00 ... (remaining 19325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.70: 8528 31.70 - 63.41: 182 63.41 - 95.11: 34 95.11 - 126.81: 4 126.81 - 158.52: 1 Dihedral angle restraints: 8749 sinusoidal: 3996 harmonic: 4753 Sorted by residual: dihedral pdb=" C4' A D 23 " pdb=" C3' A D 23 " pdb=" C2' A D 23 " pdb=" C1' A D 23 " ideal model delta sinusoidal sigma weight residual 36.35 -35.91 72.26 1 3.10e+00 1.04e-01 6.95e+02 dihedral pdb=" O4' A D 23 " pdb=" C4' A D 23 " pdb=" C3' A D 23 " pdb=" C2' A D 23 " ideal model delta sinusoidal sigma weight residual -35.15 25.29 -60.43 1 4.00e+00 6.25e-02 3.04e+02 dihedral pdb=" O4' A D 23 " pdb=" C2' A D 23 " pdb=" C1' A D 23 " pdb=" C3' A D 23 " ideal model delta sinusoidal sigma weight residual -94.41 -35.07 -59.33 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 8746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1879 0.054 - 0.109: 242 0.109 - 0.163: 53 0.163 - 0.218: 0 0.218 - 0.272: 2 Chirality restraints: 2176 Sorted by residual: chirality pdb=" C2' A D 23 " pdb=" C3' A D 23 " pdb=" O2' A D 23 " pdb=" C1' A D 23 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' A D 23 " pdb=" C4' A D 23 " pdb=" O3' A D 23 " pdb=" C2' A D 23 " both_signs ideal model delta sigma weight residual False -2.50 -2.72 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE C 41 " pdb=" N ILE C 41 " pdb=" C ILE C 41 " pdb=" CB ILE C 41 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 2173 not shown) Planarity restraints: 2361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C D 9 " -0.006 2.00e-02 2.50e+03 1.01e-02 2.29e+00 pdb=" N1 C D 9 " 0.009 2.00e-02 2.50e+03 pdb=" C2 C D 9 " -0.022 2.00e-02 2.50e+03 pdb=" O2 C D 9 " 0.013 2.00e-02 2.50e+03 pdb=" N3 C D 9 " 0.005 2.00e-02 2.50e+03 pdb=" C4 C D 9 " -0.010 2.00e-02 2.50e+03 pdb=" N4 C D 9 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C D 9 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C D 9 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 655 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.16e+00 pdb=" N PRO A 656 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 656 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 656 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A D 26 " 0.020 2.00e-02 2.50e+03 8.44e-03 1.96e+00 pdb=" N9 A D 26 " -0.017 2.00e-02 2.50e+03 pdb=" C8 A D 26 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A D 26 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A D 26 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A D 26 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A D 26 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A D 26 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A D 26 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A D 26 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A D 26 " -0.004 2.00e-02 2.50e+03 ... (remaining 2358 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 186 2.60 - 3.17: 12485 3.17 - 3.75: 20322 3.75 - 4.32: 27806 4.32 - 4.90: 47166 Nonbonded interactions: 107965 Sorted by model distance: nonbonded pdb=" OG SER A 393 " pdb=" OG1 THR A 499 " model vdw 2.019 2.440 nonbonded pdb=" OG SER B 234 " pdb="ZN ZN B 900 " model vdw 2.066 2.230 nonbonded pdb=" OG SER B 695 " pdb=" OD1 ASN B 698 " model vdw 2.079 2.440 nonbonded pdb=" NZ LYS A 192 " pdb=" OD2 ASP A 215 " model vdw 2.110 2.520 nonbonded pdb=" NE2 GLN B 272 " pdb=" O ALA B 276 " model vdw 2.144 2.520 ... (remaining 107960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 1.620 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: 0.010 Extract box with map and model: 5.200 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 45.350 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 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 : 0.003 0.029 14198 Z= 0.200 Angle : 0.488 5.410 19330 Z= 0.251 Chirality : 0.040 0.272 2176 Planarity : 0.003 0.037 2361 Dihedral : 13.470 158.517 5659 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 1.10 % Allowed : 6.93 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.22), residues: 1599 helix: 1.39 (0.21), residues: 677 sheet: -0.07 (0.49), residues: 125 loop : -2.01 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 198 HIS 0.002 0.001 HIS B 237 PHE 0.011 0.001 PHE C 13 TYR 0.009 0.001 TYR A 612 ARG 0.003 0.000 ARG A1005 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 294 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8233 (pp) REVERT: A 202 MET cc_start: 0.6643 (mmt) cc_final: 0.6441 (mmt) REVERT: A 207 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7473 (mm-40) REVERT: A 648 LYS cc_start: 0.7189 (ptmt) cc_final: 0.6876 (ttpt) REVERT: A 679 LYS cc_start: 0.7521 (tttt) cc_final: 0.7288 (tttm) REVERT: A 767 GLN cc_start: 0.7096 (tt0) cc_final: 0.6198 (tm-30) REVERT: A 915 GLN cc_start: 0.7463 (mt0) cc_final: 0.7050 (mt0) REVERT: A 973 TRP cc_start: 0.7695 (t-100) cc_final: 0.7357 (t-100) REVERT: A 986 THR cc_start: 0.9196 (t) cc_final: 0.8878 (m) REVERT: B 97 ILE cc_start: 0.8412 (pt) cc_final: 0.8201 (mt) REVERT: B 271 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7362 (mp10) REVERT: B 671 THR cc_start: 0.8029 (m) cc_final: 0.7779 (p) REVERT: E 642 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7559 (tm-30) REVERT: F 152 LYS cc_start: 0.6845 (mmtp) cc_final: 0.6624 (mmtt) outliers start: 16 outliers final: 9 residues processed: 309 average time/residue: 0.2907 time to fit residues: 126.5662 Evaluate side-chains 202 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 271 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN B 191 ASN F 102 ASN F 177 ASN ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14198 Z= 0.335 Angle : 0.669 8.461 19330 Z= 0.336 Chirality : 0.047 0.564 2176 Planarity : 0.005 0.054 2361 Dihedral : 14.247 162.235 2306 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.01 % Favored : 91.93 % Rotamer: Outliers : 2.88 % Allowed : 12.08 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1599 helix: 1.13 (0.20), residues: 676 sheet: -0.18 (0.47), residues: 132 loop : -1.84 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 198 HIS 0.004 0.001 HIS E 734 PHE 0.026 0.002 PHE C 52 TYR 0.026 0.002 TYR E 649 ARG 0.004 0.001 ARG E 751 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 201 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8342 (pp) REVERT: A 202 MET cc_start: 0.6645 (mmt) cc_final: 0.6396 (mmt) REVERT: A 207 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7387 (mm-40) REVERT: A 212 MET cc_start: 0.7531 (mtp) cc_final: 0.7100 (ttm) REVERT: A 382 MET cc_start: 0.8083 (ttt) cc_final: 0.7848 (ttt) REVERT: A 468 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7648 (mt-10) REVERT: A 679 LYS cc_start: 0.7595 (tttt) cc_final: 0.7351 (tttm) REVERT: A 716 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7515 (ttpp) REVERT: A 767 GLN cc_start: 0.7202 (tt0) cc_final: 0.6209 (tm-30) REVERT: A 973 TRP cc_start: 0.7618 (t-100) cc_final: 0.7316 (t-100) REVERT: B 79 ARG cc_start: 0.7791 (ppt170) cc_final: 0.6675 (ppt170) REVERT: B 97 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8283 (mt) REVERT: B 126 GLN cc_start: 0.6366 (tm-30) cc_final: 0.5746 (tt0) REVERT: B 244 MET cc_start: 0.8395 (tpp) cc_final: 0.8185 (tmm) REVERT: B 313 MET cc_start: 0.6106 (tmm) cc_final: 0.5455 (tmm) REVERT: B 676 GLU cc_start: 0.7605 (tp30) cc_final: 0.6682 (pm20) REVERT: C 25 LEU cc_start: 0.8334 (mp) cc_final: 0.7721 (tp) REVERT: C 48 LYS cc_start: 0.7239 (mmmm) cc_final: 0.6879 (ttpt) REVERT: E 765 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7493 (tm-30) REVERT: E 767 GLN cc_start: 0.7379 (tp40) cc_final: 0.7088 (tp40) REVERT: F 87 ASP cc_start: 0.6626 (p0) cc_final: 0.6288 (p0) REVERT: F 152 LYS cc_start: 0.6869 (mmtp) cc_final: 0.6657 (mmtt) outliers start: 42 outliers final: 25 residues processed: 231 average time/residue: 0.2454 time to fit residues: 84.8086 Evaluate side-chains 214 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain F residue 176 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 147 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN B 271 GLN B 699 GLN C 16 ASN F 127 GLN F 177 ASN ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14198 Z= 0.202 Angle : 0.571 8.289 19330 Z= 0.287 Chirality : 0.043 0.214 2176 Planarity : 0.004 0.054 2361 Dihedral : 14.153 169.740 2302 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.02 % Allowed : 13.52 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.21), residues: 1599 helix: 1.33 (0.20), residues: 682 sheet: 0.07 (0.50), residues: 113 loop : -1.71 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 198 HIS 0.003 0.001 HIS A 255 PHE 0.017 0.001 PHE C 52 TYR 0.026 0.001 TYR E 649 ARG 0.003 0.000 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 199 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8382 (pp) REVERT: A 202 MET cc_start: 0.6585 (mmt) cc_final: 0.6283 (mmt) REVERT: A 207 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7337 (mm-40) REVERT: A 212 MET cc_start: 0.7453 (mtp) cc_final: 0.6849 (mtm) REVERT: A 335 ASN cc_start: 0.6545 (m110) cc_final: 0.6331 (t0) REVERT: A 382 MET cc_start: 0.8081 (ttt) cc_final: 0.7841 (ttt) REVERT: A 408 LYS cc_start: 0.8522 (ttmt) cc_final: 0.8173 (ttmt) REVERT: A 468 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7525 (mt-10) REVERT: A 679 LYS cc_start: 0.7575 (tttt) cc_final: 0.7315 (tttm) REVERT: A 693 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5424 (mm) REVERT: A 767 GLN cc_start: 0.7204 (tt0) cc_final: 0.6148 (tm-30) REVERT: A 973 TRP cc_start: 0.7541 (t-100) cc_final: 0.7271 (t-100) REVERT: B 79 ARG cc_start: 0.7812 (ppt170) cc_final: 0.6823 (ppt170) REVERT: B 97 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8185 (mt) REVERT: B 118 ASN cc_start: 0.8152 (t0) cc_final: 0.7821 (m110) REVERT: B 126 GLN cc_start: 0.6223 (tm-30) cc_final: 0.5705 (tt0) REVERT: B 313 MET cc_start: 0.6060 (tmm) cc_final: 0.5417 (tmm) REVERT: B 676 GLU cc_start: 0.7585 (tp30) cc_final: 0.6707 (mp0) REVERT: C 25 LEU cc_start: 0.8377 (mp) cc_final: 0.7789 (tp) REVERT: C 56 ASN cc_start: 0.7650 (m-40) cc_final: 0.7361 (p0) REVERT: C 65 TYR cc_start: 0.6924 (t80) cc_final: 0.6671 (t80) REVERT: C 82 ILE cc_start: 0.8322 (mm) cc_final: 0.8072 (mm) REVERT: E 765 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7465 (tm-30) REVERT: E 788 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7241 (mm-40) outliers start: 44 outliers final: 30 residues processed: 226 average time/residue: 0.2562 time to fit residues: 85.5537 Evaluate side-chains 207 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 780 ILE Chi-restraints excluded: chain F residue 139 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 272 GLN B 700 GLN C 59 HIS ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14198 Z= 0.393 Angle : 0.665 7.282 19330 Z= 0.335 Chirality : 0.046 0.191 2176 Planarity : 0.005 0.057 2361 Dihedral : 14.311 172.202 2300 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.01 % Favored : 91.87 % Rotamer: Outliers : 4.12 % Allowed : 15.51 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.21), residues: 1599 helix: 0.98 (0.20), residues: 676 sheet: -0.21 (0.49), residues: 123 loop : -1.81 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 198 HIS 0.005 0.001 HIS C 59 PHE 0.016 0.002 PHE C 13 TYR 0.024 0.002 TYR E 649 ARG 0.004 0.001 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 180 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8311 (pp) REVERT: A 202 MET cc_start: 0.6611 (mmt) cc_final: 0.6333 (mmt) REVERT: A 207 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7378 (mm-40) REVERT: A 212 MET cc_start: 0.7582 (mtp) cc_final: 0.7146 (ttm) REVERT: A 254 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7542 (pp) REVERT: A 382 MET cc_start: 0.8279 (ttt) cc_final: 0.8045 (ttt) REVERT: A 408 LYS cc_start: 0.8555 (ttmt) cc_final: 0.8200 (ttmm) REVERT: A 468 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7627 (mt-10) REVERT: A 679 LYS cc_start: 0.7671 (tttt) cc_final: 0.7417 (tttm) REVERT: A 693 LEU cc_start: 0.5604 (OUTLIER) cc_final: 0.5312 (mm) REVERT: A 716 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7337 (ttpt) REVERT: A 767 GLN cc_start: 0.7214 (tt0) cc_final: 0.6161 (tm-30) REVERT: A 873 LYS cc_start: 0.7739 (mtpp) cc_final: 0.7480 (tttt) REVERT: A 973 TRP cc_start: 0.7659 (t-100) cc_final: 0.7339 (t-100) REVERT: A 986 THR cc_start: 0.9253 (t) cc_final: 0.8965 (m) REVERT: B 97 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8266 (mt) REVERT: B 126 GLN cc_start: 0.6123 (tm-30) cc_final: 0.5446 (tt0) REVERT: B 313 MET cc_start: 0.6269 (tmm) cc_final: 0.5875 (tmm) REVERT: B 676 GLU cc_start: 0.7520 (tp30) cc_final: 0.6683 (pm20) REVERT: C 25 LEU cc_start: 0.8310 (mp) cc_final: 0.7784 (tp) REVERT: E 788 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7376 (mm-40) outliers start: 60 outliers final: 44 residues processed: 223 average time/residue: 0.2523 time to fit residues: 83.5177 Evaluate side-chains 219 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 169 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 700 GLN Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 757 GLN Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 780 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 176 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS B 275 HIS B 700 GLN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14198 Z= 0.305 Angle : 0.616 7.713 19330 Z= 0.310 Chirality : 0.044 0.210 2176 Planarity : 0.005 0.060 2361 Dihedral : 14.307 174.686 2300 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.46 % Allowed : 15.99 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.21), residues: 1599 helix: 1.05 (0.20), residues: 682 sheet: -0.20 (0.49), residues: 126 loop : -1.78 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 198 HIS 0.004 0.001 HIS E 734 PHE 0.015 0.002 PHE C 52 TYR 0.024 0.001 TYR E 649 ARG 0.003 0.000 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 176 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8324 (pp) REVERT: A 202 MET cc_start: 0.6595 (mmt) cc_final: 0.6324 (mmt) REVERT: A 207 GLN cc_start: 0.7808 (mp10) cc_final: 0.7327 (mm-40) REVERT: A 212 MET cc_start: 0.7534 (mtp) cc_final: 0.7119 (ttm) REVERT: A 254 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7530 (pp) REVERT: A 306 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.7965 (m) REVERT: A 382 MET cc_start: 0.8330 (ttt) cc_final: 0.8106 (ttt) REVERT: A 408 LYS cc_start: 0.8472 (ttmt) cc_final: 0.8063 (ttmm) REVERT: A 468 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7633 (mt-10) REVERT: A 679 LYS cc_start: 0.7664 (tttt) cc_final: 0.7167 (tttm) REVERT: A 693 LEU cc_start: 0.5648 (OUTLIER) cc_final: 0.5286 (mm) REVERT: A 767 GLN cc_start: 0.7166 (tt0) cc_final: 0.6135 (tm-30) REVERT: A 973 TRP cc_start: 0.7611 (t-100) cc_final: 0.7302 (t-100) REVERT: A 986 THR cc_start: 0.9267 (t) cc_final: 0.8967 (m) REVERT: B 79 ARG cc_start: 0.7840 (ppt170) cc_final: 0.6745 (ppt170) REVERT: B 126 GLN cc_start: 0.6094 (tm-30) cc_final: 0.5524 (tt0) REVERT: B 313 MET cc_start: 0.6202 (tmm) cc_final: 0.5804 (tmm) REVERT: B 676 GLU cc_start: 0.7503 (tp30) cc_final: 0.6682 (pm20) REVERT: C 25 LEU cc_start: 0.8321 (mp) cc_final: 0.7794 (tp) REVERT: E 788 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7284 (mm-40) REVERT: F 216 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.5288 (tt0) outliers start: 65 outliers final: 51 residues processed: 226 average time/residue: 0.2343 time to fit residues: 80.6229 Evaluate side-chains 221 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 165 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 700 GLN Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 780 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 216 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14198 Z= 0.217 Angle : 0.567 7.360 19330 Z= 0.285 Chirality : 0.042 0.212 2176 Planarity : 0.004 0.057 2361 Dihedral : 14.149 174.788 2297 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.98 % Allowed : 16.88 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.22), residues: 1599 helix: 1.30 (0.20), residues: 675 sheet: -0.15 (0.49), residues: 126 loop : -1.68 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 198 HIS 0.003 0.001 HIS E 734 PHE 0.015 0.001 PHE C 52 TYR 0.026 0.001 TYR E 649 ARG 0.003 0.000 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 174 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8336 (pp) REVERT: A 202 MET cc_start: 0.6615 (mmt) cc_final: 0.6336 (mmt) REVERT: A 207 GLN cc_start: 0.7789 (mp10) cc_final: 0.7336 (mm-40) REVERT: A 212 MET cc_start: 0.7519 (mtp) cc_final: 0.7118 (ttm) REVERT: A 254 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7624 (pp) REVERT: A 306 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.7817 (m) REVERT: A 382 MET cc_start: 0.8324 (ttt) cc_final: 0.8098 (ttt) REVERT: A 408 LYS cc_start: 0.8452 (ttmt) cc_final: 0.8058 (ttmm) REVERT: A 679 LYS cc_start: 0.7662 (tttt) cc_final: 0.7165 (tttm) REVERT: A 693 LEU cc_start: 0.5702 (OUTLIER) cc_final: 0.5348 (mm) REVERT: A 716 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7237 (ttpt) REVERT: A 767 GLN cc_start: 0.7161 (tt0) cc_final: 0.6140 (tm-30) REVERT: A 973 TRP cc_start: 0.7514 (t-100) cc_final: 0.7211 (t-100) REVERT: A 986 THR cc_start: 0.9299 (t) cc_final: 0.8985 (m) REVERT: B 79 ARG cc_start: 0.7747 (ppt170) cc_final: 0.6686 (ppt170) REVERT: B 97 ILE cc_start: 0.8523 (pt) cc_final: 0.8180 (mt) REVERT: B 118 ASN cc_start: 0.8174 (t0) cc_final: 0.7796 (m110) REVERT: B 126 GLN cc_start: 0.6069 (tm-30) cc_final: 0.5480 (tt0) REVERT: B 239 MET cc_start: 0.1637 (mtm) cc_final: 0.1401 (mtm) REVERT: B 313 MET cc_start: 0.6080 (tmm) cc_final: 0.5675 (tmm) REVERT: B 676 GLU cc_start: 0.7381 (tp30) cc_final: 0.6616 (pm20) REVERT: C 25 LEU cc_start: 0.8280 (mp) cc_final: 0.7764 (tp) REVERT: C 65 TYR cc_start: 0.6912 (t80) cc_final: 0.6633 (t80) REVERT: E 788 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7330 (mm-40) outliers start: 58 outliers final: 44 residues processed: 222 average time/residue: 0.2342 time to fit residues: 79.2814 Evaluate side-chains 215 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 166 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 700 GLN Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 731 VAL Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 780 ILE Chi-restraints excluded: chain F residue 176 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 98 optimal weight: 0.0050 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14198 Z= 0.232 Angle : 0.567 9.388 19330 Z= 0.284 Chirality : 0.042 0.209 2176 Planarity : 0.004 0.056 2361 Dihedral : 14.101 173.472 2297 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.60 % Allowed : 16.54 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1599 helix: 1.32 (0.20), residues: 675 sheet: -0.15 (0.48), residues: 126 loop : -1.67 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 198 HIS 0.003 0.001 HIS E 734 PHE 0.028 0.002 PHE C 52 TYR 0.026 0.001 TYR E 649 ARG 0.002 0.000 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 176 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8340 (pp) REVERT: A 202 MET cc_start: 0.6578 (mmt) cc_final: 0.6278 (mmt) REVERT: A 207 GLN cc_start: 0.7784 (mp10) cc_final: 0.7346 (mm-40) REVERT: A 212 MET cc_start: 0.7453 (mtp) cc_final: 0.7051 (ttm) REVERT: A 254 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7614 (pp) REVERT: A 306 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.8101 (p) REVERT: A 382 MET cc_start: 0.8337 (ttt) cc_final: 0.8112 (ttt) REVERT: A 408 LYS cc_start: 0.8458 (ttmt) cc_final: 0.8068 (ttmm) REVERT: A 468 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7575 (mt-10) REVERT: A 679 LYS cc_start: 0.7659 (tttt) cc_final: 0.7171 (tttm) REVERT: A 693 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.5344 (mm) REVERT: A 767 GLN cc_start: 0.7187 (tt0) cc_final: 0.6156 (tm-30) REVERT: A 973 TRP cc_start: 0.7510 (t-100) cc_final: 0.7191 (t-100) REVERT: A 986 THR cc_start: 0.9283 (t) cc_final: 0.8991 (m) REVERT: B 79 ARG cc_start: 0.7729 (ppt170) cc_final: 0.6627 (ppt170) REVERT: B 97 ILE cc_start: 0.8525 (pt) cc_final: 0.8234 (mt) REVERT: B 118 ASN cc_start: 0.8173 (t0) cc_final: 0.7811 (m110) REVERT: B 126 GLN cc_start: 0.6006 (tm-30) cc_final: 0.5398 (tt0) REVERT: B 313 MET cc_start: 0.5993 (tmm) cc_final: 0.5643 (tmm) REVERT: B 676 GLU cc_start: 0.7362 (tp30) cc_final: 0.6546 (pm20) REVERT: C 25 LEU cc_start: 0.8281 (mp) cc_final: 0.7773 (tp) REVERT: C 65 TYR cc_start: 0.6941 (t80) cc_final: 0.6654 (t80) REVERT: E 665 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5794 (pp20) REVERT: E 788 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7332 (mm-40) REVERT: F 216 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.5302 (tt0) outliers start: 67 outliers final: 51 residues processed: 232 average time/residue: 0.2582 time to fit residues: 92.2297 Evaluate side-chains 225 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 168 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 700 GLN Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 665 GLU Chi-restraints excluded: chain E residue 731 VAL Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 780 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 216 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 77 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 142 optimal weight: 0.3980 chunk 150 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN C 56 ASN C 59 HIS ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14198 Z= 0.182 Angle : 0.551 9.576 19330 Z= 0.275 Chirality : 0.041 0.206 2176 Planarity : 0.004 0.055 2361 Dihedral : 14.012 172.094 2297 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.91 % Allowed : 17.71 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.22), residues: 1599 helix: 1.45 (0.20), residues: 677 sheet: -0.28 (0.47), residues: 127 loop : -1.58 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 295 HIS 0.003 0.001 HIS E 734 PHE 0.019 0.001 PHE C 52 TYR 0.026 0.001 TYR E 649 ARG 0.002 0.000 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 176 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8322 (pp) REVERT: A 202 MET cc_start: 0.6602 (mmt) cc_final: 0.6328 (mmt) REVERT: A 207 GLN cc_start: 0.7768 (mp10) cc_final: 0.7287 (mm-40) REVERT: A 212 MET cc_start: 0.7415 (mtp) cc_final: 0.7186 (mtp) REVERT: A 254 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7571 (pp) REVERT: A 306 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8158 (p) REVERT: A 382 MET cc_start: 0.8338 (ttt) cc_final: 0.8121 (ttt) REVERT: A 408 LYS cc_start: 0.8450 (ttmt) cc_final: 0.8058 (ttmm) REVERT: A 468 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7579 (mt-10) REVERT: A 679 LYS cc_start: 0.7648 (tttt) cc_final: 0.7179 (tttm) REVERT: A 693 LEU cc_start: 0.5684 (OUTLIER) cc_final: 0.5344 (mm) REVERT: A 767 GLN cc_start: 0.7121 (tt0) cc_final: 0.6121 (tm-30) REVERT: A 973 TRP cc_start: 0.7466 (t-100) cc_final: 0.7156 (t-100) REVERT: A 986 THR cc_start: 0.9289 (t) cc_final: 0.8981 (m) REVERT: B 79 ARG cc_start: 0.7600 (ppt170) cc_final: 0.6594 (ppt170) REVERT: B 97 ILE cc_start: 0.8503 (pt) cc_final: 0.8216 (mt) REVERT: B 118 ASN cc_start: 0.8131 (t0) cc_final: 0.7808 (m110) REVERT: B 126 GLN cc_start: 0.6050 (tm-30) cc_final: 0.5527 (tt0) REVERT: B 188 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5846 (tm) REVERT: B 313 MET cc_start: 0.6055 (tmm) cc_final: 0.5782 (tmm) REVERT: B 676 GLU cc_start: 0.7325 (tp30) cc_final: 0.6557 (pm20) REVERT: C 25 LEU cc_start: 0.8283 (mp) cc_final: 0.7780 (tp) REVERT: C 56 ASN cc_start: 0.7814 (m-40) cc_final: 0.7315 (p0) REVERT: C 65 TYR cc_start: 0.6804 (t80) cc_final: 0.6531 (t80) REVERT: E 665 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5820 (pp20) REVERT: E 788 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7329 (mm-40) REVERT: F 216 GLN cc_start: 0.6685 (OUTLIER) cc_final: 0.5528 (tt0) outliers start: 57 outliers final: 45 residues processed: 226 average time/residue: 0.2346 time to fit residues: 80.9331 Evaluate side-chains 215 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 163 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 700 GLN Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 665 GLU Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 780 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 216 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.6980 chunk 146 optimal weight: 0.5980 chunk 150 optimal weight: 0.0050 chunk 88 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14198 Z= 0.223 Angle : 0.571 9.792 19330 Z= 0.286 Chirality : 0.042 0.203 2176 Planarity : 0.004 0.054 2361 Dihedral : 13.994 170.535 2297 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.77 % Allowed : 17.84 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1599 helix: 1.41 (0.20), residues: 676 sheet: -0.29 (0.47), residues: 127 loop : -1.58 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 198 HIS 0.003 0.001 HIS E 734 PHE 0.018 0.002 PHE C 13 TYR 0.028 0.001 TYR E 649 ARG 0.003 0.000 ARG B 697 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 172 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8331 (pp) REVERT: A 202 MET cc_start: 0.6576 (mmt) cc_final: 0.6317 (mmt) REVERT: A 207 GLN cc_start: 0.7773 (mp10) cc_final: 0.7278 (mm-40) REVERT: A 212 MET cc_start: 0.7439 (mtp) cc_final: 0.7055 (ttm) REVERT: A 254 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7594 (pp) REVERT: A 306 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8219 (p) REVERT: A 382 MET cc_start: 0.8348 (ttt) cc_final: 0.8132 (ttt) REVERT: A 408 LYS cc_start: 0.8457 (ttmt) cc_final: 0.8062 (ttmm) REVERT: A 468 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 520 MET cc_start: 0.8243 (mmm) cc_final: 0.7603 (mmt) REVERT: A 679 LYS cc_start: 0.7655 (tttt) cc_final: 0.7179 (tttm) REVERT: A 693 LEU cc_start: 0.5684 (OUTLIER) cc_final: 0.5341 (mm) REVERT: A 767 GLN cc_start: 0.7127 (tt0) cc_final: 0.6113 (tm-30) REVERT: A 973 TRP cc_start: 0.7483 (t-100) cc_final: 0.7154 (t-100) REVERT: A 986 THR cc_start: 0.9301 (t) cc_final: 0.9018 (m) REVERT: B 79 ARG cc_start: 0.7595 (ppt170) cc_final: 0.6573 (ppt170) REVERT: B 97 ILE cc_start: 0.8528 (pt) cc_final: 0.8262 (mt) REVERT: B 118 ASN cc_start: 0.8126 (t0) cc_final: 0.7810 (m110) REVERT: B 126 GLN cc_start: 0.6046 (tm-30) cc_final: 0.5522 (tt0) REVERT: B 188 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5863 (tm) REVERT: B 313 MET cc_start: 0.6004 (tmm) cc_final: 0.5631 (tmm) REVERT: B 676 GLU cc_start: 0.7312 (tp30) cc_final: 0.6555 (pm20) REVERT: C 25 LEU cc_start: 0.8302 (mp) cc_final: 0.7821 (tp) REVERT: C 56 ASN cc_start: 0.7822 (m-40) cc_final: 0.7398 (p0) REVERT: C 65 TYR cc_start: 0.6932 (t80) cc_final: 0.6641 (t80) REVERT: E 665 GLU cc_start: 0.6227 (OUTLIER) cc_final: 0.5818 (pp20) REVERT: E 788 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7358 (mm-40) REVERT: F 216 GLN cc_start: 0.6697 (OUTLIER) cc_final: 0.5539 (tt0) outliers start: 55 outliers final: 44 residues processed: 221 average time/residue: 0.2639 time to fit residues: 88.8095 Evaluate side-chains 217 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 166 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 946 SER Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 665 GLU Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 780 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 216 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 107 optimal weight: 0.0970 chunk 162 optimal weight: 0.1980 chunk 149 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 0.0770 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 700 GLN C 59 HIS ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14198 Z= 0.143 Angle : 0.538 9.752 19330 Z= 0.268 Chirality : 0.041 0.196 2176 Planarity : 0.004 0.056 2361 Dihedral : 13.841 168.530 2297 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.61 % Allowed : 19.22 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.22), residues: 1599 helix: 1.66 (0.21), residues: 679 sheet: 0.11 (0.50), residues: 109 loop : -1.49 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 295 HIS 0.003 0.001 HIS F 109 PHE 0.019 0.001 PHE C 52 TYR 0.022 0.001 TYR E 649 ARG 0.004 0.000 ARG B 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 176 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8338 (pp) REVERT: A 202 MET cc_start: 0.6496 (mmt) cc_final: 0.6226 (mmt) REVERT: A 207 GLN cc_start: 0.7748 (mp10) cc_final: 0.7276 (mm-40) REVERT: A 212 MET cc_start: 0.7365 (mtp) cc_final: 0.7031 (ttm) REVERT: A 306 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8153 (p) REVERT: A 382 MET cc_start: 0.8346 (ttt) cc_final: 0.8136 (ttt) REVERT: A 408 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8062 (ttmm) REVERT: A 468 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7720 (mt-10) REVERT: A 679 LYS cc_start: 0.7653 (tttt) cc_final: 0.7214 (tttm) REVERT: A 693 LEU cc_start: 0.5693 (OUTLIER) cc_final: 0.5376 (mm) REVERT: A 767 GLN cc_start: 0.7073 (tt0) cc_final: 0.6137 (tm-30) REVERT: A 973 TRP cc_start: 0.7413 (t-100) cc_final: 0.7104 (t-100) REVERT: A 986 THR cc_start: 0.9298 (t) cc_final: 0.9001 (m) REVERT: B 79 ARG cc_start: 0.7519 (ppt170) cc_final: 0.6682 (ppt170) REVERT: B 97 ILE cc_start: 0.8601 (pt) cc_final: 0.8202 (mt) REVERT: B 118 ASN cc_start: 0.8032 (t0) cc_final: 0.7769 (m110) REVERT: B 126 GLN cc_start: 0.6017 (tm-30) cc_final: 0.5568 (tt0) REVERT: B 188 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.5677 (tm) REVERT: B 676 GLU cc_start: 0.7339 (tp30) cc_final: 0.6646 (mp0) REVERT: C 25 LEU cc_start: 0.8312 (mp) cc_final: 0.7869 (tp) REVERT: C 56 ASN cc_start: 0.7707 (m-40) cc_final: 0.7349 (p0) REVERT: C 65 TYR cc_start: 0.6622 (t80) cc_final: 0.6379 (t80) REVERT: E 665 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5803 (pp20) REVERT: E 788 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7358 (mm-40) REVERT: F 113 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6910 (mm-30) REVERT: F 216 GLN cc_start: 0.6645 (OUTLIER) cc_final: 0.5699 (tt0) outliers start: 38 outliers final: 26 residues processed: 207 average time/residue: 0.2370 time to fit residues: 73.9490 Evaluate side-chains 195 residues out of total 1457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 700 GLN Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 665 GLU Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 780 ILE Chi-restraints excluded: chain F residue 216 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 119 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 132 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 GLN C 59 HIS ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.158193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122226 restraints weight = 17829.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.121851 restraints weight = 15076.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.123691 restraints weight = 14447.541| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 14198 Z= 0.196 Angle : 0.804 59.200 19330 Z= 0.450 Chirality : 0.044 0.817 2176 Planarity : 0.004 0.053 2361 Dihedral : 13.840 168.531 2297 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.68 % Allowed : 18.81 % Favored : 78.52 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.22), residues: 1599 helix: 1.63 (0.21), residues: 679 sheet: 0.12 (0.50), residues: 109 loop : -1.48 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 295 HIS 0.003 0.001 HIS F 109 PHE 0.016 0.001 PHE C 84 TYR 0.023 0.001 TYR E 649 ARG 0.002 0.000 ARG F 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2954.03 seconds wall clock time: 54 minutes 34.57 seconds (3274.57 seconds total)