Starting phenix.real_space_refine on Fri Mar 15 13:31:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/03_2024/6nmd_0447.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/03_2024/6nmd_0447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/03_2024/6nmd_0447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/03_2024/6nmd_0447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/03_2024/6nmd_0447.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/03_2024/6nmd_0447.pdb" } resolution = 3.49 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= 0.000 sd= 0.005 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 P 25 5.49 5 Mg 2 5.21 5 S 35 5.16 5 C 7451 2.51 5 N 1934 2.21 5 O 2332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A ARG 737": "NH1" <-> "NH2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A GLU 755": "OE1" <-> "OE2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A GLU 885": "OE1" <-> "OE2" Residue "A GLU 947": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 11": "NH1" <-> "NH2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11779 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1202, 9931 Classifications: {'peptide': 1202} Link IDs: {'PTRANS': 26, 'TRANS': 1175} Chain breaks: 3 Chain: "G" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 535 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna2p': 8, 'rna3p': 16} Chain: "B" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1305 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 6.46, per 1000 atoms: 0.55 Number of scatterers: 11779 At special positions: 0 Unit cell: (130.68, 109.08, 105.84, 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) S 35 16.00 P 25 15.00 Mg 2 11.99 O 2332 8.00 N 1934 7.00 C 7451 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: 4.57 Conformation dependent library (CDL) restraints added in 2.0 seconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 13 sheets defined 51.9% alpha, 4.9% beta 1 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 37 through 66 removed outlier: 5.043A pdb=" N TYR A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LYS A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 73 through 83 removed outlier: 4.073A pdb=" N LEU A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 111 removed outlier: 3.737A pdb=" N GLU A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 119 removed outlier: 4.474A pdb=" N PHE A 119 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.881A pdb=" N ILE A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 124 " --> pdb=" O LYS A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 124' Processing helix chain 'A' and resid 136 through 142 removed outlier: 4.147A pdb=" N LEU A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 148 through 154 removed outlier: 4.162A pdb=" N GLY A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.846A pdb=" N ARG A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 190 removed outlier: 3.927A pdb=" N SER A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 removed outlier: 4.169A pdb=" N ASP A 194 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA A 195 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 197 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.855A pdb=" N PHE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.719A pdb=" N LYS A 265 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 312 through 327 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 357 through 371 removed outlier: 4.143A pdb=" N ILE A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 Processing helix chain 'A' and resid 396 through 404 Processing helix chain 'A' and resid 409 through 433 removed outlier: 4.363A pdb=" N LYS A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 471 Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.623A pdb=" N ASP A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.702A pdb=" N ALA A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 560 through 563 removed outlier: 4.068A pdb=" N ALA A 563 " --> pdb=" O LYS A 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 563' Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 609 through 619 Processing helix chain 'A' and resid 628 through 646 removed outlier: 4.445A pdb=" N LYS A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 635 " --> pdb=" O ASP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 652 removed outlier: 3.940A pdb=" N ASN A 651 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 663 removed outlier: 3.882A pdb=" N TYR A 663 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 677 Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'A' and resid 718 through 727 Processing helix chain 'A' and resid 786 through 790 removed outlier: 3.799A pdb=" N PHE A 789 " --> pdb=" O ASP A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 823 removed outlier: 4.058A pdb=" N ARG A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 822 " --> pdb=" O VAL A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 886 removed outlier: 3.710A pdb=" N GLU A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 4.443A pdb=" N VAL A 908 " --> pdb=" O ILE A 904 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N HIS A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 952 Processing helix chain 'A' and resid 953 through 956 Processing helix chain 'A' and resid 1020 through 1030 removed outlier: 4.398A pdb=" N LYS A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1111 through 1116 Processing helix chain 'A' and resid 1120 through 1136 removed outlier: 4.182A pdb=" N TYR A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1129 " --> pdb=" O SER A1125 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU A1130 " --> pdb=" O SER A1126 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A1133 " --> pdb=" O ALA A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1169 removed outlier: 4.165A pdb=" N ALA A1169 " --> pdb=" O ARG A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1199 removed outlier: 3.774A pdb=" N ILE A1187 " --> pdb=" O GLY A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1225 Processing helix chain 'B' and resid 3 through 20 removed outlier: 3.508A pdb=" N GLU B 10 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 4.287A pdb=" N ALA B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.528A pdb=" N GLU B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 124 through 162 removed outlier: 4.589A pdb=" N GLU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 579 through 580 removed outlier: 3.853A pdb=" N TYR A 794 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 339 Processing sheet with id=AA3, first strand: chain 'A' and resid 521 through 522 removed outlier: 3.642A pdb=" N PHE A 521 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET A 746 " --> pdb=" O PHE A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 584 through 585 Processing sheet with id=AA5, first strand: chain 'A' and resid 737 through 738 removed outlier: 3.658A pdb=" N ARG A 737 " --> pdb=" O ALA A 801 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 758 through 759 removed outlier: 3.691A pdb=" N HIS A 759 " --> pdb=" O VAL A 783 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 783 " --> pdb=" O HIS A 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 764 through 765 Processing sheet with id=AA8, first strand: chain 'A' and resid 828 through 833 removed outlier: 3.594A pdb=" N VAL A 842 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU A 839 " --> pdb=" O SER A 855 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N SER A 855 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE A 841 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLN A 853 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 843 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 858 through 862 removed outlier: 4.332A pdb=" N ILE A 868 " --> pdb=" O ASN A 861 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 922 through 925 removed outlier: 6.708A pdb=" N ILE A 922 " --> pdb=" O PHE A 994 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE A 996 " --> pdb=" O ILE A 922 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU A 924 " --> pdb=" O ILE A 996 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1047 through 1048 removed outlier: 3.844A pdb=" N LEU A1047 " --> pdb=" O TRP A1063 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP A1063 " --> pdb=" O LEU A1047 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1072 through 1073 Processing sheet with id=AB4, first strand: chain 'A' and resid 1138 through 1140 455 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 4.37 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 3834 1.36 - 1.51: 4532 1.51 - 1.66: 3643 1.66 - 1.81: 19 1.81 - 1.96: 40 Bond restraints: 12068 Sorted by residual: bond pdb=" SD MET A 626 " pdb=" CE MET A 626 " ideal model delta sigma weight residual 1.791 1.963 -0.172 2.50e-02 1.60e+03 4.71e+01 bond pdb=" SD MET A 531 " pdb=" CE MET A 531 " ideal model delta sigma weight residual 1.791 1.963 -0.172 2.50e-02 1.60e+03 4.71e+01 bond pdb=" CG MET A 531 " pdb=" SD MET A 531 " ideal model delta sigma weight residual 1.803 1.964 -0.161 2.50e-02 1.60e+03 4.13e+01 bond pdb=" CG MET A 626 " pdb=" SD MET A 626 " ideal model delta sigma weight residual 1.803 1.963 -0.160 2.50e-02 1.60e+03 4.09e+01 bond pdb=" SD MET A 603 " pdb=" CE MET A 603 " ideal model delta sigma weight residual 1.791 1.950 -0.159 2.50e-02 1.60e+03 4.05e+01 ... (remaining 12063 not shown) Histogram of bond angle deviations from ideal: 96.30 - 103.89: 164 103.89 - 111.49: 4881 111.49 - 119.08: 5015 119.08 - 126.67: 6096 126.67 - 134.27: 180 Bond angle restraints: 16336 Sorted by residual: angle pdb=" N MET A 626 " pdb=" CA MET A 626 " pdb=" C MET A 626 " ideal model delta sigma weight residual 113.16 105.11 8.05 1.24e+00 6.50e-01 4.21e+01 angle pdb=" C PHE A 220 " pdb=" CA PHE A 220 " pdb=" CB PHE A 220 " ideal model delta sigma weight residual 109.29 119.28 -9.99 1.82e+00 3.02e-01 3.01e+01 angle pdb=" CA TRP B 100 " pdb=" C TRP B 100 " pdb=" O TRP B 100 " ideal model delta sigma weight residual 121.10 115.55 5.55 1.10e+00 8.26e-01 2.54e+01 angle pdb=" C GLU A 88 " pdb=" N LYS A 89 " pdb=" CA LYS A 89 " ideal model delta sigma weight residual 122.07 129.02 -6.95 1.43e+00 4.89e-01 2.36e+01 angle pdb=" C LYS A 265 " pdb=" N THR A 266 " pdb=" CA THR A 266 " ideal model delta sigma weight residual 121.54 130.70 -9.16 1.91e+00 2.74e-01 2.30e+01 ... (remaining 16331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 6974 32.09 - 64.19: 322 64.19 - 96.28: 23 96.28 - 128.37: 0 128.37 - 160.46: 1 Dihedral angle restraints: 7320 sinusoidal: 3287 harmonic: 4033 Sorted by residual: dihedral pdb=" O4' U G 16 " pdb=" C1' U G 16 " pdb=" N1 U G 16 " pdb=" C2 U G 16 " ideal model delta sinusoidal sigma weight residual 232.00 71.54 160.46 1 1.70e+01 3.46e-03 6.45e+01 dihedral pdb=" C ASP A 625 " pdb=" N ASP A 625 " pdb=" CA ASP A 625 " pdb=" CB ASP A 625 " ideal model delta harmonic sigma weight residual -122.60 -137.60 15.00 0 2.50e+00 1.60e-01 3.60e+01 dihedral pdb=" CA PHE A 863 " pdb=" C PHE A 863 " pdb=" N ASN A 864 " pdb=" CA ASN A 864 " ideal model delta harmonic sigma weight residual -180.00 -152.72 -27.28 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 7317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1514 0.098 - 0.196: 213 0.196 - 0.294: 15 0.294 - 0.392: 3 0.392 - 0.490: 2 Chirality restraints: 1747 Sorted by residual: chirality pdb=" CA ASP A 625 " pdb=" N ASP A 625 " pdb=" C ASP A 625 " pdb=" CB ASP A 625 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CB ILE A 798 " pdb=" CA ILE A 798 " pdb=" CG1 ILE A 798 " pdb=" CG2 ILE A 798 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CB ILE B 113 " pdb=" CA ILE B 113 " pdb=" CG1 ILE B 113 " pdb=" CG2 ILE B 113 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 1744 not shown) Planarity restraints: 1999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 932 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LYS A 932 " -0.065 2.00e-02 2.50e+03 pdb=" O LYS A 932 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN A 933 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 717 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.07e+00 pdb=" C PRO A 717 " -0.046 2.00e-02 2.50e+03 pdb=" O PRO A 717 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN A 718 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 128 " -0.044 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO A 129 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.037 5.00e-02 4.00e+02 ... (remaining 1996 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 218 2.59 - 3.17: 10101 3.17 - 3.75: 18647 3.75 - 4.32: 24597 4.32 - 4.90: 39086 Nonbonded interactions: 92649 Sorted by model distance: nonbonded pdb="MG MG G 101 " pdb=" O HOH G 201 " model vdw 2.014 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 203 " model vdw 2.031 2.170 nonbonded pdb=" OP2 A G 19 " pdb="MG MG A1301 " model vdw 2.033 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 204 " model vdw 2.035 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 205 " model vdw 2.045 2.170 ... (remaining 92644 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.660 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 35.760 Find NCS groups from input model: 0.300 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: 0.000 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4586 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 : 0.013 0.172 12068 Z= 0.842 Angle : 1.111 10.494 16336 Z= 0.648 Chirality : 0.071 0.490 1747 Planarity : 0.007 0.066 1999 Dihedral : 17.366 160.463 4720 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.70 % Favored : 88.86 % Rotamer: Outliers : 2.43 % Allowed : 13.30 % Favored : 84.27 % Cbeta Deviations : 0.38 % 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: -4.62 (0.17), residues: 1346 helix: -2.71 (0.14), residues: 634 sheet: -3.20 (0.44), residues: 112 loop : -3.38 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 100 HIS 0.007 0.002 HIS B 42 PHE 0.034 0.003 PHE A1161 TYR 0.029 0.003 TYR A 237 ARG 0.005 0.001 ARG A 508 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 322 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 THR cc_start: 0.5928 (p) cc_final: 0.5474 (m) REVERT: A 189 ILE cc_start: 0.5144 (mm) cc_final: 0.4892 (tp) REVERT: A 230 THR cc_start: 0.5349 (t) cc_final: 0.4344 (p) REVERT: A 278 LYS cc_start: 0.6765 (ttmt) cc_final: 0.6405 (ttmm) REVERT: A 412 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6395 (tp30) REVERT: A 419 ILE cc_start: 0.7046 (tp) cc_final: 0.6729 (pt) REVERT: A 456 MET cc_start: 0.8104 (mtp) cc_final: 0.7698 (mtp) REVERT: A 525 PHE cc_start: 0.5230 (m-10) cc_final: 0.4614 (m-80) REVERT: A 796 LEU cc_start: 0.4979 (tt) cc_final: 0.4708 (tt) REVERT: A 899 LEU cc_start: 0.6186 (tp) cc_final: 0.5780 (tt) REVERT: A 1060 ILE cc_start: 0.5195 (mm) cc_final: 0.4111 (tt) REVERT: A 1088 GLU cc_start: 0.1620 (tm-30) cc_final: 0.0468 (tp30) REVERT: A 1131 MET cc_start: 0.6605 (mmm) cc_final: 0.6281 (mmm) REVERT: A 1174 ILE cc_start: 0.0898 (OUTLIER) cc_final: 0.0071 (mt) REVERT: A 1211 ILE cc_start: 0.3251 (OUTLIER) cc_final: 0.2971 (mp) REVERT: B 3 LYS cc_start: 0.6807 (tppt) cc_final: 0.6137 (tptp) REVERT: B 87 TYR cc_start: 0.5847 (m-80) cc_final: 0.5488 (m-80) outliers start: 30 outliers final: 6 residues processed: 347 average time/residue: 0.3040 time to fit residues: 140.6714 Evaluate side-chains 184 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 176 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain B residue 100 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 79 optimal weight: 0.0070 chunk 124 optimal weight: 5.9990 overall best weight: 1.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN A 179 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 ASN ** A 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN A1139 ASN B 20 ASN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.6735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 12068 Z= 0.291 Angle : 0.811 13.070 16336 Z= 0.426 Chirality : 0.046 0.252 1747 Planarity : 0.005 0.048 1999 Dihedral : 12.383 150.357 1863 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.13 % Favored : 92.79 % Rotamer: Outliers : 3.81 % Allowed : 18.65 % Favored : 77.53 % 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: -3.05 (0.21), residues: 1346 helix: -1.10 (0.19), residues: 642 sheet: -3.28 (0.43), residues: 108 loop : -2.80 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1063 HIS 0.005 0.001 HIS A 502 PHE 0.044 0.003 PHE A 931 TYR 0.022 0.003 TYR A 956 ARG 0.008 0.001 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 261 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 PHE cc_start: 0.6175 (m-80) cc_final: 0.5843 (m-80) REVERT: A 120 LYS cc_start: 0.7663 (mmmt) cc_final: 0.7274 (ptpp) REVERT: A 159 GLU cc_start: 0.6752 (tm-30) cc_final: 0.6423 (tm-30) REVERT: A 187 MET cc_start: 0.2905 (ttt) cc_final: 0.2529 (tpp) REVERT: A 272 LYS cc_start: 0.6754 (mttp) cc_final: 0.6358 (ttmm) REVERT: A 448 LYS cc_start: 0.8754 (mmtm) cc_final: 0.7864 (tmtt) REVERT: A 494 TYR cc_start: 0.5952 (t80) cc_final: 0.5602 (t80) REVERT: A 645 ARG cc_start: 0.7597 (mtp180) cc_final: 0.7326 (mtm-85) REVERT: A 698 LYS cc_start: 0.7703 (mttt) cc_final: 0.7471 (mtpt) REVERT: A 831 ILE cc_start: 0.8313 (mt) cc_final: 0.8081 (mm) REVERT: A 992 PHE cc_start: 0.6622 (OUTLIER) cc_final: 0.5816 (m-10) REVERT: A 995 TYR cc_start: 0.7497 (m-80) cc_final: 0.7241 (m-10) REVERT: A 1124 TYR cc_start: 0.5787 (m-80) cc_final: 0.5403 (m-80) REVERT: A 1211 ILE cc_start: 0.3941 (OUTLIER) cc_final: 0.3723 (mp) REVERT: B 3 LYS cc_start: 0.7002 (tppt) cc_final: 0.6263 (tptp) REVERT: B 15 LYS cc_start: 0.8348 (tppt) cc_final: 0.8035 (tppt) REVERT: B 29 GLU cc_start: 0.4725 (OUTLIER) cc_final: 0.2993 (mt-10) REVERT: B 100 TRP cc_start: 0.6557 (OUTLIER) cc_final: 0.5804 (p90) REVERT: B 155 ARG cc_start: 0.6493 (mmm-85) cc_final: 0.5772 (ttm-80) outliers start: 47 outliers final: 15 residues processed: 295 average time/residue: 0.2595 time to fit residues: 107.4075 Evaluate side-chains 190 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 889 ASN Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 965 CYS Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 994 PHE Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 146 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 103 optimal weight: 0.3980 chunk 84 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 42 optimal weight: 0.0470 chunk 99 optimal weight: 5.9990 overall best weight: 2.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 1.0173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 12068 Z= 0.306 Angle : 0.743 15.836 16336 Z= 0.397 Chirality : 0.045 0.230 1747 Planarity : 0.005 0.053 1999 Dihedral : 12.274 163.421 1855 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 5.60 % Allowed : 20.03 % Favored : 74.37 % 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: -2.53 (0.22), residues: 1346 helix: -0.54 (0.20), residues: 646 sheet: -3.22 (0.43), residues: 111 loop : -2.66 (0.23), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 355 HIS 0.008 0.001 HIS B 31 PHE 0.034 0.002 PHE A 655 TYR 0.029 0.002 TYR A 510 ARG 0.006 0.001 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 223 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7982 (mmmt) cc_final: 0.7427 (ptpp) REVERT: A 159 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6789 (tm-30) REVERT: A 224 PHE cc_start: 0.7371 (m-80) cc_final: 0.6735 (m-80) REVERT: A 272 LYS cc_start: 0.7380 (mttp) cc_final: 0.6848 (mtpp) REVERT: A 359 ARG cc_start: 0.7581 (tmt-80) cc_final: 0.7255 (tpt90) REVERT: A 382 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7180 (mt-10) REVERT: A 423 ASP cc_start: 0.8505 (p0) cc_final: 0.8136 (p0) REVERT: A 448 LYS cc_start: 0.8756 (mmtm) cc_final: 0.8494 (mppt) REVERT: A 466 PHE cc_start: 0.8226 (t80) cc_final: 0.7842 (t80) REVERT: A 467 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7709 (tm-30) REVERT: A 471 LYS cc_start: 0.7842 (tppt) cc_final: 0.7440 (mtpp) REVERT: A 487 TYR cc_start: 0.5453 (m-10) cc_final: 0.5171 (m-10) REVERT: A 531 MET cc_start: 0.8519 (ttm) cc_final: 0.7684 (mtp) REVERT: A 562 TYR cc_start: 0.7674 (m-80) cc_final: 0.7306 (m-80) REVERT: A 626 MET cc_start: 0.4881 (mmp) cc_final: 0.4348 (ptm) REVERT: A 630 ASN cc_start: 0.5489 (OUTLIER) cc_final: 0.4308 (t0) REVERT: A 708 ASP cc_start: 0.8349 (t70) cc_final: 0.8050 (t0) REVERT: A 735 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6369 (mp-120) REVERT: A 836 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6879 (ttm-80) REVERT: A 852 GLU cc_start: 0.7818 (tt0) cc_final: 0.7448 (tt0) REVERT: A 867 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7789 (mtp85) REVERT: A 1064 LYS cc_start: 0.5748 (tppt) cc_final: 0.5401 (tptp) REVERT: A 1086 TRP cc_start: 0.6426 (t60) cc_final: 0.6050 (t60) REVERT: A 1135 LEU cc_start: 0.6305 (OUTLIER) cc_final: 0.6097 (mp) REVERT: A 1149 PHE cc_start: 0.5994 (p90) cc_final: 0.5530 (p90) REVERT: A 1197 GLN cc_start: 0.7691 (mm110) cc_final: 0.7157 (mt0) REVERT: B 15 LYS cc_start: 0.8283 (tppt) cc_final: 0.7999 (tppt) REVERT: B 29 GLU cc_start: 0.5846 (OUTLIER) cc_final: 0.5426 (pp20) REVERT: B 30 GLN cc_start: 0.5789 (OUTLIER) cc_final: 0.5537 (mp10) REVERT: B 51 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8026 (mm) REVERT: B 58 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6575 (m-80) REVERT: B 85 SER cc_start: 0.8629 (m) cc_final: 0.7851 (p) REVERT: B 94 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8211 (p0) REVERT: B 100 TRP cc_start: 0.7257 (OUTLIER) cc_final: 0.6203 (p90) REVERT: B 121 ASP cc_start: 0.6459 (t70) cc_final: 0.6177 (p0) REVERT: B 129 GLU cc_start: 0.7489 (pt0) cc_final: 0.7013 (mp0) REVERT: B 148 GLN cc_start: 0.7489 (mm110) cc_final: 0.7204 (mm-40) REVERT: B 155 ARG cc_start: 0.7165 (mmm-85) cc_final: 0.6771 (ttm-80) REVERT: B 160 GLU cc_start: 0.5932 (tt0) cc_final: 0.5164 (pt0) outliers start: 69 outliers final: 28 residues processed: 282 average time/residue: 0.2570 time to fit residues: 100.5540 Evaluate side-chains 220 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 181 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 965 CYS Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 0.1980 chunk 13 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN A 803 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 ASN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 1.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12068 Z= 0.231 Angle : 0.642 9.861 16336 Z= 0.340 Chirality : 0.043 0.227 1747 Planarity : 0.004 0.047 1999 Dihedral : 12.214 170.483 1853 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.11 % Allowed : 22.71 % Favored : 72.18 % 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: -2.16 (0.22), residues: 1346 helix: -0.13 (0.21), residues: 643 sheet: -3.00 (0.46), residues: 109 loop : -2.62 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 534 HIS 0.004 0.001 HIS A 502 PHE 0.023 0.002 PHE A 325 TYR 0.022 0.002 TYR B 165 ARG 0.005 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 223 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7972 (mmmt) cc_final: 0.7435 (ptpp) REVERT: A 159 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6788 (tm-30) REVERT: A 224 PHE cc_start: 0.7365 (m-80) cc_final: 0.6666 (m-80) REVERT: A 272 LYS cc_start: 0.7443 (mttp) cc_final: 0.6917 (mtpp) REVERT: A 350 ASP cc_start: 0.7814 (m-30) cc_final: 0.7439 (t0) REVERT: A 423 ASP cc_start: 0.8597 (p0) cc_final: 0.8238 (p0) REVERT: A 448 LYS cc_start: 0.8838 (mmtm) cc_final: 0.8460 (mppt) REVERT: A 466 PHE cc_start: 0.8423 (t80) cc_final: 0.7909 (t80) REVERT: A 467 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 471 LYS cc_start: 0.7992 (tppt) cc_final: 0.7489 (mtpp) REVERT: A 487 TYR cc_start: 0.6003 (m-10) cc_final: 0.5529 (m-10) REVERT: A 531 MET cc_start: 0.8438 (ttm) cc_final: 0.8118 (mtp) REVERT: A 539 GLU cc_start: 0.7222 (pm20) cc_final: 0.6598 (tt0) REVERT: A 562 TYR cc_start: 0.7525 (m-80) cc_final: 0.7297 (m-80) REVERT: A 630 ASN cc_start: 0.6050 (OUTLIER) cc_final: 0.5502 (t0) REVERT: A 654 ASP cc_start: 0.7877 (t0) cc_final: 0.7582 (t0) REVERT: A 708 ASP cc_start: 0.8410 (t70) cc_final: 0.8054 (t70) REVERT: A 836 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6978 (ttm-80) REVERT: A 852 GLU cc_start: 0.7603 (tt0) cc_final: 0.7127 (tt0) REVERT: A 867 ARG cc_start: 0.8174 (ptp-110) cc_final: 0.7713 (mtp85) REVERT: A 1137 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6980 (mtt) REVERT: A 1149 PHE cc_start: 0.6743 (p90) cc_final: 0.6312 (p90) REVERT: A 1167 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.6539 (t80) REVERT: B 15 LYS cc_start: 0.8216 (tppt) cc_final: 0.8010 (tppt) REVERT: B 16 LYS cc_start: 0.6417 (OUTLIER) cc_final: 0.5859 (mtpp) REVERT: B 58 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6197 (m-80) REVERT: B 85 SER cc_start: 0.8831 (m) cc_final: 0.7562 (p) REVERT: B 92 ILE cc_start: 0.8915 (mt) cc_final: 0.8701 (mm) REVERT: B 94 ASP cc_start: 0.8315 (p0) cc_final: 0.8047 (p0) REVERT: B 100 TRP cc_start: 0.7346 (OUTLIER) cc_final: 0.6136 (p90) REVERT: B 123 ASP cc_start: 0.7052 (m-30) cc_final: 0.6763 (p0) REVERT: B 128 TYR cc_start: 0.7616 (t80) cc_final: 0.7336 (t80) REVERT: B 129 GLU cc_start: 0.7764 (pt0) cc_final: 0.7144 (mp0) REVERT: B 148 GLN cc_start: 0.7717 (mm110) cc_final: 0.7369 (mm110) outliers start: 63 outliers final: 34 residues processed: 272 average time/residue: 0.2577 time to fit residues: 98.1883 Evaluate side-chains 224 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 183 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 965 CYS Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1210 LYS Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 152 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN A1223 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 1.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12068 Z= 0.182 Angle : 0.610 11.258 16336 Z= 0.319 Chirality : 0.041 0.189 1747 Planarity : 0.004 0.044 1999 Dihedral : 11.737 173.878 1849 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.06 % Allowed : 25.47 % Favored : 70.48 % 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: -1.80 (0.23), residues: 1346 helix: 0.16 (0.21), residues: 643 sheet: -2.61 (0.47), residues: 111 loop : -2.48 (0.23), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1193 HIS 0.003 0.001 HIS B 31 PHE 0.017 0.001 PHE A 325 TYR 0.022 0.001 TYR A 57 ARG 0.005 0.001 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 218 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8611 (mmm-85) cc_final: 0.7979 (ttt90) REVERT: A 120 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7614 (ptmm) REVERT: A 123 ILE cc_start: 0.7073 (mm) cc_final: 0.6696 (mm) REVERT: A 159 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6873 (tm-30) REVERT: A 224 PHE cc_start: 0.7418 (m-80) cc_final: 0.6899 (m-80) REVERT: A 325 PHE cc_start: 0.6184 (OUTLIER) cc_final: 0.5693 (t80) REVERT: A 350 ASP cc_start: 0.7839 (m-30) cc_final: 0.7485 (t0) REVERT: A 423 ASP cc_start: 0.8520 (p0) cc_final: 0.7847 (m-30) REVERT: A 448 LYS cc_start: 0.8859 (mmtm) cc_final: 0.8508 (mppt) REVERT: A 466 PHE cc_start: 0.8485 (t80) cc_final: 0.7969 (t80) REVERT: A 467 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7595 (tm-30) REVERT: A 471 LYS cc_start: 0.8020 (tppt) cc_final: 0.7522 (mtpp) REVERT: A 561 LYS cc_start: 0.8356 (ttpp) cc_final: 0.7893 (ttpp) REVERT: A 562 TYR cc_start: 0.7557 (m-80) cc_final: 0.7013 (m-80) REVERT: A 603 MET cc_start: 0.7666 (mtp) cc_final: 0.7167 (mtm) REVERT: A 621 PHE cc_start: 0.6229 (p90) cc_final: 0.5961 (p90) REVERT: A 626 MET cc_start: 0.5565 (mmp) cc_final: 0.5207 (mmt) REVERT: A 630 ASN cc_start: 0.6111 (OUTLIER) cc_final: 0.5874 (t0) REVERT: A 638 PHE cc_start: 0.6683 (t80) cc_final: 0.6340 (t80) REVERT: A 708 ASP cc_start: 0.8299 (t70) cc_final: 0.7958 (t70) REVERT: A 836 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6987 (ttm-80) REVERT: A 852 GLU cc_start: 0.7456 (tt0) cc_final: 0.7021 (tt0) REVERT: A 949 MET cc_start: 0.7738 (tpp) cc_final: 0.7365 (mmt) REVERT: A 1104 ILE cc_start: 0.7494 (mm) cc_final: 0.6894 (tp) REVERT: A 1149 PHE cc_start: 0.6599 (p90) cc_final: 0.6298 (p90) REVERT: A 1167 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.6769 (t80) REVERT: A 1217 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7162 (mp0) REVERT: B 15 LYS cc_start: 0.8213 (tppt) cc_final: 0.7875 (tppt) REVERT: B 16 LYS cc_start: 0.6422 (OUTLIER) cc_final: 0.5940 (mtpp) REVERT: B 58 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6726 (m-80) REVERT: B 94 ASP cc_start: 0.8194 (p0) cc_final: 0.7812 (p0) REVERT: B 100 TRP cc_start: 0.7348 (OUTLIER) cc_final: 0.6070 (p90) REVERT: B 123 ASP cc_start: 0.7389 (m-30) cc_final: 0.6935 (p0) REVERT: B 148 GLN cc_start: 0.7894 (mm110) cc_final: 0.7552 (mm110) outliers start: 50 outliers final: 29 residues processed: 256 average time/residue: 0.2634 time to fit residues: 94.3264 Evaluate side-chains 224 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain A residue 1210 LYS Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 26 optimal weight: 30.0000 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 43 optimal weight: 0.3980 chunk 69 optimal weight: 5.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 1.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12068 Z= 0.390 Angle : 0.775 10.533 16336 Z= 0.411 Chirality : 0.048 0.280 1747 Planarity : 0.004 0.053 1999 Dihedral : 12.058 174.084 1849 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.79 % Allowed : 26.93 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.23 (0.22), residues: 1346 helix: -0.26 (0.20), residues: 643 sheet: -2.88 (0.44), residues: 120 loop : -2.58 (0.23), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1193 HIS 0.007 0.001 HIS B 31 PHE 0.024 0.002 PHE A 980 TYR 0.036 0.002 TYR A1068 ARG 0.008 0.001 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 213 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.7728 (t0) cc_final: 0.7447 (t0) REVERT: A 116 LYS cc_start: 0.9242 (mmmt) cc_final: 0.8626 (pttp) REVERT: A 120 LYS cc_start: 0.7796 (mmmt) cc_final: 0.7567 (ptpp) REVERT: A 159 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7203 (tt0) REVERT: A 178 GLU cc_start: 0.7656 (tp30) cc_final: 0.7396 (tp30) REVERT: A 238 ASN cc_start: 0.7883 (m-40) cc_final: 0.7229 (m110) REVERT: A 308 LEU cc_start: 0.8714 (mm) cc_final: 0.8392 (mm) REVERT: A 325 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.6244 (t80) REVERT: A 350 ASP cc_start: 0.8192 (m-30) cc_final: 0.7825 (t0) REVERT: A 423 ASP cc_start: 0.8580 (p0) cc_final: 0.7951 (m-30) REVERT: A 448 LYS cc_start: 0.8908 (mmtm) cc_final: 0.8497 (mppt) REVERT: A 467 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7764 (tm-30) REVERT: A 471 LYS cc_start: 0.8195 (tppt) cc_final: 0.7642 (mtpp) REVERT: A 494 TYR cc_start: 0.6825 (t80) cc_final: 0.6569 (t80) REVERT: A 562 TYR cc_start: 0.8126 (m-80) cc_final: 0.7923 (m-80) REVERT: A 571 LYS cc_start: 0.7415 (tmtt) cc_final: 0.7134 (tptp) REVERT: A 603 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7425 (mtm) REVERT: A 708 ASP cc_start: 0.8337 (t70) cc_final: 0.8018 (t70) REVERT: A 852 GLU cc_start: 0.7581 (tt0) cc_final: 0.7079 (tt0) REVERT: A 1056 ASP cc_start: 0.6918 (t0) cc_final: 0.6191 (t0) REVERT: A 1126 SER cc_start: 0.8888 (t) cc_final: 0.8470 (p) REVERT: A 1128 MET cc_start: 0.7070 (ptp) cc_final: 0.5865 (ppp) REVERT: A 1207 ASP cc_start: 0.7703 (p0) cc_final: 0.7262 (t70) REVERT: B 16 LYS cc_start: 0.6472 (OUTLIER) cc_final: 0.5888 (mtpp) REVERT: B 58 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.7003 (m-80) REVERT: B 100 TRP cc_start: 0.7828 (OUTLIER) cc_final: 0.6216 (p90) REVERT: B 148 GLN cc_start: 0.8187 (mm110) cc_final: 0.7900 (mm110) outliers start: 59 outliers final: 31 residues processed: 258 average time/residue: 0.2660 time to fit residues: 95.5321 Evaluate side-chains 217 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1225 SER Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 142 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 1.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12068 Z= 0.287 Angle : 0.685 10.759 16336 Z= 0.363 Chirality : 0.045 0.283 1747 Planarity : 0.004 0.044 1999 Dihedral : 11.788 176.237 1849 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.89 % Allowed : 28.30 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.93 (0.22), residues: 1346 helix: 0.07 (0.21), residues: 638 sheet: -2.92 (0.45), residues: 110 loop : -2.49 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1193 HIS 0.006 0.001 HIS B 31 PHE 0.035 0.002 PHE A1149 TYR 0.025 0.002 TYR A1068 ARG 0.004 0.001 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 199 time to evaluate : 1.313 Fit side-chains revert: symmetry clash REVERT: A 63 ASN cc_start: 0.7634 (t0) cc_final: 0.7400 (t0) REVERT: A 116 LYS cc_start: 0.9271 (mmmt) cc_final: 0.8718 (pttp) REVERT: A 159 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7261 (tp30) REVERT: A 161 MET cc_start: 0.6215 (mmp) cc_final: 0.5823 (mtp) REVERT: A 238 ASN cc_start: 0.8020 (m-40) cc_final: 0.7410 (m110) REVERT: A 325 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.5814 (t80) REVERT: A 350 ASP cc_start: 0.8150 (m-30) cc_final: 0.7727 (t0) REVERT: A 362 TRP cc_start: 0.7063 (t60) cc_final: 0.6738 (t60) REVERT: A 423 ASP cc_start: 0.8541 (p0) cc_final: 0.8008 (m-30) REVERT: A 429 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7671 (t80) REVERT: A 448 LYS cc_start: 0.8946 (mmtm) cc_final: 0.8543 (mppt) REVERT: A 466 PHE cc_start: 0.8649 (t80) cc_final: 0.8407 (t80) REVERT: A 467 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7771 (tm-30) REVERT: A 471 LYS cc_start: 0.8094 (tppt) cc_final: 0.7610 (mtpp) REVERT: A 562 TYR cc_start: 0.8006 (m-80) cc_final: 0.7781 (m-80) REVERT: A 670 TYR cc_start: 0.8691 (m-10) cc_final: 0.8440 (m-10) REVERT: A 708 ASP cc_start: 0.8326 (t70) cc_final: 0.8094 (t70) REVERT: A 808 ASN cc_start: 0.8254 (t0) cc_final: 0.7586 (t0) REVERT: A 852 GLU cc_start: 0.7527 (tt0) cc_final: 0.7046 (tt0) REVERT: A 965 CYS cc_start: 0.7310 (t) cc_final: 0.7058 (p) REVERT: A 1054 ARG cc_start: 0.7178 (mpt180) cc_final: 0.6622 (mmm-85) REVERT: A 1126 SER cc_start: 0.8977 (t) cc_final: 0.8556 (p) REVERT: A 1128 MET cc_start: 0.6715 (ptp) cc_final: 0.5819 (ppp) REVERT: A 1207 ASP cc_start: 0.7802 (p0) cc_final: 0.7156 (t70) REVERT: B 16 LYS cc_start: 0.6401 (OUTLIER) cc_final: 0.5830 (mtpp) REVERT: B 51 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8027 (mm) REVERT: B 58 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.6929 (m-80) REVERT: B 100 TRP cc_start: 0.7758 (OUTLIER) cc_final: 0.5516 (p90) REVERT: B 148 GLN cc_start: 0.8177 (mm110) cc_final: 0.7794 (mm110) outliers start: 48 outliers final: 30 residues processed: 236 average time/residue: 0.2718 time to fit residues: 90.5403 Evaluate side-chains 215 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 179 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 100 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 1.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12068 Z= 0.175 Angle : 0.635 10.467 16336 Z= 0.331 Chirality : 0.043 0.234 1747 Planarity : 0.003 0.039 1999 Dihedral : 11.579 178.745 1849 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.92 % Allowed : 29.44 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.65 (0.23), residues: 1346 helix: 0.26 (0.21), residues: 653 sheet: -2.65 (0.46), residues: 108 loop : -2.39 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A1193 HIS 0.003 0.001 HIS A 502 PHE 0.034 0.001 PHE A1149 TYR 0.024 0.001 TYR A 616 ARG 0.003 0.000 ARG A1071 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 194 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.7668 (t0) cc_final: 0.7436 (t0) REVERT: A 116 LYS cc_start: 0.9245 (mmmt) cc_final: 0.9011 (mmmm) REVERT: A 120 LYS cc_start: 0.7686 (ptpp) cc_final: 0.7486 (ptpp) REVERT: A 161 MET cc_start: 0.6342 (mmp) cc_final: 0.6067 (mtp) REVERT: A 174 ARG cc_start: 0.7318 (mmm-85) cc_final: 0.6895 (tmm-80) REVERT: A 238 ASN cc_start: 0.7937 (m-40) cc_final: 0.7318 (m110) REVERT: A 257 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7981 (pt0) REVERT: A 302 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7481 (tm-30) REVERT: A 325 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.5709 (t80) REVERT: A 350 ASP cc_start: 0.7835 (m-30) cc_final: 0.7418 (t0) REVERT: A 403 TYR cc_start: 0.5502 (OUTLIER) cc_final: 0.5044 (m-80) REVERT: A 423 ASP cc_start: 0.8589 (p0) cc_final: 0.8191 (m-30) REVERT: A 429 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.7691 (t80) REVERT: A 448 LYS cc_start: 0.8949 (mmtm) cc_final: 0.8559 (mppt) REVERT: A 466 PHE cc_start: 0.8716 (t80) cc_final: 0.8451 (t80) REVERT: A 467 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8121 (tm-30) REVERT: A 468 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8347 (t0) REVERT: A 471 LYS cc_start: 0.8137 (tppt) cc_final: 0.7825 (mmmm) REVERT: A 670 TYR cc_start: 0.8649 (m-10) cc_final: 0.8415 (m-80) REVERT: A 808 ASN cc_start: 0.8134 (t0) cc_final: 0.7493 (t0) REVERT: A 852 GLU cc_start: 0.7579 (tt0) cc_final: 0.7157 (tt0) REVERT: A 1054 ARG cc_start: 0.7511 (mpt180) cc_final: 0.6844 (mmm-85) REVERT: A 1126 SER cc_start: 0.8929 (t) cc_final: 0.8579 (p) REVERT: B 16 LYS cc_start: 0.6456 (OUTLIER) cc_final: 0.5930 (mtpp) REVERT: B 29 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5383 (pm20) REVERT: B 49 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.6968 (p0) REVERT: B 58 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7131 (m-80) REVERT: B 100 TRP cc_start: 0.7587 (OUTLIER) cc_final: 0.5087 (p90) REVERT: B 148 GLN cc_start: 0.8120 (mm110) cc_final: 0.7718 (mm110) REVERT: B 163 THR cc_start: 0.5596 (OUTLIER) cc_final: 0.5114 (p) outliers start: 36 outliers final: 23 residues processed: 222 average time/residue: 0.2557 time to fit residues: 80.0640 Evaluate side-chains 205 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 172 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 403 TYR Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 163 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 74 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 1.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12068 Z= 0.213 Angle : 0.640 8.864 16336 Z= 0.337 Chirality : 0.043 0.251 1747 Planarity : 0.003 0.041 1999 Dihedral : 11.617 179.423 1849 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.84 % Allowed : 29.85 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.55 (0.23), residues: 1346 helix: 0.29 (0.21), residues: 661 sheet: -2.59 (0.47), residues: 108 loop : -2.31 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1193 HIS 0.008 0.001 HIS A 633 PHE 0.032 0.002 PHE A1149 TYR 0.021 0.002 TYR A 616 ARG 0.003 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 179 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.6418 (mmp) cc_final: 0.6125 (mtp) REVERT: A 174 ARG cc_start: 0.7311 (mmm-85) cc_final: 0.6792 (tmm-80) REVERT: A 238 ASN cc_start: 0.7924 (m-40) cc_final: 0.7310 (m110) REVERT: A 302 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7522 (tm-30) REVERT: A 325 PHE cc_start: 0.6817 (OUTLIER) cc_final: 0.5738 (t80) REVERT: A 350 ASP cc_start: 0.7721 (m-30) cc_final: 0.7415 (t0) REVERT: A 403 TYR cc_start: 0.6047 (OUTLIER) cc_final: 0.5050 (m-80) REVERT: A 423 ASP cc_start: 0.8566 (p0) cc_final: 0.8174 (m-30) REVERT: A 429 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7672 (t80) REVERT: A 448 LYS cc_start: 0.8957 (mmtm) cc_final: 0.8563 (mppt) REVERT: A 466 PHE cc_start: 0.8693 (t80) cc_final: 0.8305 (t80) REVERT: A 467 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7923 (tm-30) REVERT: A 471 LYS cc_start: 0.8081 (tppt) cc_final: 0.7788 (mmmm) REVERT: A 596 VAL cc_start: 0.9016 (p) cc_final: 0.8798 (p) REVERT: A 612 ILE cc_start: 0.8385 (mm) cc_final: 0.8127 (pt) REVERT: A 688 LYS cc_start: 0.7060 (pttt) cc_final: 0.6813 (tppt) REVERT: A 808 ASN cc_start: 0.8184 (t0) cc_final: 0.7578 (t0) REVERT: A 852 GLU cc_start: 0.7440 (tt0) cc_final: 0.6999 (tt0) REVERT: A 867 ARG cc_start: 0.8269 (ptp-110) cc_final: 0.7840 (mtp85) REVERT: A 947 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7761 (tt0) REVERT: A 1054 ARG cc_start: 0.7501 (mpt180) cc_final: 0.6909 (mmm-85) REVERT: A 1126 SER cc_start: 0.8880 (t) cc_final: 0.8547 (p) REVERT: B 16 LYS cc_start: 0.6405 (OUTLIER) cc_final: 0.5806 (mtpp) REVERT: B 29 GLU cc_start: 0.6147 (OUTLIER) cc_final: 0.5074 (mm-30) REVERT: B 51 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8017 (mm) REVERT: B 58 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.6960 (m-80) REVERT: B 148 GLN cc_start: 0.8115 (mm110) cc_final: 0.7777 (mm110) REVERT: B 163 THR cc_start: 0.5980 (OUTLIER) cc_final: 0.5743 (p) outliers start: 35 outliers final: 25 residues processed: 208 average time/residue: 0.2606 time to fit residues: 76.2514 Evaluate side-chains 203 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 403 TYR Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 163 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 1.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12068 Z= 0.280 Angle : 0.689 11.088 16336 Z= 0.363 Chirality : 0.045 0.264 1747 Planarity : 0.004 0.040 1999 Dihedral : 11.722 178.423 1849 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.08 % Allowed : 29.76 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.72 (0.23), residues: 1346 helix: 0.13 (0.21), residues: 666 sheet: -2.70 (0.47), residues: 108 loop : -2.37 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A1193 HIS 0.006 0.001 HIS A 633 PHE 0.031 0.002 PHE A1149 TYR 0.033 0.002 TYR B 136 ARG 0.004 0.001 ARG A 182 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 182 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.6403 (mmp) cc_final: 0.6078 (mtp) REVERT: A 174 ARG cc_start: 0.7487 (mmm-85) cc_final: 0.7123 (mtp180) REVERT: A 325 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.6172 (t80) REVERT: A 350 ASP cc_start: 0.7933 (m-30) cc_final: 0.7550 (t0) REVERT: A 403 TYR cc_start: 0.6262 (OUTLIER) cc_final: 0.5081 (m-80) REVERT: A 409 SER cc_start: 0.8279 (t) cc_final: 0.8009 (p) REVERT: A 418 ILE cc_start: 0.7558 (mm) cc_final: 0.7280 (mm) REVERT: A 423 ASP cc_start: 0.8586 (p0) cc_final: 0.8206 (m-30) REVERT: A 448 LYS cc_start: 0.9053 (mmtm) cc_final: 0.8609 (mppt) REVERT: A 467 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7918 (tm-30) REVERT: A 471 LYS cc_start: 0.8090 (tppt) cc_final: 0.7799 (mmmm) REVERT: A 531 MET cc_start: 0.9098 (mtm) cc_final: 0.8783 (mtp) REVERT: A 596 VAL cc_start: 0.8999 (p) cc_final: 0.8797 (p) REVERT: A 614 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7726 (ptpp) REVERT: A 688 LYS cc_start: 0.7658 (pttt) cc_final: 0.7204 (tppt) REVERT: A 808 ASN cc_start: 0.8115 (t0) cc_final: 0.7619 (t0) REVERT: A 852 GLU cc_start: 0.7652 (tt0) cc_final: 0.7136 (tt0) REVERT: A 858 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7481 (mm-30) REVERT: A 947 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7843 (tt0) REVERT: A 1054 ARG cc_start: 0.7730 (mpt180) cc_final: 0.7091 (mmm-85) REVERT: A 1126 SER cc_start: 0.9125 (t) cc_final: 0.8729 (p) REVERT: B 16 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.5903 (mtpp) REVERT: B 28 ASP cc_start: 0.3669 (t0) cc_final: 0.3358 (t0) REVERT: B 29 GLU cc_start: 0.6335 (OUTLIER) cc_final: 0.5282 (pm20) REVERT: B 51 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8039 (mm) REVERT: B 58 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.6983 (m-80) REVERT: B 148 GLN cc_start: 0.8188 (mm110) cc_final: 0.7974 (mm110) outliers start: 38 outliers final: 27 residues processed: 215 average time/residue: 0.2509 time to fit residues: 76.8784 Evaluate side-chains 200 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 166 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 403 TYR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 146 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 111 optimal weight: 0.0010 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.166298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.123940 restraints weight = 19106.094| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.96 r_work: 0.3497 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 1.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12068 Z= 0.179 Angle : 0.643 10.255 16336 Z= 0.337 Chirality : 0.042 0.243 1747 Planarity : 0.003 0.043 1999 Dihedral : 11.584 179.716 1849 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.94 % Favored : 93.98 % Rotamer: Outliers : 2.84 % Allowed : 30.33 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.34 (0.23), residues: 1346 helix: 0.49 (0.21), residues: 648 sheet: -2.43 (0.50), residues: 103 loop : -2.20 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A1193 HIS 0.007 0.001 HIS A 633 PHE 0.029 0.002 PHE A1149 TYR 0.021 0.001 TYR A1068 ARG 0.003 0.000 ARG A1071 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2868.10 seconds wall clock time: 52 minutes 22.46 seconds (3142.46 seconds total)