Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 07:15:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/04_2023/6nmd_0447.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/04_2023/6nmd_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_0447/04_2023/6nmd_0447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/04_2023/6nmd_0447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/04_2023/6nmd_0447.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nmd_0447/04_2023/6nmd_0447.pdb" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 6.19, per 1000 atoms: 0.53 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: 4.97 Conformation dependent library (CDL) restraints added in 1.7 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: 3.12 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: 4.25 Time building geometry restraints manager: 5.35 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: 6938 32.09 - 64.19: 291 64.19 - 96.28: 20 96.28 - 128.37: 0 128.37 - 160.46: 1 Dihedral angle restraints: 7250 sinusoidal: 3217 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 7247 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: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.220 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 34.650 Find NCS groups from input model: 0.280 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.510 ------------------------------------------------------------------------------- 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 : 16.815 160.463 4650 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 % 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 *********************** 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 : 1.296 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 outliers start: 30 outliers final: 6 residues processed: 347 average time/residue: 0.3036 time to fit residues: 141.1937 Evaluate side-chains 176 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 170 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2023 time to fit residues: 3.7662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 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: 8.9990 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 363 ASN 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 990 ASN B 20 ASN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 moved from start: 0.6719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 12068 Z= 0.311 Angle : 0.806 11.594 16336 Z= 0.427 Chirality : 0.047 0.237 1747 Planarity : 0.005 0.051 1999 Dihedral : 9.916 153.061 1776 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 3.73 % 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: -3.08 (0.20), residues: 1346 helix: -1.11 (0.19), residues: 645 sheet: -3.37 (0.42), residues: 108 loop : -2.82 (0.23), residues: 593 *********************** 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 298 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 252 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 16 residues processed: 287 average time/residue: 0.2613 time to fit residues: 105.6942 Evaluate side-chains 179 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1220 time to fit residues: 5.5668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 103 optimal weight: 0.0010 chunk 84 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 overall best weight: 3.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 160 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN A 803 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN A1136 GLN A1182 ASN A1186 ASN A1215 ASN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 1.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.116 12068 Z= 0.372 Angle : 0.818 14.432 16336 Z= 0.436 Chirality : 0.049 0.251 1747 Planarity : 0.005 0.058 1999 Dihedral : 9.888 165.060 1776 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer Outliers : 5.35 % 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: -2.88 (0.21), residues: 1346 helix: -0.84 (0.19), residues: 645 sheet: -3.41 (0.39), residues: 123 loop : -2.79 (0.23), residues: 578 *********************** 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 311 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 245 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 24 residues processed: 297 average time/residue: 0.2952 time to fit residues: 122.0588 Evaluate side-chains 205 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 181 time to evaluate : 1.382 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1391 time to fit residues: 7.5999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 7.9990 chunk 93 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 chunk 59 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 706 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN A1139 ASN A1172 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 1.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 12068 Z= 0.161 Angle : 0.607 8.771 16336 Z= 0.323 Chirality : 0.042 0.216 1747 Planarity : 0.004 0.041 1999 Dihedral : 9.570 168.650 1776 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 2.68 % 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: -2.17 (0.22), residues: 1346 helix: -0.17 (0.21), residues: 646 sheet: -2.97 (0.46), residues: 109 loop : -2.61 (0.23), residues: 591 *********************** 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 244 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 211 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 237 average time/residue: 0.2721 time to fit residues: 91.0305 Evaluate side-chains 187 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 171 time to evaluate : 1.417 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1433 time to fit residues: 6.0972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 1 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 861 ASN ** 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: 0.6960 moved from start: 1.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 12068 Z= 0.283 Angle : 0.706 9.217 16336 Z= 0.374 Chirality : 0.045 0.221 1747 Planarity : 0.004 0.046 1999 Dihedral : 9.840 173.502 1776 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 3.33 % 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: -2.09 (0.22), residues: 1346 helix: -0.14 (0.21), residues: 643 sheet: -2.94 (0.47), residues: 106 loop : -2.50 (0.23), residues: 597 *********************** 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 246 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 205 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 20 residues processed: 238 average time/residue: 0.2721 time to fit residues: 90.5421 Evaluate side-chains 192 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 1.437 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1435 time to fit residues: 6.8580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 513 GLN A 577 ASN ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN A 862 ASN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 1.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 12068 Z= 0.414 Angle : 0.795 9.429 16336 Z= 0.422 Chirality : 0.050 0.242 1747 Planarity : 0.005 0.049 1999 Dihedral : 9.913 174.495 1776 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer Outliers : 2.51 % 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: -2.38 (0.22), residues: 1346 helix: -0.47 (0.20), residues: 650 sheet: -3.14 (0.45), residues: 112 loop : -2.53 (0.24), residues: 584 *********************** 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 256 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 225 time to evaluate : 1.518 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 245 average time/residue: 0.2685 time to fit residues: 91.9453 Evaluate side-chains 198 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1171 time to fit residues: 4.8879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN ** A1197 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: 0.7093 moved from start: 1.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 12068 Z= 0.290 Angle : 0.701 9.342 16336 Z= 0.374 Chirality : 0.046 0.222 1747 Planarity : 0.004 0.046 1999 Dihedral : 9.786 176.664 1776 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer Outliers : 1.62 % 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: -2.09 (0.23), residues: 1346 helix: -0.12 (0.21), residues: 643 sheet: -2.99 (0.43), residues: 122 loop : -2.48 (0.24), residues: 581 *********************** 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 211 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 5 residues processed: 201 average time/residue: 0.2812 time to fit residues: 79.0712 Evaluate side-chains 173 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 168 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3214 time to fit residues: 3.8931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 0.0870 chunk 83 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 126 optimal weight: 0.0050 overall best weight: 0.9576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN A 861 ASN A 963 ASN ** A1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7022 moved from start: 1.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 12068 Z= 0.179 Angle : 0.663 9.303 16336 Z= 0.349 Chirality : 0.043 0.236 1747 Planarity : 0.003 0.043 1999 Dihedral : 9.557 179.830 1776 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 0.97 % 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: 0.22 (0.21), residues: 638 sheet: -2.69 (0.45), residues: 120 loop : -2.24 (0.25), residues: 588 *********************** 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 207 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 195 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 200 average time/residue: 0.2825 time to fit residues: 78.7776 Evaluate side-chains 178 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 170 time to evaluate : 1.346 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1651 time to fit residues: 4.1118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.4980 chunk 123 optimal weight: 20.0000 chunk 126 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 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: 0.7003 moved from start: 1.5534 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= 0.177 Angle : 0.655 9.227 16336 Z= 0.346 Chirality : 0.043 0.244 1747 Planarity : 0.004 0.041 1999 Dihedral : 9.469 178.922 1776 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer Outliers : 0.57 % 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: -1.54 (0.23), residues: 1346 helix: 0.26 (0.21), residues: 652 sheet: -2.33 (0.46), residues: 121 loop : -2.25 (0.25), residues: 573 *********************** 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 178 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 171 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 176 average time/residue: 0.2875 time to fit residues: 70.8032 Evaluate side-chains 166 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 161 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2448 time to fit residues: 3.6463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 735 GLN ** A 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1197 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: 0.7068 moved from start: 1.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 12068 Z= 0.254 Angle : 0.697 10.812 16336 Z= 0.367 Chirality : 0.044 0.262 1747 Planarity : 0.004 0.039 1999 Dihedral : 9.580 179.697 1776 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer Outliers : 0.32 % 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: -1.58 (0.23), residues: 1346 helix: 0.24 (0.21), residues: 650 sheet: -2.37 (0.47), residues: 118 loop : -2.27 (0.25), residues: 578 ********************** 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 170 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 166 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 169 average time/residue: 0.2797 time to fit residues: 66.4303 Evaluate side-chains 162 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 1.406 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4188 time to fit residues: 3.0447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.5980 chunk 33 optimal weight: 0.0070 chunk 100 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 overall best weight: 0.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.164687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120863 restraints weight = 19277.225| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.19 r_work: 0.3413 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 1.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 12068 Z= 0.176 Angle : 0.656 9.996 16336 Z= 0.345 Chirality : 0.042 0.241 1747 Planarity : 0.003 0.037 1999 Dihedral : 9.411 178.690 1776 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer Outliers : 0.32 % 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: -1.45 (0.23), residues: 1346 helix: 0.30 (0.21), residues: 654 sheet: -1.98 (0.51), residues: 111 loop : -2.25 (0.25), residues: 581 =============================================================================== Job complete usr+sys time: 2691.91 seconds wall clock time: 49 minutes 46.67 seconds (2986.67 seconds total)