Starting phenix.real_space_refine on Sun Dec 10 08:28:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzt_29639/12_2023/8fzt_29639.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzt_29639/12_2023/8fzt_29639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzt_29639/12_2023/8fzt_29639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzt_29639/12_2023/8fzt_29639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzt_29639/12_2023/8fzt_29639.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fzt_29639/12_2023/8fzt_29639.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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: 5 Type Number sf(0) Gaussians P 149 5.49 5 S 22 5.16 5 C 8303 2.51 5 N 2436 2.21 5 O 3015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 94": "OD1" <-> "OD2" Residue "E ASP 110": "OD1" <-> "OD2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "E ASP 364": "OD1" <-> "OD2" Residue "E GLU 371": "OE1" <-> "OE2" Residue "E ASP 428": "OD1" <-> "OD2" Residue "E GLU 438": "OE1" <-> "OE2" Residue "E TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 618": "OD1" <-> "OD2" Residue "E GLU 706": not complete - not flipped Residue "E GLU 1007": "OE1" <-> "OE2" Residue "E GLU 1064": "OE1" <-> "OE2" Residue "E GLU 1175": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13925 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 10780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10780 Classifications: {'peptide': 1319} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 35, 'TRANS': 1283} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 803 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 17, 'rna3p_pyr': 20} Link IDs: {'rna2p': 1, 'rna3p': 36} Chain: "B" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1476 Classifications: {'RNA': 69} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 24} Link IDs: {'rna2p': 11, 'rna3p': 57} Chain: "C" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 616 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 8.25, per 1000 atoms: 0.59 Number of scatterers: 13925 At special positions: 0 Unit cell: (95.9, 128.1, 131.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 149 15.00 O 3015 8.00 N 2436 7.00 C 8303 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: 5.63 Conformation dependent library (CDL) restraints added in 2.4 seconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2516 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 7 sheets defined 50.6% alpha, 6.0% beta 42 base pairs and 97 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'E' and resid 59 through 87 removed outlier: 4.112A pdb=" N ARG E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE E 79 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS E 80 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR E 81 " --> pdb=" O ASN E 77 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU E 82 " --> pdb=" O ARG E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.562A pdb=" N VAL E 93 " --> pdb=" O MET E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.578A pdb=" N ARG E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 101 " --> pdb=" O PHE E 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 96 through 101' Processing helix chain 'E' and resid 122 through 132 removed outlier: 3.922A pdb=" N VAL E 126 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA E 127 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N TYR E 128 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 145 removed outlier: 4.213A pdb=" N LEU E 138 " --> pdb=" O THR E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 164 removed outlier: 3.779A pdb=" N ILE E 154 " --> pdb=" O ASP E 150 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE E 164 " --> pdb=" O HIS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 196 Processing helix chain 'E' and resid 207 through 213 removed outlier: 3.668A pdb=" N ILE E 211 " --> pdb=" O ASP E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 229 removed outlier: 3.703A pdb=" N GLN E 228 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU E 229 " --> pdb=" O LEU E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 247 Processing helix chain 'E' and resid 253 through 257 removed outlier: 3.650A pdb=" N PHE E 256 " --> pdb=" O LYS E 253 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP E 257 " --> pdb=" O SER E 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 253 through 257' Processing helix chain 'E' and resid 270 through 279 removed outlier: 3.609A pdb=" N LEU E 275 " --> pdb=" O TYR E 271 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASP E 276 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN E 277 " --> pdb=" O ASP E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 302 removed outlier: 3.593A pdb=" N LEU E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 320 Processing helix chain 'E' and resid 323 through 343 removed outlier: 5.527A pdb=" N HIS E 329 " --> pdb=" O TYR E 325 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR E 333 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU E 334 " --> pdb=" O GLN E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.744A pdb=" N ILE E 350 " --> pdb=" O LYS E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 removed outlier: 3.560A pdb=" N ASP E 364 " --> pdb=" O ALA E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 383 removed outlier: 3.668A pdb=" N PHE E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Proline residue: E 378 - end of helix removed outlier: 3.597A pdb=" N LYS E 382 " --> pdb=" O PRO E 378 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 395 removed outlier: 3.649A pdb=" N VAL E 391 " --> pdb=" O GLU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 424 removed outlier: 4.464A pdb=" N HIS E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 424 " --> pdb=" O HIS E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 Processing helix chain 'E' and resid 436 through 446 removed outlier: 3.651A pdb=" N ILE E 443 " --> pdb=" O LYS E 439 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU E 444 " --> pdb=" O ILE E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 482 removed outlier: 3.509A pdb=" N VAL E 481 " --> pdb=" O ASN E 477 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL E 482 " --> pdb=" O PHE E 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 477 through 482' Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 512 through 524 Processing helix chain 'E' and resid 541 through 552 Processing helix chain 'E' and resid 560 through 568 removed outlier: 3.803A pdb=" N LEU E 564 " --> pdb=" O THR E 560 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS E 565 " --> pdb=" O VAL E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 602 removed outlier: 4.004A pdb=" N HIS E 595 " --> pdb=" O LEU E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 609 Processing helix chain 'E' and resid 612 through 624 removed outlier: 4.231A pdb=" N LEU E 616 " --> pdb=" O ASN E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 628 through 636 removed outlier: 3.554A pdb=" N ILE E 632 " --> pdb=" O ASP E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 640 Processing helix chain 'E' and resid 644 through 653 removed outlier: 3.628A pdb=" N GLN E 650 " --> pdb=" O LYS E 646 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG E 653 " --> pdb=" O LYS E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 685 Processing helix chain 'E' and resid 692 through 698 removed outlier: 3.676A pdb=" N HIS E 698 " --> pdb=" O MET E 694 " (cutoff:3.500A) Processing helix chain 'E' and resid 703 through 714 Processing helix chain 'E' and resid 720 through 727 Processing helix chain 'E' and resid 730 through 751 removed outlier: 3.656A pdb=" N LYS E 734 " --> pdb=" O SER E 730 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET E 751 " --> pdb=" O LEU E 747 " (cutoff:3.500A) Processing helix chain 'E' and resid 777 through 792 removed outlier: 3.516A pdb=" N LEU E 791 " --> pdb=" O GLY E 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 802 through 808 Processing helix chain 'E' and resid 808 through 818 Processing helix chain 'E' and resid 861 through 865 removed outlier: 3.547A pdb=" N ARG E 864 " --> pdb=" O ASP E 861 " (cutoff:3.500A) Processing helix chain 'E' and resid 873 through 889 removed outlier: 7.017A pdb=" N ASN E 881 " --> pdb=" O LYS E 877 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR E 882 " --> pdb=" O LYS E 878 " (cutoff:3.500A) Processing helix chain 'E' and resid 893 through 906 removed outlier: 3.775A pdb=" N GLU E 904 " --> pdb=" O LEU E 900 " (cutoff:3.500A) Processing helix chain 'E' and resid 910 through 922 Processing helix chain 'E' and resid 925 through 940 removed outlier: 4.087A pdb=" N LYS E 929 " --> pdb=" O ARG E 925 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN E 940 " --> pdb=" O ASP E 936 " (cutoff:3.500A) Processing helix chain 'E' and resid 960 through 971 removed outlier: 4.089A pdb=" N SER E 964 " --> pdb=" O SER E 960 " (cutoff:3.500A) Processing helix chain 'E' and resid 981 through 1001 removed outlier: 4.002A pdb=" N ALA E 991 " --> pdb=" O ALA E 987 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 992 " --> pdb=" O TYR E 988 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 993 " --> pdb=" O LEU E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 1004 through 1009 Processing helix chain 'E' and resid 1031 through 1041 Processing helix chain 'E' and resid 1078 through 1087 Processing helix chain 'E' and resid 1127 through 1132 Processing helix chain 'E' and resid 1170 through 1177 Processing helix chain 'E' and resid 1177 through 1186 removed outlier: 3.605A pdb=" N PHE E1181 " --> pdb=" O ASN E1177 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS E1185 " --> pdb=" O PHE E1181 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY E1186 " --> pdb=" O LEU E1182 " (cutoff:3.500A) Processing helix chain 'E' and resid 1229 through 1242 removed outlier: 3.730A pdb=" N VAL E1233 " --> pdb=" O PRO E1229 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS E1241 " --> pdb=" O TYR E1237 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR E1242 " --> pdb=" O LEU E1238 " (cutoff:3.500A) Processing helix chain 'E' and resid 1250 through 1262 removed outlier: 3.833A pdb=" N GLN E1254 " --> pdb=" O GLU E1250 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS E1255 " --> pdb=" O ASP E1251 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU E1260 " --> pdb=" O GLN E1256 " (cutoff:3.500A) Processing helix chain 'E' and resid 1265 through 1278 Processing helix chain 'E' and resid 1284 through 1298 removed outlier: 3.618A pdb=" N ARG E1298 " --> pdb=" O TYR E1294 " (cutoff:3.500A) Processing helix chain 'E' and resid 1301 through 1306 Processing helix chain 'E' and resid 1308 through 1313 Processing helix chain 'E' and resid 1340 through 1344 Processing sheet with id=AA1, first strand: chain 'E' and resid 954 through 957 removed outlier: 3.586A pdb=" N VAL E1095 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 29 through 32 Processing sheet with id=AA3, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.725A pdb=" N LEU E 35 " --> pdb=" O ARG E1359 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ASP E1361 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU E1203 " --> pdb=" O ILE E1348 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU E1219 " --> pdb=" O ALA E1215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 837 through 840 Processing sheet with id=AA5, first strand: chain 'E' and resid 1063 through 1065 Processing sheet with id=AA6, first strand: chain 'E' and resid 1160 through 1167 removed outlier: 7.018A pdb=" N VAL E1160 " --> pdb=" O VAL E1146 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL E1146 " --> pdb=" O VAL E1160 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU E1162 " --> pdb=" O LEU E1144 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU E1144 " --> pdb=" O GLU E1162 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU E1164 " --> pdb=" O SER E1142 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER E1142 " --> pdb=" O LEU E1164 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE E1166 " --> pdb=" O ALA E1140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 1324 through 1325 removed outlier: 3.574A pdb=" N PHE E1324 " --> pdb=" O ILE E1331 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 210 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 97 stacking parallelities Total time for adding SS restraints: 6.97 Time building geometry restraints manager: 6.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3972 1.34 - 1.46: 4051 1.46 - 1.59: 6125 1.59 - 1.71: 295 1.71 - 1.84: 42 Bond restraints: 14485 Sorted by residual: bond pdb=" C GLY E1319 " pdb=" O GLY E1319 " ideal model delta sigma weight residual 1.236 1.266 -0.030 5.30e-03 3.56e+04 3.25e+01 bond pdb=" CG1 ILE E1050 " pdb=" CD1 ILE E1050 " ideal model delta sigma weight residual 1.513 1.602 -0.089 3.90e-02 6.57e+02 5.16e+00 bond pdb=" CA THR E1051 " pdb=" C THR E1051 " ideal model delta sigma weight residual 1.525 1.566 -0.041 2.10e-02 2.27e+03 3.84e+00 bond pdb=" N THR E1051 " pdb=" CA THR E1051 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.72e+00 bond pdb=" CB GLU E1049 " pdb=" CG GLU E1049 " ideal model delta sigma weight residual 1.520 1.577 -0.057 3.00e-02 1.11e+03 3.60e+00 ... (remaining 14480 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.76: 1054 106.76 - 113.57: 8095 113.57 - 120.38: 5568 120.38 - 127.19: 5095 127.19 - 134.00: 378 Bond angle restraints: 20190 Sorted by residual: angle pdb=" N ILE E1050 " pdb=" CA ILE E1050 " pdb=" C ILE E1050 " ideal model delta sigma weight residual 112.96 119.55 -6.59 1.00e+00 1.00e+00 4.34e+01 angle pdb=" C THR E 957 " pdb=" N LEU E 958 " pdb=" CA LEU E 958 " ideal model delta sigma weight residual 121.90 116.74 5.16 1.26e+00 6.30e-01 1.68e+01 angle pdb=" C LEU E 958 " pdb=" CA LEU E 958 " pdb=" CB LEU E 958 " ideal model delta sigma weight residual 112.31 106.60 5.71 1.53e+00 4.27e-01 1.39e+01 angle pdb=" CB MET E 781 " pdb=" CG MET E 781 " pdb=" SD MET E 781 " ideal model delta sigma weight residual 112.70 122.93 -10.23 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C THR E1048 " pdb=" N GLU E1049 " pdb=" CA GLU E1049 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 ... (remaining 20185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 8105 35.42 - 70.84: 554 70.84 - 106.26: 39 106.26 - 141.68: 0 141.68 - 177.10: 3 Dihedral angle restraints: 8701 sinusoidal: 4821 harmonic: 3880 Sorted by residual: dihedral pdb=" CA HIS E1297 " pdb=" C HIS E1297 " pdb=" N ARG E1298 " pdb=" CA ARG E1298 " ideal model delta harmonic sigma weight residual 180.00 153.32 26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA LYS E 356 " pdb=" C LYS E 356 " pdb=" N ASN E 357 " pdb=" CA ASN E 357 " ideal model delta harmonic sigma weight residual 180.00 154.07 25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA TYR E 325 " pdb=" C TYR E 325 " pdb=" N ASP E 326 " pdb=" CA ASP E 326 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 8698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1517 0.031 - 0.062: 547 0.062 - 0.092: 180 0.092 - 0.123: 68 0.123 - 0.154: 16 Chirality restraints: 2328 Sorted by residual: chirality pdb=" CA VAL E 20 " pdb=" N VAL E 20 " pdb=" C VAL E 20 " pdb=" CB VAL E 20 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" P C A 4 " pdb=" OP1 C A 4 " pdb=" OP2 C A 4 " pdb=" O5' C A 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.26 0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" C1' A B 23 " pdb=" O4' A B 23 " pdb=" C2' A B 23 " pdb=" N9 A B 23 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 2325 not shown) Planarity restraints: 2034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E1001 " 0.056 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO E1002 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO E1002 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO E1002 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 502 " 0.044 5.00e-02 4.00e+02 6.77e-02 7.32e+00 pdb=" N PRO E 503 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 503 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 503 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E1242 " -0.015 2.00e-02 2.50e+03 1.75e-02 6.12e+00 pdb=" CG TYR E1242 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR E1242 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR E1242 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR E1242 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E1242 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR E1242 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR E1242 " -0.005 2.00e-02 2.50e+03 ... (remaining 2031 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1370 2.74 - 3.28: 12045 3.28 - 3.82: 21628 3.82 - 4.36: 25090 4.36 - 4.90: 41541 Nonbonded interactions: 101674 Sorted by model distance: nonbonded pdb=" N GLU E 438 " pdb=" OE1 GLU E 438 " model vdw 2.205 2.520 nonbonded pdb=" NH1 ARG E 395 " pdb=" OD2 ASP E 397 " model vdw 2.210 2.520 nonbonded pdb=" O SER E1136 " pdb=" OG SER E1136 " model vdw 2.251 2.440 nonbonded pdb=" OD1 ASN E1066 " pdb=" OG1 THR E1069 " model vdw 2.254 2.440 nonbonded pdb=" O2' A A 8 " pdb=" OP1 A A 9 " model vdw 2.310 2.440 ... (remaining 101669 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: 5.720 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: 0.000 Extract box with map and model: 13.590 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 43.460 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 : 0.004 0.089 14485 Z= 0.226 Angle : 0.628 10.233 20190 Z= 0.342 Chirality : 0.039 0.154 2328 Planarity : 0.005 0.085 2034 Dihedral : 20.431 177.095 6185 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.68 % Allowed : 28.81 % Favored : 70.51 % 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: -1.36 (0.23), residues: 1303 helix: 0.23 (0.22), residues: 604 sheet: 0.18 (0.56), residues: 99 loop : -2.36 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 659 HIS 0.005 0.001 HIS E 983 PHE 0.017 0.001 PHE E 966 TYR 0.039 0.002 TYR E1242 ARG 0.018 0.001 ARG E 629 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 194 time to evaluate : 1.217 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 200 average time/residue: 0.3441 time to fit residues: 95.4569 Evaluate side-chains 198 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 1.241 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1909 time to fit residues: 3.2047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 0.0570 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 112 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 84 optimal weight: 40.0000 chunk 130 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 295 ASN E 668 ASN E 726 ASN ** E 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14485 Z= 0.175 Angle : 0.532 7.750 20190 Z= 0.286 Chirality : 0.037 0.141 2328 Planarity : 0.004 0.065 2034 Dihedral : 17.942 179.209 3394 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.54 % Allowed : 27.03 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.23), residues: 1303 helix: 0.63 (0.22), residues: 618 sheet: 0.54 (0.57), residues: 96 loop : -2.25 (0.23), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 659 HIS 0.004 0.001 HIS E 412 PHE 0.016 0.001 PHE E 966 TYR 0.012 0.001 TYR E 325 ARG 0.004 0.000 ARG E 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 194 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 211 average time/residue: 0.3225 time to fit residues: 94.8237 Evaluate side-chains 201 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 187 time to evaluate : 1.637 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.1790 time to fit residues: 5.8689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 0.0070 chunk 89 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 726 ASN ** E 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14485 Z= 0.255 Angle : 0.584 9.779 20190 Z= 0.310 Chirality : 0.039 0.197 2328 Planarity : 0.004 0.063 2034 Dihedral : 17.951 178.880 3394 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.03 % Allowed : 27.03 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.23), residues: 1303 helix: 0.70 (0.22), residues: 617 sheet: 0.55 (0.57), residues: 93 loop : -2.27 (0.22), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 659 HIS 0.005 0.001 HIS E 328 PHE 0.020 0.002 PHE E 966 TYR 0.013 0.001 TYR E 5 ARG 0.005 0.000 ARG E 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 1.447 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 207 average time/residue: 0.3227 time to fit residues: 92.4043 Evaluate side-chains 204 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.1541 time to fit residues: 5.2271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14485 Z= 0.376 Angle : 0.676 9.729 20190 Z= 0.356 Chirality : 0.043 0.189 2328 Planarity : 0.005 0.066 2034 Dihedral : 18.125 178.478 3394 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.71 % Allowed : 26.19 % Favored : 71.10 % 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: -1.09 (0.23), residues: 1303 helix: 0.49 (0.22), residues: 618 sheet: 0.33 (0.55), residues: 95 loop : -2.32 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 659 HIS 0.008 0.002 HIS E 328 PHE 0.027 0.002 PHE E 966 TYR 0.017 0.002 TYR E 5 ARG 0.006 0.000 ARG E 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 1.320 Fit side-chains outliers start: 32 outliers final: 16 residues processed: 211 average time/residue: 0.3225 time to fit residues: 94.0946 Evaluate side-chains 211 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 195 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.1879 time to fit residues: 6.6617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 103 optimal weight: 0.0270 chunk 57 optimal weight: 9.9990 chunk 118 optimal weight: 0.5980 chunk 96 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 124 optimal weight: 0.0870 chunk 35 optimal weight: 0.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 369 GLN ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14485 Z= 0.149 Angle : 0.513 10.006 20190 Z= 0.275 Chirality : 0.036 0.155 2328 Planarity : 0.004 0.052 2034 Dihedral : 17.905 178.785 3394 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.85 % Allowed : 26.95 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.23), residues: 1303 helix: 0.86 (0.22), residues: 617 sheet: 0.54 (0.54), residues: 104 loop : -2.26 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 659 HIS 0.003 0.001 HIS E 412 PHE 0.012 0.001 PHE E 966 TYR 0.016 0.001 TYR E 325 ARG 0.002 0.000 ARG E 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 188 time to evaluate : 1.284 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 193 average time/residue: 0.3288 time to fit residues: 87.7991 Evaluate side-chains 190 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 184 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.2248 time to fit residues: 3.9090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 369 GLN ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14485 Z= 0.390 Angle : 0.682 10.380 20190 Z= 0.357 Chirality : 0.043 0.191 2328 Planarity : 0.005 0.069 2034 Dihedral : 18.143 178.870 3394 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 1.53 % Allowed : 27.54 % Favored : 70.93 % 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: -1.00 (0.23), residues: 1303 helix: 0.65 (0.22), residues: 611 sheet: 0.18 (0.55), residues: 97 loop : -2.31 (0.22), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 659 HIS 0.008 0.002 HIS E 328 PHE 0.026 0.002 PHE E 966 TYR 0.018 0.002 TYR E 5 ARG 0.005 0.000 ARG E 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 191 time to evaluate : 1.403 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 202 average time/residue: 0.3315 time to fit residues: 91.6163 Evaluate side-chains 197 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1242 time to fit residues: 3.6177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.4980 chunk 79 optimal weight: 50.0000 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 77 optimal weight: 40.0000 chunk 138 optimal weight: 4.9990 chunk 86 optimal weight: 30.0000 chunk 84 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 85 optimal weight: 20.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 369 GLN ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 14485 Z= 0.415 Angle : 0.705 12.026 20190 Z= 0.370 Chirality : 0.044 0.195 2328 Planarity : 0.005 0.068 2034 Dihedral : 18.223 178.091 3394 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.95 % Allowed : 27.20 % Favored : 70.85 % 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: -1.23 (0.23), residues: 1303 helix: 0.41 (0.22), residues: 611 sheet: 0.18 (0.54), residues: 95 loop : -2.39 (0.22), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 659 HIS 0.008 0.002 HIS E 328 PHE 0.027 0.002 PHE E 966 TYR 0.019 0.002 TYR E 5 ARG 0.005 0.000 ARG E 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 196 time to evaluate : 1.228 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 210 average time/residue: 0.3312 time to fit residues: 95.5518 Evaluate side-chains 204 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 1.413 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.1338 time to fit residues: 5.0016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14485 Z= 0.204 Angle : 0.576 11.677 20190 Z= 0.305 Chirality : 0.038 0.153 2328 Planarity : 0.004 0.062 2034 Dihedral : 17.962 177.995 3394 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.76 % Allowed : 28.05 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.23), residues: 1303 helix: 0.80 (0.22), residues: 610 sheet: 0.08 (0.55), residues: 97 loop : -2.30 (0.22), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 659 HIS 0.005 0.001 HIS E 328 PHE 0.017 0.001 PHE E 966 TYR 0.015 0.001 TYR E 325 ARG 0.003 0.000 ARG E 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 187 time to evaluate : 1.374 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 191 average time/residue: 0.3318 time to fit residues: 87.9135 Evaluate side-chains 191 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 185 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1346 time to fit residues: 3.2078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 56 optimal weight: 0.2980 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 84 optimal weight: 40.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 GLN ** E 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14485 Z= 0.187 Angle : 0.554 11.699 20190 Z= 0.290 Chirality : 0.037 0.157 2328 Planarity : 0.004 0.059 2034 Dihedral : 17.864 178.564 3394 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.59 % Allowed : 28.05 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.23), residues: 1303 helix: 1.03 (0.22), residues: 610 sheet: 0.22 (0.55), residues: 97 loop : -2.25 (0.22), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 659 HIS 0.004 0.001 HIS E 641 PHE 0.015 0.001 PHE E 966 TYR 0.016 0.001 TYR E 325 ARG 0.004 0.000 ARG E 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 185 time to evaluate : 1.393 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 188 average time/residue: 0.3240 time to fit residues: 84.4753 Evaluate side-chains 188 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 185 time to evaluate : 1.392 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1265 time to fit residues: 2.6185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 50.0000 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14485 Z= 0.297 Angle : 0.632 11.862 20190 Z= 0.331 Chirality : 0.040 0.169 2328 Planarity : 0.004 0.062 2034 Dihedral : 17.978 178.366 3394 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.42 % Allowed : 28.56 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.23), residues: 1303 helix: 0.88 (0.22), residues: 611 sheet: 0.16 (0.55), residues: 97 loop : -2.29 (0.22), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 659 HIS 0.006 0.001 HIS E 328 PHE 0.022 0.002 PHE E 966 TYR 0.015 0.002 TYR E 5 ARG 0.005 0.000 ARG E 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 188 time to evaluate : 1.219 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 191 average time/residue: 0.3248 time to fit residues: 86.0666 Evaluate side-chains 192 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 1.411 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1291 time to fit residues: 2.9792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 20.0000 chunk 100 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.176375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.130335 restraints weight = 18583.854| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.27 r_work: 0.3142 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14485 Z= 0.192 Angle : 0.565 11.791 20190 Z= 0.297 Chirality : 0.037 0.151 2328 Planarity : 0.004 0.070 2034 Dihedral : 17.869 178.073 3394 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.17 % Allowed : 28.73 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.23), residues: 1303 helix: 1.03 (0.22), residues: 610 sheet: 0.53 (0.55), residues: 94 loop : -2.26 (0.22), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 659 HIS 0.004 0.001 HIS E 412 PHE 0.016 0.001 PHE E 966 TYR 0.016 0.001 TYR E 325 ARG 0.003 0.000 ARG E 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3081.65 seconds wall clock time: 61 minutes 25.92 seconds (3685.92 seconds total)