Starting phenix.real_space_refine on Sat Dec 9 18:20:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0z_0585/12_2023/6o0z_0585.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0z_0585/12_2023/6o0z_0585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0z_0585/12_2023/6o0z_0585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0z_0585/12_2023/6o0z_0585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0z_0585/12_2023/6o0z_0585.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o0z_0585/12_2023/6o0z_0585.pdb" } resolution = 3.3 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= 0.043 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 134 5.49 5 S 15 5.16 5 C 7080 2.51 5 N 2132 2.21 5 O 2551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 70": "NH1" <-> "NH2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 353": "OD1" <-> "OD2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A ARG 467": "NH1" <-> "NH2" Residue "A ASP 483": "OD1" <-> "OD2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A GLU 746": "OE1" <-> "OE2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A ARG 967": "NH1" <-> "NH2" Residue "A GLU 977": "OE1" <-> "OE2" Residue "A ARG 1078": "NH1" <-> "NH2" Residue "A ARG 1084": "NH1" <-> "NH2" Residue "A GLU 1150": "OE1" <-> "OE2" Residue "A ARG 1210": "NH1" <-> "NH2" Residue "A ARG 1279": "NH1" <-> "NH2" Residue "A ARG 1298": "NH1" <-> "NH2" 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: 11912 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9063 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 1288, 9063 Classifications: {'peptide': 1288} Incomplete info: {'truncation_to_alanine': 391} Link IDs: {'PTRANS': 34, 'TRANS': 1253} Chain breaks: 11 Unresolved non-hydrogen bonds: 1545 Unresolved non-hydrogen angles: 1919 Unresolved non-hydrogen dihedrals: 1252 Unresolved non-hydrogen chiralities: 106 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 3, 'TYR:plan': 12, 'ASN:plan1': 32, 'TRP:plan': 1, 'ASP:plan': 45, 'PHE:plan': 16, 'GLU:plan': 61, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 883 Chain: "B" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 2058 Classifications: {'RNA': 96} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 34} Link IDs: {'rna2p': 11, 'rna3p': 84} Chain: "C" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 563 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 228 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Time building chain proxies: 7.52, per 1000 atoms: 0.63 Number of scatterers: 11912 At special positions: 0 Unit cell: (140.448, 127.072, 98.648, 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 15 16.00 P 134 15.00 O 2551 8.00 N 2132 7.00 C 7080 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: 5.75 Conformation dependent library (CDL) restraints added in 1.9 seconds 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 7 sheets defined 52.7% alpha, 6.3% beta 49 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 4.98 Creating SS restraints... Processing helix chain 'A' and resid 59 through 86 Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.960A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 4.018A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.608A pdb=" N PHE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 removed outlier: 3.592A pdb=" N ILE A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLN A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'A' and resid 269 through 281 removed outlier: 4.594A pdb=" N ASP A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 315 through 342 removed outlier: 3.557A pdb=" N ALA A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.520A pdb=" N ILE A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.352A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.628A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.572A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.618A pdb=" N VAL A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.676A pdb=" N SER A 487 " --> pdb=" O ASP A 483 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 543 through 556 removed outlier: 4.275A pdb=" N ALA A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 573 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 605 through 609 removed outlier: 3.524A pdb=" N ASP A 608 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN A 609 " --> pdb=" O PHE A 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 605 through 609' Processing helix chain 'A' and resid 610 through 626 removed outlier: 4.013A pdb=" N ASP A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 621 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 638 Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 678 through 685 removed outlier: 3.602A pdb=" N SER A 685 " --> pdb=" O ASP A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 703 through 711 removed outlier: 3.690A pdb=" N ASP A 707 " --> pdb=" O THR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.798A pdb=" N ASN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.545A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 792 removed outlier: 3.562A pdb=" N GLY A 792 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 817 removed outlier: 3.974A pdb=" N TYR A 812 " --> pdb=" O ASN A 808 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR A 814 " --> pdb=" O LYS A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 872 through 879 Processing helix chain 'A' and resid 881 through 889 Processing helix chain 'A' and resid 893 through 902 Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' Processing helix chain 'A' and resid 909 through 922 Processing helix chain 'A' and resid 925 through 940 removed outlier: 3.857A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 removed outlier: 4.131A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.870A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 3.747A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 removed outlier: 3.690A pdb=" N PHE A1181 " --> pdb=" O ASN A1177 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A1186 " --> pdb=" O LEU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 4.029A pdb=" N ILE A1195 " --> pdb=" O LYS A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 removed outlier: 3.592A pdb=" N HIS A1241 " --> pdb=" O TYR A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1261 Processing helix chain 'A' and resid 1264 through 1280 removed outlier: 3.906A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1302 through 1312 removed outlier: 4.172A pdb=" N GLU A1307 " --> pdb=" O ARG A1303 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN A1308 " --> pdb=" O GLU A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1315 No H-bonds generated for 'chain 'A' and resid 1313 through 1315' Processing helix chain 'A' and resid 1341 through 1344 Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.201A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A1095 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.251A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 839 through 840 Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.760A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 122 hydrogen bonds 240 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 7.21 Time building geometry restraints manager: 6.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2133 1.33 - 1.45: 3597 1.45 - 1.57: 6375 1.57 - 1.69: 266 1.69 - 1.81: 28 Bond restraints: 12399 Sorted by residual: bond pdb=" C LEU A1198 " pdb=" O LEU A1198 " ideal model delta sigma weight residual 1.249 1.236 0.013 8.50e-03 1.38e+04 2.41e+00 bond pdb=" O5' DC C 20 " pdb=" C5' DC C 20 " ideal model delta sigma weight residual 1.423 1.379 0.044 3.00e-02 1.11e+03 2.11e+00 bond pdb=" CG LYS A1334 " pdb=" CD LYS A1334 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" C1' DC C 20 " pdb=" N1 DC C 20 " ideal model delta sigma weight residual 1.490 1.527 -0.037 3.00e-02 1.11e+03 1.49e+00 bond pdb=" C ILE A1110 " pdb=" N LEU A1111 " ideal model delta sigma weight residual 1.339 1.273 0.067 5.57e-02 3.22e+02 1.44e+00 ... (remaining 12394 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.51: 989 106.51 - 113.43: 6988 113.43 - 120.34: 4753 120.34 - 127.26: 4393 127.26 - 134.17: 348 Bond angle restraints: 17471 Sorted by residual: angle pdb=" C3' A B 68 " pdb=" O3' A B 68 " pdb=" P A B 69 " ideal model delta sigma weight residual 120.20 126.75 -6.55 1.50e+00 4.44e-01 1.90e+01 angle pdb=" C LYS A 862 " pdb=" N ASN A 863 " pdb=" CA ASN A 863 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" O3' A B 68 " pdb=" C3' A B 68 " pdb=" C2' A B 68 " ideal model delta sigma weight residual 113.70 119.68 -5.98 1.50e+00 4.44e-01 1.59e+01 angle pdb=" CA LYS A1334 " pdb=" CB LYS A1334 " pdb=" CG LYS A1334 " ideal model delta sigma weight residual 114.10 107.11 6.99 2.00e+00 2.50e-01 1.22e+01 angle pdb=" C3' A B 42 " pdb=" O3' A B 42 " pdb=" P G B 43 " ideal model delta sigma weight residual 120.20 125.37 -5.17 1.50e+00 4.44e-01 1.19e+01 ... (remaining 17466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.56: 6915 34.56 - 69.13: 358 69.13 - 103.69: 27 103.69 - 138.25: 0 138.25 - 172.81: 3 Dihedral angle restraints: 7303 sinusoidal: 3526 harmonic: 3777 Sorted by residual: dihedral pdb=" O4' C B 70 " pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sinusoidal sigma weight residual 200.00 43.08 156.92 1 1.50e+01 4.44e-03 8.19e+01 dihedral pdb=" CA ASP A 861 " pdb=" C ASP A 861 " pdb=" N LYS A 862 " pdb=" CA LYS A 862 " ideal model delta harmonic sigma weight residual 180.00 157.81 22.19 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA SER A1040 " pdb=" C SER A1040 " pdb=" N ASN A1041 " pdb=" CA ASN A1041 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 7300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1835 0.062 - 0.123: 261 0.123 - 0.185: 28 0.185 - 0.247: 2 0.247 - 0.309: 2 Chirality restraints: 2128 Sorted by residual: chirality pdb=" C3' A B 42 " pdb=" C4' A B 42 " pdb=" O3' A B 42 " pdb=" C2' A B 42 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C3' A B 38 " pdb=" C4' A B 38 " pdb=" O3' A B 38 " pdb=" C2' A B 38 " both_signs ideal model delta sigma weight residual False -2.48 -2.22 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL A1149 " pdb=" CA VAL A1149 " pdb=" CG1 VAL A1149 " pdb=" CG2 VAL A1149 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.10e-01 ... (remaining 2125 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 474 " -0.035 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 475 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 475 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 475 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1228 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO A1229 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A1229 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1229 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1342 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C VAL A1342 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A1342 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A1343 " -0.011 2.00e-02 2.50e+03 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3643 2.82 - 3.34: 9736 3.34 - 3.86: 20451 3.86 - 4.38: 21925 4.38 - 4.90: 35065 Nonbonded interactions: 90820 Sorted by model distance: nonbonded pdb=" OG SER A 469 " pdb=" OE1 GLU A 471 " model vdw 2.302 2.440 nonbonded pdb=" O TYR A 521 " pdb=" OG1 THR A 525 " model vdw 2.308 2.440 nonbonded pdb=" O LYS A 141 " pdb=" OG SER A 145 " model vdw 2.328 2.440 nonbonded pdb=" OG SER A1109 " pdb=" OP2 DG C 11 " model vdw 2.334 2.440 nonbonded pdb=" N2 G B 73 " pdb=" OP2 A B 76 " model vdw 2.337 2.520 ... (remaining 90815 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=0.49 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: 1.490 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: 6.490 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 42.880 Find NCS groups from input model: 0.300 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: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 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 : 0.006 0.067 12399 Z= 0.364 Angle : 0.716 8.255 17471 Z= 0.395 Chirality : 0.044 0.309 2128 Planarity : 0.005 0.052 1752 Dihedral : 18.491 172.814 4843 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.27 % Allowed : 8.34 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.18), residues: 1264 helix: -2.68 (0.15), residues: 608 sheet: -0.72 (0.46), residues: 127 loop : -3.20 (0.21), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A 167 PHE 0.016 0.002 PHE A1324 TYR 0.014 0.002 TYR A 325 ARG 0.005 0.000 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 1.287 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 0.2827 time to fit residues: 29.1098 Evaluate side-chains 51 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 1.107 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1153 time to fit residues: 1.6712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 113 HIS ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 420 HIS A 426 GLN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN A1272 GLN ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12399 Z= 0.238 Angle : 0.500 6.133 17471 Z= 0.275 Chirality : 0.036 0.168 2128 Planarity : 0.004 0.059 1752 Dihedral : 19.149 171.856 3133 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.09 % Allowed : 11.08 % Favored : 87.82 % 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: -2.25 (0.22), residues: 1264 helix: -0.61 (0.20), residues: 624 sheet: -0.46 (0.47), residues: 127 loop : -2.88 (0.23), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1074 HIS 0.003 0.001 HIS A 160 PHE 0.018 0.001 PHE A 518 TYR 0.010 0.001 TYR A 325 ARG 0.007 0.000 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 1.278 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.2082 time to fit residues: 20.9501 Evaluate side-chains 53 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1079 time to fit residues: 2.5564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 0.0770 chunk 35 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 overall best weight: 2.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS A 990 ASN ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12399 Z= 0.238 Angle : 0.492 6.281 17471 Z= 0.267 Chirality : 0.036 0.159 2128 Planarity : 0.003 0.057 1752 Dihedral : 19.079 173.795 3133 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.82 % Allowed : 14.36 % Favored : 84.82 % 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: -1.22 (0.24), residues: 1264 helix: 0.46 (0.22), residues: 614 sheet: -0.57 (0.47), residues: 136 loop : -2.51 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1074 HIS 0.003 0.001 HIS A 160 PHE 0.009 0.001 PHE A 432 TYR 0.010 0.001 TYR A 325 ARG 0.003 0.000 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 1.212 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 0.2112 time to fit residues: 19.1453 Evaluate side-chains 51 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 1.185 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1114 time to fit residues: 1.9621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 10.0000 chunk 95 optimal weight: 30.0000 chunk 66 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 60 optimal weight: 0.0570 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 112 optimal weight: 0.0570 overall best weight: 2.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12399 Z= 0.205 Angle : 0.472 6.026 17471 Z= 0.256 Chirality : 0.035 0.155 2128 Planarity : 0.003 0.056 1752 Dihedral : 19.027 173.912 3133 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.96 % Allowed : 15.60 % Favored : 83.45 % 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: -0.74 (0.24), residues: 1264 helix: 0.92 (0.22), residues: 616 sheet: -0.42 (0.47), residues: 137 loop : -2.35 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1074 HIS 0.003 0.001 HIS A 160 PHE 0.018 0.001 PHE A 518 TYR 0.012 0.001 TYR A 271 ARG 0.002 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 1.257 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.2220 time to fit residues: 20.7430 Evaluate side-chains 52 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1061 time to fit residues: 2.2766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 100 optimal weight: 0.0270 chunk 55 optimal weight: 30.0000 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 34 optimal weight: 0.0970 chunk 45 optimal weight: 5.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN A 990 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12399 Z= 0.133 Angle : 0.443 6.052 17471 Z= 0.240 Chirality : 0.034 0.145 2128 Planarity : 0.003 0.053 1752 Dihedral : 18.918 173.108 3133 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.09 % Allowed : 16.01 % Favored : 82.90 % 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: -0.38 (0.25), residues: 1264 helix: 1.23 (0.22), residues: 616 sheet: -0.20 (0.48), residues: 135 loop : -2.20 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1074 HIS 0.002 0.000 HIS A 160 PHE 0.011 0.001 PHE A 432 TYR 0.010 0.001 TYR A 271 ARG 0.001 0.000 ARG A1078 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 1.187 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 0.2038 time to fit residues: 20.4222 Evaluate side-chains 55 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 1.350 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1167 time to fit residues: 2.5290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 8.9990 chunk 26 optimal weight: 30.0000 chunk 79 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 GLN ** A1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.077 12399 Z= 0.621 Angle : 0.700 7.897 17471 Z= 0.369 Chirality : 0.043 0.187 2128 Planarity : 0.004 0.059 1752 Dihedral : 19.282 178.170 3133 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.92 % Allowed : 16.01 % Favored : 82.08 % 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: -0.79 (0.24), residues: 1264 helix: 0.88 (0.22), residues: 614 sheet: -0.50 (0.47), residues: 138 loop : -2.35 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1074 HIS 0.005 0.001 HIS A 167 PHE 0.020 0.002 PHE A 518 TYR 0.018 0.002 TYR A 325 ARG 0.003 0.001 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 1.261 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 61 average time/residue: 0.2046 time to fit residues: 20.5683 Evaluate side-chains 53 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1070 time to fit residues: 3.0787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.9980 chunk 77 optimal weight: 50.0000 chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 114 optimal weight: 0.9980 chunk 75 optimal weight: 40.0000 chunk 134 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 82 optimal weight: 50.0000 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12399 Z= 0.320 Angle : 0.542 7.302 17471 Z= 0.290 Chirality : 0.038 0.165 2128 Planarity : 0.003 0.057 1752 Dihedral : 19.138 177.360 3133 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.82 % Allowed : 17.24 % Favored : 81.94 % 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: -0.48 (0.24), residues: 1264 helix: 1.16 (0.22), residues: 616 sheet: -0.43 (0.47), residues: 138 loop : -2.22 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1074 HIS 0.004 0.001 HIS A 160 PHE 0.010 0.001 PHE A1174 TYR 0.012 0.001 TYR A 325 ARG 0.001 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 1.233 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.2102 time to fit residues: 18.4065 Evaluate side-chains 55 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1011 time to fit residues: 2.3651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 30.0000 chunk 80 optimal weight: 40.0000 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 40.0000 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 122 optimal weight: 0.0270 chunk 129 optimal weight: 5.9990 overall best weight: 1.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12399 Z= 0.187 Angle : 0.478 6.782 17471 Z= 0.258 Chirality : 0.036 0.155 2128 Planarity : 0.003 0.053 1752 Dihedral : 19.024 175.446 3133 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.27 % Allowed : 18.19 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1264 helix: 1.48 (0.22), residues: 617 sheet: -0.26 (0.48), residues: 137 loop : -2.11 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 476 HIS 0.003 0.001 HIS A 160 PHE 0.010 0.001 PHE A1174 TYR 0.010 0.001 TYR A 155 ARG 0.001 0.000 ARG A 938 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 1.252 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 0.2555 time to fit residues: 22.8312 Evaluate side-chains 50 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1157 time to fit residues: 1.7992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.0030 chunk 125 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 75 optimal weight: 50.0000 chunk 54 optimal weight: 50.0000 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 82 optimal weight: 50.0000 chunk 132 optimal weight: 6.9990 overall best weight: 3.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12399 Z= 0.377 Angle : 0.572 8.784 17471 Z= 0.304 Chirality : 0.039 0.168 2128 Planarity : 0.003 0.057 1752 Dihedral : 19.116 177.488 3133 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.55 % Allowed : 17.92 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1264 helix: 1.34 (0.22), residues: 617 sheet: -0.36 (0.48), residues: 138 loop : -2.10 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1074 HIS 0.003 0.001 HIS A 167 PHE 0.025 0.001 PHE A 518 TYR 0.013 0.001 TYR A 325 ARG 0.002 0.000 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 1.188 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 53 average time/residue: 0.2159 time to fit residues: 18.7339 Evaluate side-chains 48 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1062 time to fit residues: 1.6870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 30.0000 chunk 63 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 68 optimal weight: 0.4980 chunk 88 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12399 Z= 0.181 Angle : 0.485 7.997 17471 Z= 0.260 Chirality : 0.036 0.155 2128 Planarity : 0.003 0.054 1752 Dihedral : 19.000 176.008 3133 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.14 % Allowed : 18.06 % Favored : 81.81 % 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: 0.00 (0.25), residues: 1264 helix: 1.56 (0.22), residues: 617 sheet: -0.22 (0.48), residues: 137 loop : -1.98 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1074 HIS 0.003 0.001 HIS A 160 PHE 0.010 0.001 PHE A1174 TYR 0.010 0.001 TYR A 155 ARG 0.001 0.000 ARG A1078 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 1.066 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.2274 time to fit residues: 19.3948 Evaluate side-chains 49 residues out of total 1163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.252 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 20 optimal weight: 50.0000 chunk 97 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.088185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.059820 restraints weight = 36426.810| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.92 r_work: 0.2779 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12399 Z= 0.140 Angle : 0.464 8.843 17471 Z= 0.248 Chirality : 0.035 0.146 2128 Planarity : 0.003 0.053 1752 Dihedral : 18.917 174.843 3133 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.27 % Allowed : 18.19 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1264 helix: 1.72 (0.22), residues: 618 sheet: -0.02 (0.49), residues: 135 loop : -1.88 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1074 HIS 0.002 0.000 HIS A 723 PHE 0.011 0.001 PHE A1327 TYR 0.008 0.001 TYR A 155 ARG 0.001 0.000 ARG A1078 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2090.77 seconds wall clock time: 38 minutes 57.48 seconds (2337.48 seconds total)