Starting phenix.real_space_refine on Sat Dec 9 22:11:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtg_0065/12_2023/6gtg_0065.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtg_0065/12_2023/6gtg_0065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtg_0065/12_2023/6gtg_0065.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtg_0065/12_2023/6gtg_0065.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtg_0065/12_2023/6gtg_0065.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtg_0065/12_2023/6gtg_0065.pdb" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 91 5.49 5 Mg 4 5.21 5 S 21 5.16 5 C 7709 2.51 5 N 2100 2.21 5 O 2613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 43": "NH1" <-> "NH2" Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1166": "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: 12538 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1298, 10633 Classifications: {'peptide': 1298} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 28, 'TRANS': 1269} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 872 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 18, 'rna3p_pyr': 15} Link IDs: {'rna2p': 8, 'rna3p': 32} Chain: "C" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 374 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.41, per 1000 atoms: 0.59 Number of scatterers: 12538 At special positions: 0 Unit cell: (103.168, 131.456, 102.336, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 91 15.00 Mg 4 11.99 O 2613 8.00 N 2100 7.00 C 7709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.12 Conformation dependent library (CDL) restraints added in 2.0 seconds 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 8 sheets defined 38.1% alpha, 5.4% beta 18 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 4.73 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 74 through 85 removed outlier: 3.980A pdb=" N ASN A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 110 removed outlier: 3.738A pdb=" N ILE A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.775A pdb=" N PHE A 119 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS A 120 " --> pdb=" O GLU A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 120' Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.552A pdb=" N LYS A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 removed outlier: 3.732A pdb=" N ILE A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.555A pdb=" N LYS A 180 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.642A pdb=" N ILE A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.241A pdb=" N ASN A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 236 through 240 removed outlier: 4.120A pdb=" N ALA A 239 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU A 240 " --> pdb=" O ASP A 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 236 through 240' Processing helix chain 'A' and resid 265 through 272 removed outlier: 4.154A pdb=" N ASN A 270 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 304 through 312 removed outlier: 4.627A pdb=" N GLN A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 311 " --> pdb=" O TYR A 307 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 319 removed outlier: 3.548A pdb=" N LYS A 318 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR A 319 " --> pdb=" O LEU A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 319' Processing helix chain 'A' and resid 344 through 349 removed outlier: 4.299A pdb=" N VAL A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 344 through 349' Processing helix chain 'A' and resid 350 through 360 removed outlier: 3.777A pdb=" N TYR A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.836A pdb=" N THR A 373 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 374 " --> pdb=" O LYS A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 374' Processing helix chain 'A' and resid 397 through 407 removed outlier: 3.514A pdb=" N GLN A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 removed outlier: 3.540A pdb=" N VAL A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 464 removed outlier: 3.759A pdb=" N LEU A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA A 459 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.142A pdb=" N ILE A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE A 482 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 516 through 520 removed outlier: 3.504A pdb=" N GLU A 520 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 535 removed outlier: 3.545A pdb=" N LEU A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 539 Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.732A pdb=" N PHE A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 4.080A pdb=" N TYR A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 642 through 648 removed outlier: 3.510A pdb=" N ILE A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 673 removed outlier: 3.527A pdb=" N LEU A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Proline residue: A 670 - end of helix Processing helix chain 'A' and resid 678 through 683 removed outlier: 4.013A pdb=" N TYR A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.963A pdb=" N ASN A 693 " --> pdb=" O LEU A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 723 removed outlier: 4.513A pdb=" N ASP A 722 " --> pdb=" O ARG A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 759 removed outlier: 4.172A pdb=" N GLU A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 758 " --> pdb=" O TYR A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 779 Processing helix chain 'A' and resid 888 through 891 removed outlier: 4.362A pdb=" N SER A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 888 through 891' Processing helix chain 'A' and resid 895 through 907 removed outlier: 3.931A pdb=" N GLU A 899 " --> pdb=" O LYS A 895 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 971 removed outlier: 3.759A pdb=" N SER A 966 " --> pdb=" O LYS A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 999 removed outlier: 3.877A pdb=" N GLN A 987 " --> pdb=" O GLY A 983 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 997 " --> pdb=" O ALA A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1016 removed outlier: 4.462A pdb=" N GLY A1015 " --> pdb=" O GLY A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1019 No H-bonds generated for 'chain 'A' and resid 1017 through 1019' Processing helix chain 'A' and resid 1025 through 1033 removed outlier: 3.541A pdb=" N GLU A1033 " --> pdb=" O LYS A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1109 removed outlier: 3.550A pdb=" N GLN A1106 " --> pdb=" O VAL A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 4.115A pdb=" N ASN A1132 " --> pdb=" O ASP A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1181 removed outlier: 3.538A pdb=" N LEU A1174 " --> pdb=" O PRO A1170 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS A1176 " --> pdb=" O LYS A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1198 removed outlier: 3.917A pdb=" N ILE A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A1198 " --> pdb=" O ALA A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1215 removed outlier: 4.456A pdb=" N THR A1208 " --> pdb=" O PHE A1204 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER A1209 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR A1213 " --> pdb=" O SER A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1246 removed outlier: 3.626A pdb=" N ALA A1246 " --> pdb=" O SER A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1266 removed outlier: 3.508A pdb=" N GLY A1258 " --> pdb=" O ALA A1254 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A1259 " --> pdb=" O ASP A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1275 removed outlier: 3.519A pdb=" N ASN A1275 " --> pdb=" O GLY A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1297 removed outlier: 3.605A pdb=" N GLN A1296 " --> pdb=" O PHE A1292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.764A pdb=" N PHE A 596 " --> pdb=" O TYR A 832 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 4.020A pdb=" N LYS A 823 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 23 removed outlier: 4.772A pdb=" N TYR A 628 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 655 through 661 Processing sheet with id=AA5, first strand: chain 'A' and resid 915 through 916 removed outlier: 3.548A pdb=" N ILE A 916 " --> pdb=" O VAL A1004 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN A1006 " --> pdb=" O ILE A 916 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 925 through 927 removed outlier: 3.829A pdb=" N ASP A 939 " --> pdb=" O TYR A 926 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 943 through 944 removed outlier: 3.590A pdb=" N THR A 951 " --> pdb=" O ILE A 944 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1116 through 1117 235 hydrogen bonds defined for protein. 639 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 5.12 Time building geometry restraints manager: 6.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2387 1.33 - 1.45: 3612 1.45 - 1.57: 6761 1.57 - 1.69: 179 1.69 - 1.81: 33 Bond restraints: 12972 Sorted by residual: bond pdb=" C LEU A 669 " pdb=" N PRO A 670 " ideal model delta sigma weight residual 1.334 1.362 -0.028 8.40e-03 1.42e+04 1.13e+01 bond pdb=" C ILE A 485 " pdb=" N PRO A 486 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.42e+00 bond pdb=" CB ASP A 917 " pdb=" CG ASP A 917 " ideal model delta sigma weight residual 1.516 1.453 0.063 2.50e-02 1.60e+03 6.40e+00 bond pdb=" CB ASP A1046 " pdb=" CG ASP A1046 " ideal model delta sigma weight residual 1.516 1.578 -0.062 2.50e-02 1.60e+03 6.21e+00 bond pdb=" CD LYS A 981 " pdb=" CE LYS A 981 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.44e+00 ... (remaining 12967 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.10: 506 105.10 - 112.34: 6145 112.34 - 119.58: 4912 119.58 - 126.83: 5975 126.83 - 134.07: 326 Bond angle restraints: 17864 Sorted by residual: angle pdb=" N ILE A 575 " pdb=" CA ILE A 575 " pdb=" C ILE A 575 " ideal model delta sigma weight residual 112.29 106.36 5.93 9.40e-01 1.13e+00 3.97e+01 angle pdb=" C LEU A1151 " pdb=" N ILE A1152 " pdb=" CA ILE A1152 " ideal model delta sigma weight residual 121.97 131.45 -9.48 1.80e+00 3.09e-01 2.78e+01 angle pdb=" C PHE A1045 " pdb=" N ASP A1046 " pdb=" CA ASP A1046 " ideal model delta sigma weight residual 124.82 134.07 -9.25 1.78e+00 3.16e-01 2.70e+01 angle pdb=" N VAL A 821 " pdb=" CA VAL A 821 " pdb=" C VAL A 821 " ideal model delta sigma weight residual 112.96 107.89 5.07 1.00e+00 1.00e+00 2.57e+01 angle pdb=" N ILE A 728 " pdb=" CA ILE A 728 " pdb=" C ILE A 728 " ideal model delta sigma weight residual 113.39 106.99 6.40 1.47e+00 4.63e-01 1.89e+01 ... (remaining 17859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 6919 17.77 - 35.53: 499 35.53 - 53.30: 211 53.30 - 71.06: 61 71.06 - 88.83: 15 Dihedral angle restraints: 7705 sinusoidal: 3851 harmonic: 3854 Sorted by residual: dihedral pdb=" CA ASP A 313 " pdb=" C ASP A 313 " pdb=" N LYS A 314 " pdb=" CA LYS A 314 " ideal model delta harmonic sigma weight residual -180.00 -147.48 -32.52 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA LYS A1047 " pdb=" C LYS A1047 " pdb=" N THR A1048 " pdb=" CA THR A1048 " ideal model delta harmonic sigma weight residual -180.00 -152.65 -27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA LEU A 537 " pdb=" C LEU A 537 " pdb=" N HIS A 538 " pdb=" CA HIS A 538 " ideal model delta harmonic sigma weight residual 180.00 153.97 26.03 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 7702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1282 0.052 - 0.104: 546 0.104 - 0.155: 108 0.155 - 0.207: 18 0.207 - 0.259: 6 Chirality restraints: 1960 Sorted by residual: chirality pdb=" CB ILE A 545 " pdb=" CA ILE A 545 " pdb=" CG1 ILE A 545 " pdb=" CG2 ILE A 545 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CG LEU A1008 " pdb=" CB LEU A1008 " pdb=" CD1 LEU A1008 " pdb=" CD2 LEU A1008 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB ILE A1191 " pdb=" CA ILE A1191 " pdb=" CG1 ILE A1191 " pdb=" CG2 ILE A1191 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1957 not shown) Planarity restraints: 1969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 178 " 0.028 2.00e-02 2.50e+03 2.08e-02 8.65e+00 pdb=" CG TYR A 178 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR A 178 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 178 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 178 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 178 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 178 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 178 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 669 " -0.048 5.00e-02 4.00e+02 7.26e-02 8.42e+00 pdb=" N PRO A 670 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 225 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.78e+00 pdb=" N PRO A 226 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 226 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 226 " -0.040 5.00e-02 4.00e+02 ... (remaining 1966 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 181 2.62 - 3.19: 10365 3.19 - 3.76: 19620 3.76 - 4.33: 28663 4.33 - 4.90: 44599 Nonbonded interactions: 103428 Sorted by model distance: nonbonded pdb=" O2' C B 20 " pdb=" O3' A B 21 " model vdw 2.051 2.440 nonbonded pdb=" O ARG A 800 " pdb="MG MG A1401 " model vdw 2.141 2.170 nonbonded pdb=" N7 A B -12 " pdb="MG MG B 101 " model vdw 2.177 2.250 nonbonded pdb=" O PHE A 941 " pdb=" OH TYR A 984 " model vdw 2.192 2.440 nonbonded pdb=" OH TYR A 822 " pdb=" O VAL A1051 " model vdw 2.274 2.440 ... (remaining 103423 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: 1.210 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: 0.040 Extract box with map and model: 3.720 Check model and map are aligned: 0.200 Set scattering table: 0.170 Process input model: 42.490 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 : 0.009 0.075 12972 Z= 0.535 Angle : 1.069 14.251 17864 Z= 0.579 Chirality : 0.058 0.259 1960 Planarity : 0.007 0.073 1969 Dihedral : 15.733 88.828 5215 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.51 % Favored : 85.49 % Rotamer: Outliers : 0.69 % Allowed : 6.57 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.96 (0.16), residues: 1296 helix: -4.71 (0.09), residues: 486 sheet: -2.84 (0.52), residues: 82 loop : -3.66 (0.18), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP A1142 HIS 0.018 0.004 HIS A 881 PHE 0.035 0.003 PHE A 258 TYR 0.050 0.004 TYR A 178 ARG 0.014 0.002 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 282 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 290 average time/residue: 0.2956 time to fit residues: 118.4776 Evaluate side-chains 173 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1203 time to fit residues: 2.4653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN A 148 ASN A 183 HIS A 185 ASN A 268 ASN A 291 ASN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN A 538 HIS A 638 ASN A 693 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 ASN A1043 ASN ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1156 ASN ** A1187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1249 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12972 Z= 0.188 Angle : 0.628 8.924 17864 Z= 0.348 Chirality : 0.040 0.177 1960 Planarity : 0.005 0.066 1969 Dihedral : 17.269 89.207 2501 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 2.25 % Allowed : 13.14 % Favored : 84.62 % 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: -4.98 (0.18), residues: 1296 helix: -3.54 (0.16), residues: 504 sheet: -2.44 (0.52), residues: 87 loop : -3.32 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 141 HIS 0.006 0.001 HIS A1161 PHE 0.022 0.002 PHE A 681 TYR 0.023 0.002 TYR A 659 ARG 0.004 0.001 ARG A 918 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 210 average time/residue: 0.2565 time to fit residues: 78.1450 Evaluate side-chains 170 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 1.440 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1203 time to fit residues: 5.1684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 124 optimal weight: 0.4980 chunk 134 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN A 464 ASN A 693 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12972 Z= 0.186 Angle : 0.588 8.107 17864 Z= 0.324 Chirality : 0.039 0.181 1960 Planarity : 0.004 0.068 1969 Dihedral : 16.987 88.822 2501 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 1.73 % Allowed : 14.26 % Favored : 84.01 % 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: -4.55 (0.19), residues: 1296 helix: -2.99 (0.18), residues: 530 sheet: -2.22 (0.51), residues: 87 loop : -3.20 (0.20), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 141 HIS 0.006 0.001 HIS A1161 PHE 0.011 0.001 PHE A1109 TYR 0.021 0.002 TYR A1228 ARG 0.003 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 186 average time/residue: 0.2748 time to fit residues: 73.6887 Evaluate side-chains 156 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1282 time to fit residues: 4.0420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 83 optimal weight: 0.0270 chunk 125 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 580 ASN A 602 ASN A 683 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 GLN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12972 Z= 0.331 Angle : 0.663 9.330 17864 Z= 0.359 Chirality : 0.043 0.206 1960 Planarity : 0.004 0.063 1969 Dihedral : 17.146 87.303 2501 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.81 % Favored : 87.19 % Rotamer: Outliers : 3.11 % Allowed : 14.17 % Favored : 82.71 % 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: -4.35 (0.20), residues: 1296 helix: -2.80 (0.19), residues: 532 sheet: -2.28 (0.50), residues: 88 loop : -3.09 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 808 HIS 0.008 0.002 HIS A1161 PHE 0.019 0.002 PHE A 888 TYR 0.022 0.002 TYR A 178 ARG 0.004 0.001 ARG A1298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 167 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 24 residues processed: 183 average time/residue: 0.2694 time to fit residues: 71.2457 Evaluate side-chains 168 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.395 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1331 time to fit residues: 7.6808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 118 optimal weight: 0.0070 chunk 33 optimal weight: 0.9980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 24 GLN A 602 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12972 Z= 0.178 Angle : 0.565 7.787 17864 Z= 0.312 Chirality : 0.039 0.171 1960 Planarity : 0.004 0.063 1969 Dihedral : 16.686 87.452 2501 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.16 % Allowed : 14.78 % Favored : 83.06 % 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: -4.00 (0.21), residues: 1296 helix: -2.44 (0.20), residues: 523 sheet: -2.10 (0.52), residues: 90 loop : -2.96 (0.21), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 141 HIS 0.005 0.001 HIS A1161 PHE 0.018 0.001 PHE A1010 TYR 0.025 0.002 TYR A 112 ARG 0.002 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.393 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 174 average time/residue: 0.2851 time to fit residues: 72.4851 Evaluate side-chains 146 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 1.381 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1302 time to fit residues: 4.4661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 50.0000 chunk 69 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12972 Z= 0.354 Angle : 0.672 9.593 17864 Z= 0.364 Chirality : 0.045 0.240 1960 Planarity : 0.004 0.062 1969 Dihedral : 17.077 86.471 2501 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer: Outliers : 2.07 % Allowed : 16.34 % Favored : 81.59 % 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: -4.05 (0.21), residues: 1296 helix: -2.48 (0.20), residues: 524 sheet: -2.14 (0.53), residues: 88 loop : -2.99 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP A 141 HIS 0.007 0.002 HIS A1161 PHE 0.020 0.002 PHE A 596 TYR 0.023 0.002 TYR A 178 ARG 0.003 0.001 ARG A1298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 169 average time/residue: 0.2763 time to fit residues: 67.4465 Evaluate side-chains 152 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 1.438 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1431 time to fit residues: 5.0430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 ASN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12972 Z= 0.188 Angle : 0.575 7.942 17864 Z= 0.317 Chirality : 0.040 0.179 1960 Planarity : 0.004 0.055 1969 Dihedral : 16.686 87.378 2501 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 0.78 % Allowed : 18.32 % Favored : 80.90 % 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: -3.78 (0.21), residues: 1296 helix: -2.18 (0.21), residues: 510 sheet: -2.01 (0.54), residues: 90 loop : -2.90 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 141 HIS 0.005 0.001 HIS A1161 PHE 0.024 0.001 PHE A1010 TYR 0.026 0.002 TYR A 112 ARG 0.006 0.000 ARG A1166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 153 average time/residue: 0.2537 time to fit residues: 57.2813 Evaluate side-chains 138 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.344 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1185 time to fit residues: 2.0931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12972 Z= 0.236 Angle : 0.591 7.906 17864 Z= 0.324 Chirality : 0.041 0.232 1960 Planarity : 0.004 0.069 1969 Dihedral : 16.711 86.036 2501 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 1.12 % Allowed : 18.93 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.22), residues: 1296 helix: -2.00 (0.22), residues: 505 sheet: -1.86 (0.55), residues: 88 loop : -2.82 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 141 HIS 0.005 0.001 HIS A1161 PHE 0.020 0.002 PHE A1010 TYR 0.022 0.002 TYR A 112 ARG 0.006 0.001 ARG A1166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 151 average time/residue: 0.2528 time to fit residues: 56.3024 Evaluate side-chains 150 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.436 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1286 time to fit residues: 4.6633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 ASN ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12972 Z= 0.291 Angle : 0.632 9.817 17864 Z= 0.342 Chirality : 0.043 0.207 1960 Planarity : 0.004 0.069 1969 Dihedral : 16.853 86.011 2501 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 0.95 % Allowed : 18.50 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.22), residues: 1296 helix: -1.97 (0.22), residues: 501 sheet: -1.93 (0.54), residues: 90 loop : -2.83 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 141 HIS 0.006 0.001 HIS A1161 PHE 0.021 0.002 PHE A1010 TYR 0.028 0.002 TYR A 112 ARG 0.005 0.001 ARG A1166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 153 average time/residue: 0.2728 time to fit residues: 60.9024 Evaluate side-chains 146 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 1.347 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1230 time to fit residues: 3.3424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 6.9990 chunk 79 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN A 404 GLN A 599 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12972 Z= 0.179 Angle : 0.569 8.558 17864 Z= 0.311 Chirality : 0.040 0.175 1960 Planarity : 0.004 0.067 1969 Dihedral : 16.512 86.225 2501 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 0.35 % Allowed : 19.27 % Favored : 80.38 % 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: -3.47 (0.22), residues: 1296 helix: -1.85 (0.22), residues: 502 sheet: -1.81 (0.55), residues: 89 loop : -2.79 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 141 HIS 0.006 0.001 HIS A 843 PHE 0.021 0.001 PHE A1010 TYR 0.025 0.002 TYR A 112 ARG 0.006 0.000 ARG A1166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 152 average time/residue: 0.2533 time to fit residues: 56.7684 Evaluate side-chains 136 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1215 time to fit residues: 2.2790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.0470 chunk 33 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN A 404 GLN A 464 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.188469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.151007 restraints weight = 13915.154| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.24 r_work: 0.3585 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12972 Z= 0.167 Angle : 0.550 7.026 17864 Z= 0.302 Chirality : 0.039 0.171 1960 Planarity : 0.004 0.070 1969 Dihedral : 16.401 83.964 2501 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 0.52 % Allowed : 19.53 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.22), residues: 1296 helix: -1.50 (0.23), residues: 488 sheet: -1.52 (0.56), residues: 86 loop : -2.78 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 141 HIS 0.004 0.001 HIS A1161 PHE 0.018 0.001 PHE A 362 TYR 0.025 0.001 TYR A 112 ARG 0.005 0.000 ARG A1166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2644.77 seconds wall clock time: 52 minutes 51.88 seconds (3171.88 seconds total)