Starting phenix.real_space_refine on Sun Apr 7 15:27:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtf_0064/04_2024/6gtf_0064.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtf_0064/04_2024/6gtf_0064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtf_0064/04_2024/6gtf_0064.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtf_0064/04_2024/6gtf_0064.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtf_0064/04_2024/6gtf_0064.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gtf_0064/04_2024/6gtf_0064.pdb" } resolution = 3.63 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= 0.006 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 66 5.49 5 S 17 5.16 5 C 6602 2.51 5 N 1908 2.21 5 O 2278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 740": "NH1" <-> "NH2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A TYR 822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1081": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1185": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10871 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 9496 Classifications: {'peptide': 1280} Incomplete info: {'backbone_only': 239, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 28, 'TRANS': 1251} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1107 Unresolved non-hydrogen angles: 1576 Unresolved non-hydrogen dihedrals: 714 Unresolved non-hydrogen chiralities: 310 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 17, 'TRP:plan': 1, 'ASP:plan': 25, 'PHE:plan': 14, 'GLU:plan': 23, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 545 Chain: "B" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 616 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 10} Link IDs: {'rna2p': 8, 'rna3p': 20} Chain: "C" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 427 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 6.28, per 1000 atoms: 0.58 Number of scatterers: 10871 At special positions: 0 Unit cell: (100.672, 133.12, 103.168, 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 17 16.00 P 66 15.00 O 2278 8.00 N 1908 7.00 C 6602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.79 Conformation dependent library (CDL) restraints added in 1.9 seconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 4 sheets defined 35.9% alpha, 4.1% beta 4 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 removed outlier: 4.069A pdb=" N ARG A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.540A pdb=" N ILE A 65 " --> pdb=" O ILE A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 74 through 89 removed outlier: 3.848A pdb=" N VAL A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 114 removed outlier: 3.705A pdb=" N GLN A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.617A pdb=" N LEU A 122 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 123' Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.895A pdb=" N ASN A 148 " --> pdb=" O GLN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 171 removed outlier: 3.604A pdb=" N ILE A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.738A pdb=" N ARG A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 187 " --> pdb=" O HIS A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 182 through 187' Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.564A pdb=" N LYS A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 313 through 319 removed outlier: 3.744A pdb=" N LYS A 317 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 removed outlier: 4.147A pdb=" N MET A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.903A pdb=" N ASP A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.827A pdb=" N GLU A 419 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 removed outlier: 3.851A pdb=" N GLU A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 4.173A pdb=" N ALA A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 493 removed outlier: 3.503A pdb=" N GLU A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.967A pdb=" N GLN A 507 " --> pdb=" O ILE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 522 Processing helix chain 'A' and resid 523 through 528 removed outlier: 3.629A pdb=" N ASP A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 539 through 544 removed outlier: 4.346A pdb=" N ILE A 542 " --> pdb=" O LYS A 539 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 543 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS A 544 " --> pdb=" O LYS A 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 539 through 544' Processing helix chain 'A' and resid 561 through 572 removed outlier: 3.519A pdb=" N GLU A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 567 " --> pdb=" O LEU A 563 " (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 634 through 638 removed outlier: 3.577A pdb=" N ASN A 638 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 649 removed outlier: 3.503A pdb=" N ILE A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 673 removed outlier: 3.814A pdb=" N PHE A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 683 removed outlier: 3.600A pdb=" N TYR A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 removed outlier: 3.543A pdb=" N LEU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 693 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 728 removed outlier: 5.370A pdb=" N PHE A 720 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN A 726 " --> pdb=" O ASP A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 Processing helix chain 'A' and resid 755 through 760 Processing helix chain 'A' and resid 770 through 779 removed outlier: 3.677A pdb=" N ILE A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 removed outlier: 4.588A pdb=" N PHE A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.257A pdb=" N SER A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 907 removed outlier: 3.964A pdb=" N LEU A 902 " --> pdb=" O ASP A 898 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 954 No H-bonds generated for 'chain 'A' and resid 952 through 954' Processing helix chain 'A' and resid 955 through 962 removed outlier: 3.646A pdb=" N ILE A 960 " --> pdb=" O LYS A 956 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 999 removed outlier: 3.847A pdb=" N MET A 980 " --> pdb=" O ASN A 976 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 981 " --> pdb=" O ILE A 977 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU A 982 " --> pdb=" O LYS A 978 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLN A 987 " --> pdb=" O GLY A 983 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 988 " --> pdb=" O TYR A 984 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 989 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N HIS A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 995 " --> pdb=" O GLU A 991 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 996 " --> pdb=" O ILE A 992 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 997 " --> pdb=" O ALA A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1033 removed outlier: 3.593A pdb=" N LYS A1029 " --> pdb=" O GLN A1025 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1110 removed outlier: 3.710A pdb=" N GLN A1106 " --> pdb=" O VAL A1102 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1181 removed outlier: 3.655A pdb=" N GLU A1175 " --> pdb=" O THR A1171 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS A1176 " --> pdb=" O LYS A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1197 removed outlier: 4.269A pdb=" N ILE A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1212 removed outlier: 3.791A pdb=" N LYS A1206 " --> pdb=" O LYS A1202 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A1207 " --> pdb=" O PHE A1203 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER A1209 " --> pdb=" O ALA A1205 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A1210 " --> pdb=" O LYS A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1275 removed outlier: 4.113A pdb=" N HIS A1261 " --> pdb=" O ASN A1257 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A1262 " --> pdb=" O GLY A1258 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY A1263 " --> pdb=" O ALA A1259 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET A1268 " --> pdb=" O LEU A1264 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A1269 " --> pdb=" O LYS A1265 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN A1275 " --> pdb=" O GLY A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1295 removed outlier: 4.525A pdb=" N GLU A1293 " --> pdb=" O GLU A1289 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A1295 " --> pdb=" O TYR A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing sheet with id=AA1, first strand: chain 'A' and resid 596 through 598 removed outlier: 4.029A pdb=" N PHE A 596 " --> pdb=" O TYR A 832 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU A 830 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 878 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 11.970A pdb=" N ALA A 619 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N TYR A 659 " --> pdb=" O ALA A 619 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU A 621 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 657 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 912 through 913 removed outlier: 6.582A pdb=" N HIS A 912 " --> pdb=" O ILE A1002 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 927 through 928 Processing sheet with id=AA4, first strand: chain 'A' and resid 1125 through 1129 removed outlier: 3.562A pdb=" N ILE A1144 " --> pdb=" O PHE A1126 " (cutoff:3.500A) 198 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 8 hydrogen bonds 12 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2010 1.32 - 1.44: 3170 1.44 - 1.57: 5874 1.57 - 1.69: 129 1.69 - 1.81: 27 Bond restraints: 11210 Sorted by residual: bond pdb=" CB TRP A 808 " pdb=" CG TRP A 808 " ideal model delta sigma weight residual 1.498 1.392 0.106 3.10e-02 1.04e+03 1.17e+01 bond pdb=" CB ARG A 18 " pdb=" CG ARG A 18 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 6.92e+00 bond pdb=" CB PHE A 941 " pdb=" CG PHE A 941 " ideal model delta sigma weight residual 1.502 1.447 0.055 2.30e-02 1.89e+03 5.74e+00 bond pdb=" C1' DC C 4 " pdb=" N1 DC C 4 " ideal model delta sigma weight residual 1.490 1.420 0.070 3.00e-02 1.11e+03 5.44e+00 bond pdb=" CB GLN A 24 " pdb=" CG GLN A 24 " ideal model delta sigma weight residual 1.520 1.451 0.069 3.00e-02 1.11e+03 5.28e+00 ... (remaining 11205 not shown) Histogram of bond angle deviations from ideal: 97.79 - 105.12: 393 105.12 - 112.45: 5110 112.45 - 119.78: 4418 119.78 - 127.11: 5153 127.11 - 134.44: 198 Bond angle restraints: 15272 Sorted by residual: angle pdb=" C GLN A1245 " pdb=" N ALA A1246 " pdb=" CA ALA A1246 " ideal model delta sigma weight residual 120.94 134.44 -13.50 1.90e+00 2.77e-01 5.05e+01 angle pdb=" C GLY A 892 " pdb=" N ALA A 893 " pdb=" CA ALA A 893 " ideal model delta sigma weight residual 122.35 130.65 -8.30 1.46e+00 4.69e-01 3.23e+01 angle pdb=" N PHE A 211 " pdb=" CA PHE A 211 " pdb=" C PHE A 211 " ideal model delta sigma weight residual 114.75 108.13 6.62 1.26e+00 6.30e-01 2.76e+01 angle pdb=" CA GLU A 41 " pdb=" CB GLU A 41 " pdb=" CG GLU A 41 " ideal model delta sigma weight residual 114.10 124.31 -10.21 2.00e+00 2.50e-01 2.61e+01 angle pdb=" N VAL A 253 " pdb=" CA VAL A 253 " pdb=" C VAL A 253 " ideal model delta sigma weight residual 110.05 104.77 5.28 1.09e+00 8.42e-01 2.35e+01 ... (remaining 15267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.78: 5650 18.78 - 37.56: 462 37.56 - 56.34: 186 56.34 - 75.11: 62 75.11 - 93.89: 12 Dihedral angle restraints: 6372 sinusoidal: 3057 harmonic: 3315 Sorted by residual: dihedral pdb=" CA ASP A1227 " pdb=" C ASP A1227 " pdb=" N TYR A1228 " pdb=" CA TYR A1228 " ideal model delta harmonic sigma weight residual 180.00 -147.66 -32.34 0 5.00e+00 4.00e-02 4.18e+01 dihedral pdb=" CA LYS A1084 " pdb=" C LYS A1084 " pdb=" N ILE A1085 " pdb=" CA ILE A1085 " ideal model delta harmonic sigma weight residual -180.00 -148.64 -31.36 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CA ASP A 40 " pdb=" C ASP A 40 " pdb=" N GLU A 41 " pdb=" CA GLU A 41 " ideal model delta harmonic sigma weight residual -180.00 -149.10 -30.90 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 6369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1123 0.069 - 0.138: 342 0.138 - 0.207: 52 0.207 - 0.276: 5 0.276 - 0.344: 3 Chirality restraints: 1525 Sorted by residual: chirality pdb=" C1' U B -16 " pdb=" O4' U B -16 " pdb=" C2' U B -16 " pdb=" N1 U B -16 " both_signs ideal model delta sigma weight residual False 2.47 2.12 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB ILE A 974 " pdb=" CA ILE A 974 " pdb=" CG1 ILE A 974 " pdb=" CG2 ILE A 974 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CG LEU A 914 " pdb=" CB LEU A 914 " pdb=" CD1 LEU A 914 " pdb=" CD2 LEU A 914 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 1522 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 669 " -0.061 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO A 670 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1231 " 0.050 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PRO A1232 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A1232 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1232 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C B -11 " -0.036 2.00e-02 2.50e+03 1.92e-02 8.27e+00 pdb=" N1 C B -11 " 0.042 2.00e-02 2.50e+03 pdb=" C2 C B -11 " 0.007 2.00e-02 2.50e+03 pdb=" O2 C B -11 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C B -11 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C B -11 " -0.010 2.00e-02 2.50e+03 pdb=" N4 C B -11 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C B -11 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C B -11 " 0.006 2.00e-02 2.50e+03 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 211 2.60 - 3.18: 9059 3.18 - 3.75: 16871 3.75 - 4.33: 23040 4.33 - 4.90: 35787 Nonbonded interactions: 84968 Sorted by model distance: nonbonded pdb=" OE2 GLU A 920 " pdb=" OH TYR A1024 " model vdw 2.030 2.440 nonbonded pdb=" OE2 GLU A 594 " pdb=" N LYS A 834 " model vdw 2.101 2.520 nonbonded pdb=" N ALA A 665 " pdb=" OE2 GLU A 758 " model vdw 2.111 2.520 nonbonded pdb=" OP2 A B -18 " pdb=" N4 C B -11 " model vdw 2.121 2.520 nonbonded pdb=" NZ LYS A1221 " pdb=" OD2 ASP A1227 " model vdw 2.186 2.520 ... (remaining 84963 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.460 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 33.750 Find NCS groups from input model: 0.260 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 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 : 0.010 0.106 11210 Z= 0.590 Angle : 1.173 14.437 15272 Z= 0.651 Chirality : 0.065 0.344 1525 Planarity : 0.007 0.092 1810 Dihedral : 17.174 93.892 4392 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.54 % Favored : 84.46 % Rotamer: Outliers : 0.43 % Allowed : 5.17 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -5.84 (0.17), residues: 1274 helix: -4.50 (0.11), residues: 458 sheet: -3.90 (0.40), residues: 106 loop : -3.52 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP A1142 HIS 0.018 0.004 HIS A 881 PHE 0.036 0.004 PHE A 596 TYR 0.046 0.004 TYR A 178 ARG 0.012 0.002 ARG A 833 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 VAL cc_start: 0.7886 (m) cc_final: 0.7560 (m) REVERT: A 112 TYR cc_start: 0.7950 (t80) cc_final: 0.7607 (t80) REVERT: A 118 LYS cc_start: 0.8187 (mttp) cc_final: 0.7930 (mttp) REVERT: A 246 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8532 (pt) REVERT: A 248 TYR cc_start: 0.7795 (m-10) cc_final: 0.7426 (m-10) REVERT: A 642 ASP cc_start: 0.7619 (p0) cc_final: 0.7063 (p0) REVERT: A 667 LYS cc_start: 0.7622 (mtmm) cc_final: 0.7394 (ttmm) REVERT: A 846 LYS cc_start: 0.9096 (mtmp) cc_final: 0.8787 (pttm) REVERT: A 859 LYS cc_start: 0.8988 (mmtt) cc_final: 0.8602 (mmtm) REVERT: A 1218 ARG cc_start: 0.7951 (ttt180) cc_final: 0.6891 (ttp80) REVERT: A 1240 PHE cc_start: 0.7605 (m-10) cc_final: 0.7188 (m-80) outliers start: 4 outliers final: 1 residues processed: 216 average time/residue: 0.3334 time to fit residues: 94.6862 Evaluate side-chains 132 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 862 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 40 optimal weight: 50.0000 chunk 63 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 24 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN A 271 ASN ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 ASN A 694 HIS A 697 HIS A 759 ASN A 779 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS A 843 HIS A 887 ASN A 922 HIS A 942 ASN A 952 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN A1043 ASN ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11210 Z= 0.188 Angle : 0.662 7.039 15272 Z= 0.364 Chirality : 0.044 0.296 1525 Planarity : 0.005 0.069 1810 Dihedral : 19.784 101.334 2208 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 2.59 % Allowed : 11.96 % Favored : 85.45 % 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: -5.01 (0.19), residues: 1274 helix: -3.52 (0.16), residues: 496 sheet: -3.46 (0.42), residues: 106 loop : -3.17 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 175 HIS 0.003 0.001 HIS A1261 PHE 0.013 0.002 PHE A1241 TYR 0.037 0.002 TYR A1099 ARG 0.004 0.000 ARG A1053 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.6265 (ttm110) cc_final: 0.5638 (ttm110) REVERT: A 112 TYR cc_start: 0.8144 (t80) cc_final: 0.7849 (t80) REVERT: A 180 LYS cc_start: 0.6499 (OUTLIER) cc_final: 0.6089 (tttt) REVERT: A 248 TYR cc_start: 0.7599 (m-10) cc_final: 0.7134 (m-10) REVERT: A 321 MET cc_start: 0.4371 (tpp) cc_final: 0.4171 (tpt) REVERT: A 846 LYS cc_start: 0.9064 (mtmp) cc_final: 0.8757 (pttm) REVERT: A 859 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8586 (mmtm) REVERT: A 921 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.6036 (pmm150) REVERT: A 1071 THR cc_start: 0.7844 (t) cc_final: 0.7506 (m) REVERT: A 1218 ARG cc_start: 0.8077 (ttt180) cc_final: 0.7000 (ttp80) REVERT: A 1221 LYS cc_start: 0.6558 (mmtt) cc_final: 0.6219 (tptt) outliers start: 24 outliers final: 11 residues processed: 170 average time/residue: 0.2992 time to fit residues: 68.2039 Evaluate side-chains 134 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1063 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 33 optimal weight: 30.0000 chunk 120 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 107 optimal weight: 0.0010 chunk 119 optimal weight: 3.9990 chunk 41 optimal weight: 50.0000 chunk 97 optimal weight: 7.9990 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 GLN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11210 Z= 0.373 Angle : 0.778 9.091 15272 Z= 0.418 Chirality : 0.049 0.343 1525 Planarity : 0.005 0.071 1810 Dihedral : 19.844 101.827 2206 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.21 % Favored : 85.79 % Rotamer: Outliers : 4.53 % Allowed : 13.36 % Favored : 82.11 % 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: -4.78 (0.20), residues: 1274 helix: -3.09 (0.18), residues: 499 sheet: -3.71 (0.40), residues: 105 loop : -3.18 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 175 HIS 0.010 0.002 HIS A 183 PHE 0.026 0.003 PHE A 888 TYR 0.029 0.003 TYR A1099 ARG 0.005 0.001 ARG A 833 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 124 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6965 (mp0) REVERT: A 859 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8584 (mmtm) REVERT: A 922 HIS cc_start: 0.4527 (OUTLIER) cc_final: 0.4038 (m90) REVERT: A 982 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7914 (mp0) REVERT: A 1130 TYR cc_start: 0.3685 (OUTLIER) cc_final: 0.2399 (m-80) REVERT: A 1218 ARG cc_start: 0.8219 (ttt180) cc_final: 0.7108 (ttp80) REVERT: A 1221 LYS cc_start: 0.6630 (mmtt) cc_final: 0.6304 (tptt) REVERT: A 1270 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7987 (mm) outliers start: 42 outliers final: 28 residues processed: 152 average time/residue: 0.2834 time to fit residues: 58.6617 Evaluate side-chains 144 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 922 HIS Chi-restraints excluded: chain A residue 938 GLN Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 GLN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11210 Z= 0.314 Angle : 0.714 8.065 15272 Z= 0.385 Chirality : 0.048 0.324 1525 Planarity : 0.004 0.058 1810 Dihedral : 19.727 102.500 2206 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer: Outliers : 5.28 % Allowed : 15.52 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.21), residues: 1274 helix: -2.74 (0.19), residues: 506 sheet: -3.70 (0.40), residues: 105 loop : -3.14 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 175 HIS 0.004 0.001 HIS A 697 PHE 0.025 0.002 PHE A 888 TYR 0.028 0.003 TYR A 773 ARG 0.005 0.001 ARG A 833 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 120 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ILE cc_start: 0.8737 (mm) cc_final: 0.8493 (mm) REVERT: A 265 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7079 (mt-10) REVERT: A 859 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8364 (tmtt) REVERT: A 982 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7992 (mp0) REVERT: A 1071 THR cc_start: 0.7957 (t) cc_final: 0.7547 (m) REVERT: A 1130 TYR cc_start: 0.3754 (OUTLIER) cc_final: 0.2476 (m-80) REVERT: A 1218 ARG cc_start: 0.8083 (ttt180) cc_final: 0.6835 (ttp80) REVERT: A 1270 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7945 (mm) outliers start: 49 outliers final: 34 residues processed: 155 average time/residue: 0.2573 time to fit residues: 55.2759 Evaluate side-chains 147 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 916 ILE Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 938 GLN Chi-restraints excluded: chain A residue 947 ASP Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1227 ASP Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 53 optimal weight: 0.0970 chunk 109 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11210 Z= 0.207 Angle : 0.621 8.091 15272 Z= 0.339 Chirality : 0.044 0.271 1525 Planarity : 0.004 0.060 1810 Dihedral : 19.498 99.420 2206 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 4.85 % Allowed : 17.78 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.21), residues: 1274 helix: -2.46 (0.20), residues: 511 sheet: -3.63 (0.41), residues: 103 loop : -3.01 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 175 HIS 0.003 0.001 HIS A 697 PHE 0.024 0.002 PHE A 888 TYR 0.027 0.002 TYR A 773 ARG 0.003 0.000 ARG A 833 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 120 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 TYR cc_start: 0.7057 (p90) cc_final: 0.6324 (p90) REVERT: A 265 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6811 (mt-10) REVERT: A 859 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8572 (mmtm) REVERT: A 982 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7765 (mp0) REVERT: A 1071 THR cc_start: 0.7933 (t) cc_final: 0.7557 (m) REVERT: A 1130 TYR cc_start: 0.3583 (OUTLIER) cc_final: 0.2549 (m-80) REVERT: A 1198 GLU cc_start: 0.8410 (tp30) cc_final: 0.8155 (tp30) REVERT: A 1270 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7932 (mm) outliers start: 45 outliers final: 31 residues processed: 151 average time/residue: 0.2580 time to fit residues: 53.8540 Evaluate side-chains 144 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 819 ASP Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1227 ASP Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 50.0000 chunk 115 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 106 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 40.0000 chunk 67 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 HIS A 938 GLN ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 11210 Z= 0.393 Angle : 0.767 9.170 15272 Z= 0.414 Chirality : 0.050 0.336 1525 Planarity : 0.005 0.068 1810 Dihedral : 19.669 104.865 2206 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 26.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Rotamer: Outliers : 5.50 % Allowed : 18.75 % Favored : 75.75 % 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: -4.32 (0.21), residues: 1274 helix: -2.36 (0.20), residues: 505 sheet: -3.85 (0.39), residues: 103 loop : -3.16 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 175 HIS 0.006 0.002 HIS A1261 PHE 0.027 0.002 PHE A1128 TYR 0.029 0.003 TYR A 773 ARG 0.005 0.001 ARG A 833 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 115 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6907 (mp0) REVERT: A 638 ASN cc_start: 0.8496 (p0) cc_final: 0.8257 (p0) REVERT: A 859 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8457 (tmtt) REVERT: A 982 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8127 (mp0) REVERT: A 1099 TYR cc_start: 0.3406 (OUTLIER) cc_final: 0.2308 (t80) REVERT: A 1108 PHE cc_start: 0.8137 (m-10) cc_final: 0.7757 (m-10) REVERT: A 1130 TYR cc_start: 0.3752 (OUTLIER) cc_final: 0.2517 (m-80) REVERT: A 1198 GLU cc_start: 0.8445 (tp30) cc_final: 0.7876 (tm-30) REVERT: A 1270 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7844 (mm) outliers start: 51 outliers final: 38 residues processed: 150 average time/residue: 0.2616 time to fit residues: 54.7455 Evaluate side-chains 153 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 112 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 SER Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 938 GLN Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1099 TYR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1227 ASP Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11210 Z= 0.179 Angle : 0.609 8.283 15272 Z= 0.333 Chirality : 0.043 0.258 1525 Planarity : 0.003 0.050 1810 Dihedral : 19.303 95.072 2206 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 4.31 % Allowed : 20.58 % Favored : 75.11 % 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: -3.83 (0.22), residues: 1274 helix: -1.94 (0.22), residues: 502 sheet: -3.44 (0.42), residues: 103 loop : -2.92 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 175 HIS 0.003 0.001 HIS A 697 PHE 0.022 0.001 PHE A 888 TYR 0.028 0.002 TYR A1099 ARG 0.004 0.000 ARG A 746 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6638 (mt-10) REVERT: A 834 LYS cc_start: 0.7733 (mtmt) cc_final: 0.7523 (mtmm) REVERT: A 859 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8569 (mmtm) REVERT: A 925 TYR cc_start: 0.7680 (t80) cc_final: 0.7198 (t80) REVERT: A 935 ILE cc_start: 0.5841 (OUTLIER) cc_final: 0.5629 (pt) REVERT: A 982 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7881 (mp0) REVERT: A 1071 THR cc_start: 0.7819 (t) cc_final: 0.7426 (m) REVERT: A 1099 TYR cc_start: 0.3582 (OUTLIER) cc_final: 0.2385 (t80) REVERT: A 1198 GLU cc_start: 0.8383 (tp30) cc_final: 0.8142 (tp30) REVERT: A 1270 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7868 (mm) outliers start: 40 outliers final: 31 residues processed: 151 average time/residue: 0.2627 time to fit residues: 54.7930 Evaluate side-chains 146 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 944 ILE Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1099 TYR Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1227 ASP Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 38 optimal weight: 50.0000 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN ** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 GLN ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 GLN ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 11210 Z= 0.411 Angle : 0.796 9.379 15272 Z= 0.429 Chirality : 0.050 0.335 1525 Planarity : 0.005 0.057 1810 Dihedral : 19.551 102.463 2206 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 27.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.84 % Favored : 85.16 % Rotamer: Outliers : 5.50 % Allowed : 20.58 % Favored : 73.92 % 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: -4.08 (0.21), residues: 1274 helix: -2.09 (0.21), residues: 503 sheet: -3.69 (0.41), residues: 104 loop : -3.10 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 141 HIS 0.007 0.002 HIS A1261 PHE 0.025 0.003 PHE A 888 TYR 0.029 0.003 TYR A1099 ARG 0.008 0.001 ARG A 964 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 116 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 GLU cc_start: 0.7241 (mm-30) cc_final: 0.7007 (mt-10) REVERT: A 594 GLU cc_start: 0.7034 (pm20) cc_final: 0.6816 (mm-30) REVERT: A 638 ASN cc_start: 0.8527 (p0) cc_final: 0.8326 (p0) REVERT: A 834 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7321 (mtmm) REVERT: A 859 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8528 (tmtt) REVERT: A 982 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8191 (mp0) REVERT: A 1071 THR cc_start: 0.8056 (t) cc_final: 0.7597 (m) REVERT: A 1099 TYR cc_start: 0.3477 (OUTLIER) cc_final: 0.2403 (t80) REVERT: A 1198 GLU cc_start: 0.8451 (tp30) cc_final: 0.7890 (tm-30) REVERT: A 1270 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7748 (mm) outliers start: 51 outliers final: 44 residues processed: 150 average time/residue: 0.2668 time to fit residues: 55.8546 Evaluate side-chains 154 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 108 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 938 GLN Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1099 TYR Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1227 ASP Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 93 optimal weight: 0.0770 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN A 617 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11210 Z= 0.172 Angle : 0.616 8.611 15272 Z= 0.339 Chirality : 0.043 0.243 1525 Planarity : 0.004 0.043 1810 Dihedral : 19.153 93.080 2206 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.02 % Allowed : 22.41 % Favored : 74.57 % 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: -3.55 (0.22), residues: 1274 helix: -1.61 (0.23), residues: 494 sheet: -3.36 (0.43), residues: 103 loop : -2.83 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP A 141 HIS 0.005 0.001 HIS A 58 PHE 0.022 0.002 PHE A 888 TYR 0.033 0.002 TYR A1099 ARG 0.006 0.001 ARG A 746 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.7555 (t0) cc_final: 0.7295 (t0) REVERT: A 265 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6530 (mt-10) REVERT: A 773 TYR cc_start: 0.8851 (t80) cc_final: 0.8546 (t80) REVERT: A 859 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8577 (mmtm) REVERT: A 982 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7960 (mp0) REVERT: A 1071 THR cc_start: 0.7793 (t) cc_final: 0.7383 (m) REVERT: A 1099 TYR cc_start: 0.3364 (OUTLIER) cc_final: 0.2503 (t80) REVERT: A 1198 GLU cc_start: 0.8396 (tp30) cc_final: 0.7816 (tm-30) REVERT: A 1270 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7849 (mm) outliers start: 28 outliers final: 24 residues processed: 138 average time/residue: 0.2742 time to fit residues: 51.9405 Evaluate side-chains 138 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 1000 ASN Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1099 TYR Chi-restraints excluded: chain A residue 1185 TYR Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1227 ASP Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 121 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 0.0270 chunk 83 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11210 Z= 0.167 Angle : 0.600 9.921 15272 Z= 0.324 Chirality : 0.042 0.232 1525 Planarity : 0.004 0.036 1810 Dihedral : 18.977 88.899 2206 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.37 % Allowed : 23.38 % Favored : 74.25 % 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: -3.31 (0.22), residues: 1274 helix: -1.40 (0.24), residues: 488 sheet: -3.00 (0.46), residues: 101 loop : -2.73 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 141 HIS 0.004 0.001 HIS A 58 PHE 0.022 0.001 PHE A 888 TYR 0.033 0.002 TYR A1099 ARG 0.004 0.000 ARG A 746 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.7621 (t0) cc_final: 0.7385 (t0) REVERT: A 773 TYR cc_start: 0.8851 (t80) cc_final: 0.8516 (t80) REVERT: A 859 LYS cc_start: 0.8897 (mmtt) cc_final: 0.8629 (mmtm) REVERT: A 918 ARG cc_start: 0.5791 (mmt-90) cc_final: 0.3597 (ttp-170) REVERT: A 925 TYR cc_start: 0.7696 (t80) cc_final: 0.7245 (t80) REVERT: A 982 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7906 (mp0) REVERT: A 1099 TYR cc_start: 0.3454 (OUTLIER) cc_final: 0.2734 (t80) REVERT: A 1198 GLU cc_start: 0.8388 (tp30) cc_final: 0.7799 (tm-30) REVERT: A 1270 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7828 (mm) outliers start: 22 outliers final: 17 residues processed: 128 average time/residue: 0.2593 time to fit residues: 46.0185 Evaluate side-chains 128 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 667 LYS Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 921 ARG Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1099 TYR Chi-restraints excluded: chain A residue 1221 LYS Chi-restraints excluded: chain A residue 1227 ASP Chi-restraints excluded: chain A residue 1241 PHE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1286 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 29 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 40.0000 chunk 108 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.2980 chunk 92 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.154615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.121641 restraints weight = 24704.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.125642 restraints weight = 11895.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.128201 restraints weight = 7410.054| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11210 Z= 0.167 Angle : 0.588 10.167 15272 Z= 0.318 Chirality : 0.042 0.236 1525 Planarity : 0.003 0.035 1810 Dihedral : 18.862 87.709 2206 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.59 % Allowed : 23.49 % Favored : 73.92 % 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: -3.17 (0.23), residues: 1274 helix: -1.30 (0.24), residues: 488 sheet: -3.04 (0.45), residues: 105 loop : -2.61 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP A 141 HIS 0.005 0.001 HIS A1261 PHE 0.021 0.001 PHE A 888 TYR 0.045 0.002 TYR A 112 ARG 0.004 0.000 ARG A 746 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2230.70 seconds wall clock time: 41 minutes 51.23 seconds (2511.23 seconds total)