Starting phenix.real_space_refine on Wed Feb 21 06:54:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eec_9041/02_2024/6eec_9041_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eec_9041/02_2024/6eec_9041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eec_9041/02_2024/6eec_9041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eec_9041/02_2024/6eec_9041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eec_9041/02_2024/6eec_9041_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eec_9041/02_2024/6eec_9041_neut_trim_updated.pdb" } resolution = 3.55 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= 0.006 sd= 0.103 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 128 5.49 5 Mg 1 5.21 5 S 99 5.16 5 C 18335 2.51 5 N 5337 2.21 5 O 5994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 144": "NH1" <-> "NH2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ARG 467": "NH1" <-> "NH2" Residue "C ARG 482": "NH1" <-> "NH2" Residue "C ARG 791": "NH1" <-> "NH2" Residue "C ARG 855": "NH1" <-> "NH2" Residue "C ARG 925": "NH1" <-> "NH2" Residue "C ARG 1067": "NH1" <-> "NH2" Residue "D PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 572": "NH1" <-> "NH2" Residue "D ASP 660": "OD1" <-> "OD2" Residue "D ARG 841": "NH1" <-> "NH2" Residue "D ARG 876": "NH1" <-> "NH2" Residue "D ARG 940": "NH1" <-> "NH2" Residue "D PHE 1061": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 213": "NH1" <-> "NH2" Residue "F ARG 229": "NH1" <-> "NH2" Residue "F ARG 278": "NH1" <-> "NH2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F ARG 418": "NH1" <-> "NH2" Residue "F ARG 500": "NH1" <-> "NH2" Residue "F ARG 524": "NH1" <-> "NH2" Residue "J ARG 109": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29896 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1759 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 220} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 8593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8593 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 9873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 9873 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 57, 'TRANS': 1204} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2518 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 310} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 881 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1336 Classifications: {'DNA': 65} Link IDs: {'rna3p': 64} Chain: "P" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1289 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain breaks: 1 Chain: "M" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 153} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'C0L': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19132 SG CYS D 891 108.225 61.944 83.263 1.00 76.82 S ATOM 19699 SG CYS D 968 104.599 62.438 85.049 1.00 78.10 S ATOM 19741 SG CYS D 975 105.542 63.855 82.129 1.00 73.35 S ATOM 19759 SG CYS D 978 105.701 60.556 81.261 1.00 75.60 S ATOM 12574 SG CYS D 60 79.742 106.887 124.743 1.00 98.08 S ATOM 12592 SG CYS D 62 78.833 107.222 128.102 1.00 98.16 S ATOM 12727 SG CYS D 78 80.787 104.199 127.363 1.00 91.64 S Time building chain proxies: 15.43, per 1000 atoms: 0.52 Number of scatterers: 29896 At special positions: 0 Unit cell: (131.3, 180.7, 191.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 99 16.00 P 128 15.00 Mg 1 11.99 O 5994 8.00 N 5337 7.00 C 18335 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: 13.38 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " Number of angles added : 6 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 114 helices and 32 sheets defined 36.8% alpha, 9.2% beta 56 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 14.11 Creating SS restraints... Processing helix chain 'A' and resid 31 through 42 Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.617A pdb=" N SER A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 204 through 224 removed outlier: 3.908A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 45 removed outlier: 3.725A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 4.025A pdb=" N SER B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.595A pdb=" N ALA B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 65 removed outlier: 4.305A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 77 removed outlier: 3.694A pdb=" N ALA C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 119 through 125 Processing helix chain 'C' and resid 234 through 240 Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.862A pdb=" N ASP C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 310 through 319 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 381 through 406 removed outlier: 4.077A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 417 No H-bonds generated for 'chain 'C' and resid 414 through 417' Processing helix chain 'C' and resid 421 through 431 Processing helix chain 'C' and resid 445 through 451 Processing helix chain 'C' and resid 470 through 473 No H-bonds generated for 'chain 'C' and resid 470 through 473' Processing helix chain 'C' and resid 535 through 538 No H-bonds generated for 'chain 'C' and resid 535 through 538' Processing helix chain 'C' and resid 591 through 593 No H-bonds generated for 'chain 'C' and resid 591 through 593' Processing helix chain 'C' and resid 597 through 599 No H-bonds generated for 'chain 'C' and resid 597 through 599' Processing helix chain 'C' and resid 602 through 611 Processing helix chain 'C' and resid 630 through 636 removed outlier: 4.222A pdb=" N ALA C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 743 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 923 through 925 No H-bonds generated for 'chain 'C' and resid 923 through 925' Processing helix chain 'C' and resid 929 through 942 Processing helix chain 'C' and resid 955 through 957 No H-bonds generated for 'chain 'C' and resid 955 through 957' Processing helix chain 'C' and resid 982 through 990 Processing helix chain 'C' and resid 1037 through 1039 No H-bonds generated for 'chain 'C' and resid 1037 through 1039' Processing helix chain 'C' and resid 1070 through 1078 Processing helix chain 'C' and resid 1083 through 1090 Processing helix chain 'C' and resid 1096 through 1108 removed outlier: 4.274A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1119 through 1131 Processing helix chain 'D' and resid 17 through 23 removed outlier: 3.911A pdb=" N GLN D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 removed outlier: 4.238A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 186 removed outlier: 4.685A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 227 Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 258 through 266 Processing helix chain 'D' and resid 270 through 283 Processing helix chain 'D' and resid 286 through 304 removed outlier: 3.757A pdb=" N LEU D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 322 through 325 Processing helix chain 'D' and resid 340 through 360 Processing helix chain 'D' and resid 364 through 382 Processing helix chain 'D' and resid 394 through 396 No H-bonds generated for 'chain 'D' and resid 394 through 396' Processing helix chain 'D' and resid 402 through 405 No H-bonds generated for 'chain 'D' and resid 402 through 405' Processing helix chain 'D' and resid 445 through 462 removed outlier: 4.251A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS D 453 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Proline residue: D 454 - end of helix Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'D' and resid 481 through 491 removed outlier: 3.642A pdb=" N GLU D 488 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 532 No H-bonds generated for 'chain 'D' and resid 529 through 532' Processing helix chain 'D' and resid 549 through 557 Processing helix chain 'D' and resid 579 through 589 removed outlier: 3.835A pdb=" N THR D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 623 Processing helix chain 'D' and resid 644 through 650 Processing helix chain 'D' and resid 657 through 659 No H-bonds generated for 'chain 'D' and resid 657 through 659' Processing helix chain 'D' and resid 668 through 676 Processing helix chain 'D' and resid 690 through 703 Processing helix chain 'D' and resid 706 through 727 removed outlier: 3.760A pdb=" N GLN D 711 " --> pdb=" O ILE D 707 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 761 Processing helix chain 'D' and resid 767 through 792 Processing helix chain 'D' and resid 798 through 804 removed outlier: 4.107A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 817 Processing helix chain 'D' and resid 846 through 880 removed outlier: 3.862A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR D 872 " --> pdb=" O ALA D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 916 No H-bonds generated for 'chain 'D' and resid 914 through 916' Processing helix chain 'D' and resid 946 through 955 Processing helix chain 'D' and resid 995 through 1009 Proline residue: D1006 - end of helix removed outlier: 5.100A pdb=" N GLN D1009 " --> pdb=" O GLU D1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1036 Processing helix chain 'D' and resid 1118 through 1144 Proline residue: D1127 - end of helix removed outlier: 3.872A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1163 removed outlier: 3.820A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG D1163 " --> pdb=" O ARG D1159 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1194 Processing helix chain 'D' and resid 1210 through 1215 Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 4.436A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1229 through 1239 Processing helix chain 'D' and resid 1265 through 1268 No H-bonds generated for 'chain 'D' and resid 1265 through 1268' Processing helix chain 'D' and resid 1276 through 1281 Processing helix chain 'E' and resid 34 through 36 No H-bonds generated for 'chain 'E' and resid 34 through 36' Processing helix chain 'E' and resid 40 through 43 No H-bonds generated for 'chain 'E' and resid 40 through 43' Processing helix chain 'E' and resid 50 through 71 Processing helix chain 'E' and resid 91 through 101 Processing helix chain 'F' and resid 211 through 218 removed outlier: 3.804A pdb=" N ALA F 215 " --> pdb=" O ALA F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 237 removed outlier: 4.233A pdb=" N LYS F 237 " --> pdb=" O LYS F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 265 Processing helix chain 'F' and resid 275 through 309 removed outlier: 5.377A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG F 309 " --> pdb=" O SER F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 334 Processing helix chain 'F' and resid 343 through 361 removed outlier: 4.690A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 390 Processing helix chain 'F' and resid 396 through 403 Processing helix chain 'F' and resid 407 through 416 removed outlier: 4.109A pdb=" N LEU F 411 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU F 412 " --> pdb=" O GLU F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 438 Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 469 through 479 Processing helix chain 'F' and resid 489 through 496 Processing helix chain 'F' and resid 500 through 514 Processing helix chain 'F' and resid 524 through 526 No H-bonds generated for 'chain 'F' and resid 524 through 526' Processing helix chain 'J' and resid 81 through 88 removed outlier: 3.880A pdb=" N ARG J 88 " --> pdb=" O MET J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 109 Processing helix chain 'M' and resid 51 through 56 removed outlier: 4.470A pdb=" N GLU M 54 " --> pdb=" O GLU M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 74 Processing helix chain 'M' and resid 85 through 98 Processing helix chain 'M' and resid 101 through 117 removed outlier: 3.525A pdb=" N GLU M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 142 Processing helix chain 'M' and resid 147 through 159 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 13 Processing sheet with id= B, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.084A pdb=" N SER A 53 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.759A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 47 through 49 Processing sheet with id= E, first strand: chain 'B' and resid 53 through 55 Processing sheet with id= F, first strand: chain 'B' and resid 93 through 100 removed outlier: 4.002A pdb=" N VAL B 93 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 99 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 134 " --> pdb=" O LYS B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.746A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 171 through 175 removed outlier: 6.847A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 103 through 106 Processing sheet with id= J, first strand: chain 'C' and resid 110 through 112 removed outlier: 4.066A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 166 through 168 Processing sheet with id= L, first strand: chain 'C' and resid 178 through 181 Processing sheet with id= M, first strand: chain 'C' and resid 184 through 192 removed outlier: 3.882A pdb=" N ASP C 188 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 454 through 456 Processing sheet with id= O, first strand: chain 'C' and resid 528 through 531 Processing sheet with id= P, first strand: chain 'C' and resid 558 through 562 Processing sheet with id= Q, first strand: chain 'C' and resid 667 through 671 removed outlier: 3.531A pdb=" N GLU C 652 " --> pdb=" O THR C 659 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N MET C 661 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE C 650 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 716 through 722 removed outlier: 3.716A pdb=" N LEU C 719 " --> pdb=" O MET C1028 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 886 " --> pdb=" O MET C1031 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 885 " --> pdb=" O GLY C 893 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 806 through 808 Processing sheet with id= T, first strand: chain 'C' and resid 642 through 644 removed outlier: 5.632A pdb=" N ALA C 644 " --> pdb=" O VAL C 701 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL C 701 " --> pdb=" O ALA C 644 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 735 through 737 removed outlier: 7.272A pdb=" N LEU C 737 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE C 898 " --> pdb=" O LEU C 737 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 748 through 760 removed outlier: 3.720A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 93 through 96 Processing sheet with id= X, first strand: chain 'D' and resid 233 through 235 removed outlier: 4.297A pdb=" N GLN D 233 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 427 through 429 Processing sheet with id= Z, first strand: chain 'D' and resid 430 through 432 removed outlier: 6.187A pdb=" N ILE D 522 " --> pdb=" O VAL D 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'D' and resid 495 through 497 Processing sheet with id= AB, first strand: chain 'D' and resid 633 through 637 removed outlier: 3.550A pdb=" N VAL D 635 " --> pdb=" O ALA D 664 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA D 664 " --> pdb=" O VAL D 635 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.321A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 27 through 33 Processing sheet with id= AE, first strand: chain 'J' and resid 53 through 55 Processing sheet with id= AF, first strand: chain 'M' and resid 9 through 11 removed outlier: 7.000A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE M 22 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TYR M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N THR M 24 " --> pdb=" O LYS M 32 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LYS M 32 " --> pdb=" O THR M 24 " (cutoff:3.500A) 950 hydrogen bonds defined for protein. 2742 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 145 hydrogen bonds 290 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 12.43 Time building geometry restraints manager: 13.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 4909 1.27 - 1.41: 7366 1.41 - 1.54: 17933 1.54 - 1.67: 278 1.67 - 1.81: 175 Bond restraints: 30661 Sorted by residual: bond pdb=" C23 C0L C1201 " pdb=" O24 C0L C1201 " ideal model delta sigma weight residual 1.204 1.390 -0.186 2.00e-02 2.50e+03 8.61e+01 bond pdb=" CA TRP D 656 " pdb=" C TRP D 656 " ideal model delta sigma weight residual 1.524 1.412 0.112 1.26e-02 6.30e+03 7.84e+01 bond pdb=" CA ARG D 389 " pdb=" C ARG D 389 " ideal model delta sigma weight residual 1.523 1.430 0.093 1.06e-02 8.90e+03 7.64e+01 bond pdb=" CA ALA D 661 " pdb=" C ALA D 661 " ideal model delta sigma weight residual 1.521 1.414 0.107 1.24e-02 6.50e+03 7.51e+01 bond pdb=" CA SER F 305 " pdb=" C SER F 305 " ideal model delta sigma weight residual 1.523 1.412 0.111 1.30e-02 5.92e+03 7.34e+01 ... (remaining 30656 not shown) Histogram of bond angle deviations from ideal: 93.21 - 102.66: 333 102.66 - 112.11: 16723 112.11 - 121.56: 18053 121.56 - 131.01: 6859 131.01 - 140.46: 108 Bond angle restraints: 42076 Sorted by residual: angle pdb=" C LEU F 306 " pdb=" N ALA F 307 " pdb=" CA ALA F 307 " ideal model delta sigma weight residual 120.63 103.71 16.92 1.61e+00 3.86e-01 1.10e+02 angle pdb=" N ASP C 307 " pdb=" CA ASP C 307 " pdb=" C ASP C 307 " ideal model delta sigma weight residual 110.06 122.75 -12.69 1.43e+00 4.89e-01 7.87e+01 angle pdb=" N THR C 288 " pdb=" CA THR C 288 " pdb=" C THR C 288 " ideal model delta sigma weight residual 108.02 93.21 14.81 1.75e+00 3.27e-01 7.16e+01 angle pdb=" N LEU C 281 " pdb=" CA LEU C 281 " pdb=" C LEU C 281 " ideal model delta sigma weight residual 111.36 102.21 9.15 1.09e+00 8.42e-01 7.05e+01 angle pdb=" N VAL F 448 " pdb=" CA VAL F 448 " pdb=" C VAL F 448 " ideal model delta sigma weight residual 112.96 105.13 7.83 1.00e+00 1.00e+00 6.13e+01 ... (remaining 42071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 17712 35.53 - 71.07: 660 71.07 - 106.60: 17 106.60 - 142.14: 3 142.14 - 177.67: 8 Dihedral angle restraints: 18400 sinusoidal: 8352 harmonic: 10048 Sorted by residual: dihedral pdb=" CA PRO C 975 " pdb=" C PRO C 975 " pdb=" N VAL C 976 " pdb=" CA VAL C 976 " ideal model delta harmonic sigma weight residual 180.00 -150.89 -29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LYS C 229 " pdb=" C LYS C 229 " pdb=" N ARG C 230 " pdb=" CA ARG C 230 " ideal model delta harmonic sigma weight residual 180.00 150.96 29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" C GLN D 657 " pdb=" N GLN D 657 " pdb=" CA GLN D 657 " pdb=" CB GLN D 657 " ideal model delta harmonic sigma weight residual -122.60 -136.69 14.09 0 2.50e+00 1.60e-01 3.17e+01 ... (remaining 18397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 4755 0.149 - 0.297: 27 0.297 - 0.446: 4 0.446 - 0.594: 1 0.594 - 0.743: 2 Chirality restraints: 4789 Sorted by residual: chirality pdb=" CA GLN D 657 " pdb=" N GLN D 657 " pdb=" C GLN D 657 " pdb=" CB GLN D 657 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CA ASP D 660 " pdb=" N ASP D 660 " pdb=" C ASP D 660 " pdb=" CB ASP D 660 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA ASN D 384 " pdb=" N ASN D 384 " pdb=" C ASN D 384 " pdb=" CB ASN D 384 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.55e+00 ... (remaining 4786 not shown) Planarity restraints: 5084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 274 " -0.019 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C LEU C 274 " 0.069 2.00e-02 2.50e+03 pdb=" O LEU C 274 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU C 275 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN D 657 " 0.065 5.00e-02 4.00e+02 9.57e-02 1.47e+01 pdb=" N PRO D 658 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 658 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 658 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 396 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" CG ASN D 396 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN D 396 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN D 396 " -0.021 2.00e-02 2.50e+03 ... (remaining 5081 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 222 2.44 - 3.06: 22911 3.06 - 3.67: 46380 3.67 - 4.29: 68177 4.29 - 4.90: 108683 Nonbonded interactions: 246373 Sorted by model distance: nonbonded pdb=" O ALA C 273 " pdb=" N ASP C 276 " model vdw 1.828 2.520 nonbonded pdb=" OD2 ASP D 383 " pdb=" NE ARG D 386 " model vdw 1.857 2.520 nonbonded pdb=" N GLU C 466 " pdb=" OE1 GLU C 466 " model vdw 1.865 2.520 nonbonded pdb=" O THR C 294 " pdb=" OD1 ASN C 298 " model vdw 1.906 3.040 nonbonded pdb=" O ASP C 271 " pdb=" CD1 LEU C 275 " model vdw 1.913 3.460 ... (remaining 246368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 or (resid 186 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 2 \ 23 or (resid 224 and (name N or name CA or name C or name O or name CB )) or res \ id 225 through 226)) selection = (chain 'B' and resid 2 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 5.260 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 94.540 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 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 : 0.011 0.186 30661 Z= 0.683 Angle : 1.024 22.031 42076 Z= 0.582 Chirality : 0.054 0.743 4789 Planarity : 0.006 0.096 5084 Dihedral : 16.058 177.673 11936 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 36.23 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.64 % Favored : 88.07 % Rotamer: Outliers : 0.55 % Allowed : 3.70 % Favored : 95.75 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % 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: -3.74 (0.12), residues: 3488 helix: -1.43 (0.12), residues: 1361 sheet: -3.58 (0.22), residues: 394 loop : -3.13 (0.13), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP F 283 HIS 0.015 0.002 HIS D 494 PHE 0.040 0.003 PHE C 187 TYR 0.046 0.003 TYR E 56 ARG 0.014 0.001 ARG D 506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 470 time to evaluate : 3.298 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 177 LYS cc_start: 0.8879 (pttt) cc_final: 0.8650 (ptmm) REVERT: B 177 LYS cc_start: 0.9071 (ptpp) cc_final: 0.8760 (ptpp) REVERT: B 195 ASP cc_start: 0.7732 (t0) cc_final: 0.7247 (t70) REVERT: B 226 ASN cc_start: 0.8686 (t160) cc_final: 0.8482 (t0) REVERT: C 258 MET cc_start: 0.8465 (mmm) cc_final: 0.8075 (mmt) REVERT: C 271 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8490 (t70) REVERT: C 293 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: C 355 MET cc_start: 0.8068 (tmm) cc_final: 0.7616 (tmm) REVERT: C 393 MET cc_start: 0.8938 (mmt) cc_final: 0.8649 (mmt) REVERT: C 394 SER cc_start: 0.9123 (m) cc_final: 0.8918 (p) REVERT: C 441 ASP cc_start: 0.8376 (t70) cc_final: 0.8087 (t0) REVERT: C 467 ARG cc_start: 0.8449 (mmt180) cc_final: 0.8247 (mmt-90) REVERT: C 630 MET cc_start: 0.8985 (mmm) cc_final: 0.8713 (tpp) REVERT: C 645 GLU cc_start: 0.8549 (tp30) cc_final: 0.8305 (tp30) REVERT: C 661 MET cc_start: 0.8613 (tpt) cc_final: 0.8221 (tpt) REVERT: C 779 GLU cc_start: 0.8382 (tt0) cc_final: 0.7737 (tp30) REVERT: D 118 LEU cc_start: 0.9095 (mt) cc_final: 0.8856 (mt) REVERT: D 211 ARG cc_start: 0.7918 (mmt-90) cc_final: 0.7510 (mtp-110) REVERT: D 1106 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7637 (mm-30) REVERT: E 70 GLN cc_start: 0.6995 (tt0) cc_final: 0.6704 (tt0) REVERT: E 88 GLN cc_start: 0.8390 (tp40) cc_final: 0.7998 (tp40) REVERT: F 220 GLU cc_start: 0.8007 (tt0) cc_final: 0.7604 (tp30) REVERT: F 258 TYR cc_start: 0.8952 (t80) cc_final: 0.8663 (t80) REVERT: F 306 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8961 (mt) REVERT: F 411 LEU cc_start: 0.9043 (mt) cc_final: 0.8759 (pp) REVERT: F 511 MET cc_start: 0.9193 (tpt) cc_final: 0.8619 (tpp) REVERT: J 58 ASN cc_start: 0.9176 (t0) cc_final: 0.8472 (t0) REVERT: J 84 MET cc_start: 0.8505 (mpp) cc_final: 0.7548 (mpp) REVERT: M 4 LYS cc_start: 0.7794 (mtmm) cc_final: 0.7511 (mttt) REVERT: M 7 ASP cc_start: 0.7849 (m-30) cc_final: 0.7516 (m-30) REVERT: M 41 GLN cc_start: 0.8155 (tt0) cc_final: 0.7838 (tm-30) REVERT: M 124 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8029 (mm-30) outliers start: 16 outliers final: 8 residues processed: 485 average time/residue: 0.4744 time to fit residues: 349.4124 Evaluate side-chains 266 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 255 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 293 GLN Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain F residue 306 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 0.9990 chunk 271 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 280 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 325 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 124 HIS B 79 ASN B 226 ASN C 81 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN C 298 ASN C 419 ASN C 435 GLN C 841 HIS C 875 GLN C 920 HIS C1035 HIS C1054 GLN D 239 ASN D 307 ASN D 396 ASN D 416 ASN D 494 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 687 GLN D 693 GLN ** D 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 797 ASN D1001 GLN D1139 GLN E 106 HIS F 388 GLN J 21 ASN M 14 HIS M 102 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 30661 Z= 0.243 Angle : 0.683 8.341 42076 Z= 0.355 Chirality : 0.044 0.213 4789 Planarity : 0.005 0.099 5084 Dihedral : 20.280 177.712 5293 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.54 % Favored : 93.41 % Rotamer: Outliers : 2.02 % Allowed : 8.56 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.14), residues: 3488 helix: -0.08 (0.14), residues: 1349 sheet: -2.85 (0.24), residues: 388 loop : -2.38 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 70 HIS 0.006 0.001 HIS C 751 PHE 0.016 0.002 PHE D 721 TYR 0.018 0.002 TYR D 134 ARG 0.015 0.001 ARG F 487 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 324 time to evaluate : 3.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8766 (pttt) cc_final: 0.8552 (ptmm) REVERT: B 177 LYS cc_start: 0.8974 (ptpp) cc_final: 0.8760 (ptpp) REVERT: B 195 ASP cc_start: 0.7516 (t0) cc_final: 0.7275 (t0) REVERT: C 103 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8549 (ptt) REVERT: C 281 LEU cc_start: 0.9440 (tp) cc_final: 0.9239 (tt) REVERT: C 355 MET cc_start: 0.7991 (tmm) cc_final: 0.7533 (tmm) REVERT: C 394 SER cc_start: 0.9015 (m) cc_final: 0.8781 (p) REVERT: C 404 MET cc_start: 0.8622 (ttt) cc_final: 0.8067 (ttm) REVERT: C 441 ASP cc_start: 0.8162 (t70) cc_final: 0.7921 (t0) REVERT: C 463 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8872 (pt) REVERT: C 584 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8263 (ptp90) REVERT: C 586 MET cc_start: 0.9171 (ptm) cc_final: 0.8619 (ptm) REVERT: C 702 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8721 (tp) REVERT: C 779 GLU cc_start: 0.8201 (tt0) cc_final: 0.7633 (tp30) REVERT: C 1071 MET cc_start: 0.8747 (mtp) cc_final: 0.8493 (mtt) REVERT: D 92 MET cc_start: 0.8977 (mtm) cc_final: 0.8772 (mtm) REVERT: D 623 ASP cc_start: 0.7947 (m-30) cc_final: 0.7594 (t0) REVERT: E 70 GLN cc_start: 0.7110 (tt0) cc_final: 0.6774 (tt0) REVERT: E 88 GLN cc_start: 0.8185 (tp40) cc_final: 0.7773 (tp40) REVERT: F 220 GLU cc_start: 0.7986 (tt0) cc_final: 0.7527 (tp30) REVERT: F 258 TYR cc_start: 0.8906 (t80) cc_final: 0.8627 (t80) REVERT: F 511 MET cc_start: 0.8918 (tpt) cc_final: 0.8635 (tpp) REVERT: J 76 LYS cc_start: 0.8220 (pmtt) cc_final: 0.7684 (pttt) REVERT: J 84 MET cc_start: 0.8553 (mpp) cc_final: 0.7418 (mpp) REVERT: M 4 LYS cc_start: 0.8014 (mtmm) cc_final: 0.7563 (mmtt) REVERT: M 7 ASP cc_start: 0.7799 (m-30) cc_final: 0.7544 (m-30) REVERT: M 37 LEU cc_start: 0.9246 (tt) cc_final: 0.9027 (tp) REVERT: M 72 GLN cc_start: 0.8822 (tt0) cc_final: 0.8501 (tm-30) outliers start: 59 outliers final: 32 residues processed: 365 average time/residue: 0.4198 time to fit residues: 247.3908 Evaluate side-chains 293 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 257 time to evaluate : 3.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 795 GLU Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 437 ASP Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 21 ASN Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 83 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 180 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 325 optimal weight: 9.9990 chunk 351 optimal weight: 7.9990 chunk 290 optimal weight: 40.0000 chunk 322 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 HIS C 941 HIS D 499 ASN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 657 GLN D 674 ASN ** D 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1251 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 30661 Z= 0.543 Angle : 0.759 14.291 42076 Z= 0.394 Chirality : 0.047 0.251 4789 Planarity : 0.005 0.101 5084 Dihedral : 20.055 175.762 5271 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.72 % Favored : 91.20 % Rotamer: Outliers : 3.66 % Allowed : 10.48 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.14), residues: 3488 helix: 0.16 (0.14), residues: 1357 sheet: -2.65 (0.24), residues: 401 loop : -2.19 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 656 HIS 0.007 0.001 HIS C 751 PHE 0.017 0.002 PHE A 63 TYR 0.041 0.002 TYR D 915 ARG 0.009 0.001 ARG C 888 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 250 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8890 (pttt) cc_final: 0.8625 (ptmm) REVERT: B 165 ASP cc_start: 0.8238 (m-30) cc_final: 0.7848 (m-30) REVERT: B 177 LYS cc_start: 0.9043 (ptpp) cc_final: 0.8790 (ptpp) REVERT: B 195 ASP cc_start: 0.7611 (t0) cc_final: 0.7376 (t0) REVERT: C 191 ILE cc_start: 0.9204 (mt) cc_final: 0.8947 (tp) REVERT: C 394 SER cc_start: 0.9195 (m) cc_final: 0.8845 (p) REVERT: C 404 MET cc_start: 0.8615 (ttt) cc_final: 0.8086 (ttp) REVERT: C 441 ASP cc_start: 0.8244 (t70) cc_final: 0.7953 (t0) REVERT: C 463 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9002 (pt) REVERT: C 584 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8128 (ptp90) REVERT: C 586 MET cc_start: 0.9192 (ptm) cc_final: 0.8682 (ptm) REVERT: C 702 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8856 (tp) REVERT: C 736 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9092 (mp) REVERT: C 779 GLU cc_start: 0.8265 (tt0) cc_final: 0.7711 (tp30) REVERT: C 1051 MET cc_start: 0.8300 (mmm) cc_final: 0.7899 (mmm) REVERT: C 1071 MET cc_start: 0.9042 (mtp) cc_final: 0.8688 (mtt) REVERT: D 623 ASP cc_start: 0.7978 (m-30) cc_final: 0.7590 (t0) REVERT: E 70 GLN cc_start: 0.7124 (tt0) cc_final: 0.6830 (tt0) REVERT: E 88 GLN cc_start: 0.8123 (tp40) cc_final: 0.7744 (tp40) REVERT: F 220 GLU cc_start: 0.8162 (tt0) cc_final: 0.7692 (tp30) REVERT: F 297 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7741 (mp0) REVERT: F 460 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8578 (tm) REVERT: J 76 LYS cc_start: 0.8228 (pmtt) cc_final: 0.7695 (pttt) REVERT: M 4 LYS cc_start: 0.7877 (mtmm) cc_final: 0.7467 (mmtt) REVERT: M 7 ASP cc_start: 0.7923 (m-30) cc_final: 0.7619 (m-30) outliers start: 107 outliers final: 65 residues processed: 330 average time/residue: 0.3961 time to fit residues: 214.8185 Evaluate side-chains 304 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 234 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 736 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 437 ASP Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 83 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 321 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 218 optimal weight: 0.9990 chunk 326 optimal weight: 5.9990 chunk 346 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 309 optimal weight: 0.0870 chunk 93 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 674 ASN ** D 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN F 325 ASN J 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30661 Z= 0.179 Angle : 0.599 14.109 42076 Z= 0.312 Chirality : 0.042 0.212 4789 Planarity : 0.004 0.049 5084 Dihedral : 19.882 179.185 5271 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.53 % Favored : 94.44 % Rotamer: Outliers : 2.64 % Allowed : 12.50 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3488 helix: 0.78 (0.14), residues: 1358 sheet: -2.25 (0.25), residues: 397 loop : -1.80 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 656 HIS 0.004 0.001 HIS D 854 PHE 0.011 0.001 PHE D1226 TYR 0.028 0.001 TYR F 258 ARG 0.016 0.000 ARG D1143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 278 time to evaluate : 3.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8865 (pttt) cc_final: 0.8573 (ptmm) REVERT: B 165 ASP cc_start: 0.8244 (m-30) cc_final: 0.7821 (m-30) REVERT: B 195 ASP cc_start: 0.7562 (t0) cc_final: 0.7331 (t0) REVERT: C 154 MET cc_start: 0.8600 (tpp) cc_final: 0.8063 (mpp) REVERT: C 191 ILE cc_start: 0.9135 (mt) cc_final: 0.8860 (tp) REVERT: C 281 LEU cc_start: 0.9327 (tp) cc_final: 0.9126 (tt) REVERT: C 394 SER cc_start: 0.9045 (m) cc_final: 0.8720 (p) REVERT: C 404 MET cc_start: 0.8572 (ttt) cc_final: 0.8344 (ttp) REVERT: C 441 ASP cc_start: 0.7950 (t70) cc_final: 0.7718 (t0) REVERT: C 584 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8170 (ptp90) REVERT: C 586 MET cc_start: 0.9149 (ptm) cc_final: 0.8582 (ppp) REVERT: C 702 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8771 (tp) REVERT: C 779 GLU cc_start: 0.8166 (tt0) cc_final: 0.7623 (tp30) REVERT: C 1051 MET cc_start: 0.8220 (mmm) cc_final: 0.7815 (mmm) REVERT: C 1071 MET cc_start: 0.8722 (mtp) cc_final: 0.8323 (mtt) REVERT: D 37 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8806 (ptp-110) REVERT: D 862 ASP cc_start: 0.8475 (t70) cc_final: 0.8063 (t0) REVERT: E 88 GLN cc_start: 0.8243 (tp40) cc_final: 0.7779 (tp40) REVERT: F 220 GLU cc_start: 0.7942 (tt0) cc_final: 0.7502 (tp30) REVERT: F 297 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7649 (mp0) REVERT: J 76 LYS cc_start: 0.7948 (pmtt) cc_final: 0.7538 (pttt) REVERT: M 4 LYS cc_start: 0.7972 (mtmm) cc_final: 0.7577 (mmtt) REVERT: M 7 ASP cc_start: 0.7751 (m-30) cc_final: 0.7494 (m-30) REVERT: M 127 MET cc_start: 0.8560 (ttm) cc_final: 0.8337 (ttt) outliers start: 77 outliers final: 36 residues processed: 342 average time/residue: 0.4011 time to fit residues: 226.7061 Evaluate side-chains 268 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 229 time to evaluate : 3.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 437 ASP Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain M residue 71 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 288 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 257 optimal weight: 0.0970 chunk 142 optimal weight: 0.0000 chunk 295 optimal weight: 9.9990 chunk 239 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 310 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS ** D 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 30661 Z= 0.299 Angle : 0.615 12.252 42076 Z= 0.319 Chirality : 0.042 0.188 4789 Planarity : 0.004 0.051 5084 Dihedral : 19.759 178.058 5271 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.54 % Favored : 93.43 % Rotamer: Outliers : 3.56 % Allowed : 13.29 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3488 helix: 0.94 (0.14), residues: 1348 sheet: -2.03 (0.25), residues: 390 loop : -1.67 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 656 HIS 0.006 0.001 HIS D 854 PHE 0.013 0.002 PHE J 44 TYR 0.019 0.001 TYR F 258 ARG 0.014 0.000 ARG D1143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 230 time to evaluate : 3.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8897 (pttt) cc_final: 0.8599 (ptmm) REVERT: C 191 ILE cc_start: 0.9126 (mt) cc_final: 0.8823 (tp) REVERT: C 258 MET cc_start: 0.8114 (mmm) cc_final: 0.7798 (mmm) REVERT: C 394 SER cc_start: 0.9103 (m) cc_final: 0.8767 (p) REVERT: C 441 ASP cc_start: 0.8005 (t70) cc_final: 0.7768 (t0) REVERT: C 463 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9051 (pt) REVERT: C 584 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8188 (ptp90) REVERT: C 586 MET cc_start: 0.9161 (ptm) cc_final: 0.8509 (ppp) REVERT: C 661 MET cc_start: 0.8603 (tpt) cc_final: 0.8265 (tpt) REVERT: C 702 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8791 (tp) REVERT: C 779 GLU cc_start: 0.8163 (tt0) cc_final: 0.7635 (tp30) REVERT: C 1051 MET cc_start: 0.8259 (mmm) cc_final: 0.7833 (mmm) REVERT: C 1071 MET cc_start: 0.8907 (mtp) cc_final: 0.8439 (mtt) REVERT: D 862 ASP cc_start: 0.8482 (t70) cc_final: 0.8060 (t0) REVERT: F 220 GLU cc_start: 0.8066 (tt0) cc_final: 0.7591 (tp30) REVERT: F 257 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9089 (mp) REVERT: F 297 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7775 (mt-10) REVERT: F 424 ASP cc_start: 0.8569 (m-30) cc_final: 0.8318 (m-30) REVERT: J 76 LYS cc_start: 0.8008 (pmtt) cc_final: 0.7590 (pttt) REVERT: M 4 LYS cc_start: 0.8006 (mtmm) cc_final: 0.7588 (mmtt) REVERT: M 7 ASP cc_start: 0.7758 (m-30) cc_final: 0.7491 (m-30) REVERT: M 41 GLN cc_start: 0.7551 (tt0) cc_final: 0.7309 (tm-30) outliers start: 104 outliers final: 68 residues processed: 311 average time/residue: 0.4045 time to fit residues: 211.1569 Evaluate side-chains 291 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 219 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1235 ASP Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 437 ASP Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 21 ASN Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 71 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 116 optimal weight: 0.9990 chunk 311 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 346 optimal weight: 7.9990 chunk 287 optimal weight: 0.3980 chunk 160 optimal weight: 0.1980 chunk 28 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30661 Z= 0.173 Angle : 0.564 11.795 42076 Z= 0.294 Chirality : 0.040 0.152 4789 Planarity : 0.004 0.065 5084 Dihedral : 19.619 179.551 5267 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.50 % Rotamer: Outliers : 2.67 % Allowed : 14.28 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 3488 helix: 1.15 (0.15), residues: 1352 sheet: -1.72 (0.26), residues: 380 loop : -1.50 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 656 HIS 0.004 0.001 HIS D 854 PHE 0.011 0.001 PHE A 63 TYR 0.032 0.001 TYR F 258 ARG 0.006 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 257 time to evaluate : 4.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8855 (pttt) cc_final: 0.8514 (ptmm) REVERT: B 109 ASP cc_start: 0.8220 (t0) cc_final: 0.7932 (t0) REVERT: B 123 MET cc_start: 0.8215 (tmm) cc_final: 0.7521 (tmm) REVERT: B 165 ASP cc_start: 0.8158 (m-30) cc_final: 0.7750 (m-30) REVERT: C 103 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8542 (ptt) REVERT: C 154 MET cc_start: 0.8524 (tpp) cc_final: 0.8155 (tpp) REVERT: C 191 ILE cc_start: 0.9045 (mt) cc_final: 0.8731 (tp) REVERT: C 394 SER cc_start: 0.9076 (m) cc_final: 0.8743 (p) REVERT: C 404 MET cc_start: 0.8440 (ttp) cc_final: 0.8183 (ttp) REVERT: C 441 ASP cc_start: 0.7890 (t70) cc_final: 0.7633 (t0) REVERT: C 463 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9070 (pt) REVERT: C 584 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8168 (ptp90) REVERT: C 586 MET cc_start: 0.9132 (ptm) cc_final: 0.8469 (ppp) REVERT: C 661 MET cc_start: 0.8525 (tpt) cc_final: 0.8211 (tpt) REVERT: C 702 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8760 (tp) REVERT: C 779 GLU cc_start: 0.8133 (tt0) cc_final: 0.7617 (tp30) REVERT: C 1051 MET cc_start: 0.8224 (mmm) cc_final: 0.7797 (mmm) REVERT: C 1071 MET cc_start: 0.8847 (mtp) cc_final: 0.8365 (mtt) REVERT: D 862 ASP cc_start: 0.8424 (t70) cc_final: 0.8056 (t0) REVERT: D 1139 GLN cc_start: 0.8778 (mm-40) cc_final: 0.7941 (mm-40) REVERT: E 88 GLN cc_start: 0.8070 (tp40) cc_final: 0.7718 (tp40) REVERT: F 220 GLU cc_start: 0.7996 (tt0) cc_final: 0.7517 (tp30) REVERT: F 258 TYR cc_start: 0.9023 (t80) cc_final: 0.8796 (t80) REVERT: F 282 MET cc_start: 0.8836 (mmm) cc_final: 0.8626 (mmm) REVERT: F 427 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8181 (pt) REVERT: F 465 ASP cc_start: 0.8739 (m-30) cc_final: 0.8469 (m-30) REVERT: J 76 LYS cc_start: 0.7954 (pmtt) cc_final: 0.7467 (pttt) REVERT: M 4 LYS cc_start: 0.8039 (mtmm) cc_final: 0.7609 (mmtt) REVERT: M 7 ASP cc_start: 0.7740 (m-30) cc_final: 0.7528 (m-30) REVERT: M 41 GLN cc_start: 0.7409 (tt0) cc_final: 0.7100 (tm-30) outliers start: 78 outliers final: 51 residues processed: 317 average time/residue: 0.3896 time to fit residues: 207.4715 Evaluate side-chains 284 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 228 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1235 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 437 ASP Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 21 ASN Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 71 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 333 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 252 optimal weight: 0.4980 chunk 195 optimal weight: 0.5980 chunk 291 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 345 optimal weight: 20.0000 chunk 215 optimal weight: 0.1980 chunk 210 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30661 Z= 0.199 Angle : 0.571 17.324 42076 Z= 0.295 Chirality : 0.041 0.219 4789 Planarity : 0.004 0.053 5084 Dihedral : 19.487 178.570 5267 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.61 % Rotamer: Outliers : 2.95 % Allowed : 14.45 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 3488 helix: 1.25 (0.15), residues: 1351 sheet: -1.55 (0.26), residues: 372 loop : -1.44 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP D 656 HIS 0.005 0.001 HIS D 854 PHE 0.012 0.001 PHE A 63 TYR 0.019 0.001 TYR F 258 ARG 0.004 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 245 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8864 (pttt) cc_final: 0.8525 (ptmm) REVERT: A 213 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8576 (ttpt) REVERT: B 123 MET cc_start: 0.8221 (tmm) cc_final: 0.7514 (tmm) REVERT: B 165 ASP cc_start: 0.8122 (m-30) cc_final: 0.7716 (m-30) REVERT: C 103 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8475 (ptt) REVERT: C 154 MET cc_start: 0.8537 (tpp) cc_final: 0.8153 (mpp) REVERT: C 191 ILE cc_start: 0.9037 (mt) cc_final: 0.8722 (tp) REVERT: C 394 SER cc_start: 0.9086 (m) cc_final: 0.8743 (p) REVERT: C 404 MET cc_start: 0.8413 (ttp) cc_final: 0.8071 (ttp) REVERT: C 441 ASP cc_start: 0.7863 (t70) cc_final: 0.7639 (t0) REVERT: C 463 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9082 (pt) REVERT: C 584 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8207 (ptp90) REVERT: C 586 MET cc_start: 0.9114 (ptm) cc_final: 0.8391 (ppp) REVERT: C 587 VAL cc_start: 0.9463 (OUTLIER) cc_final: 0.9194 (m) REVERT: C 661 MET cc_start: 0.8520 (tpt) cc_final: 0.8219 (tpt) REVERT: C 702 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8787 (tp) REVERT: C 779 GLU cc_start: 0.8139 (tt0) cc_final: 0.7625 (tp30) REVERT: C 1051 MET cc_start: 0.8235 (mmm) cc_final: 0.7804 (mmm) REVERT: D 862 ASP cc_start: 0.8395 (t70) cc_final: 0.8156 (t0) REVERT: D 975 CYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7718 (p) REVERT: D 1112 MET cc_start: 0.8666 (tpp) cc_final: 0.8305 (tpp) REVERT: D 1139 GLN cc_start: 0.8654 (mm-40) cc_final: 0.6962 (mm-40) REVERT: D 1235 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8088 (m-30) REVERT: E 88 GLN cc_start: 0.8055 (tp40) cc_final: 0.7742 (tp40) REVERT: F 220 GLU cc_start: 0.8030 (tt0) cc_final: 0.7516 (tp30) REVERT: F 257 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8891 (mp) REVERT: F 427 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8170 (pt) REVERT: J 76 LYS cc_start: 0.7960 (pmtt) cc_final: 0.7468 (pttt) REVERT: M 4 LYS cc_start: 0.8038 (mtmm) cc_final: 0.7611 (mmtt) REVERT: M 41 GLN cc_start: 0.7369 (tt0) cc_final: 0.7065 (tm-30) REVERT: M 112 TRP cc_start: 0.8420 (t-100) cc_final: 0.7947 (t60) outliers start: 86 outliers final: 63 residues processed: 313 average time/residue: 0.3945 time to fit residues: 204.7126 Evaluate side-chains 303 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 230 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1235 ASP Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 437 ASP Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 21 ASN Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 71 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 213 optimal weight: 0.3980 chunk 137 optimal weight: 8.9990 chunk 206 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 235 optimal weight: 0.5980 chunk 170 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 271 optimal weight: 10.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1139 GLN E 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30661 Z= 0.224 Angle : 0.580 14.273 42076 Z= 0.302 Chirality : 0.041 0.215 4789 Planarity : 0.004 0.055 5084 Dihedral : 19.423 178.043 5267 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.65 % Favored : 94.32 % Rotamer: Outliers : 3.05 % Allowed : 14.73 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3488 helix: 1.31 (0.15), residues: 1352 sheet: -1.50 (0.26), residues: 384 loop : -1.42 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP D 656 HIS 0.005 0.001 HIS D 854 PHE 0.014 0.001 PHE C 430 TYR 0.032 0.001 TYR D 915 ARG 0.017 0.000 ARG D1143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 236 time to evaluate : 3.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8867 (pttt) cc_final: 0.8531 (ptmm) REVERT: B 165 ASP cc_start: 0.8160 (m-30) cc_final: 0.7738 (m-30) REVERT: C 103 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8430 (ptt) REVERT: C 154 MET cc_start: 0.8578 (tpp) cc_final: 0.8098 (mpp) REVERT: C 191 ILE cc_start: 0.9036 (mt) cc_final: 0.8704 (tp) REVERT: C 394 SER cc_start: 0.9088 (m) cc_final: 0.8749 (p) REVERT: C 404 MET cc_start: 0.8434 (ttp) cc_final: 0.8131 (ttp) REVERT: C 441 ASP cc_start: 0.7889 (t70) cc_final: 0.7655 (t0) REVERT: C 463 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9098 (pt) REVERT: C 584 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8188 (ptp90) REVERT: C 586 MET cc_start: 0.9130 (ptm) cc_final: 0.8392 (ppp) REVERT: C 587 VAL cc_start: 0.9469 (OUTLIER) cc_final: 0.9192 (m) REVERT: C 661 MET cc_start: 0.8533 (tpt) cc_final: 0.8195 (tpt) REVERT: C 702 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8773 (tp) REVERT: C 779 GLU cc_start: 0.8218 (tt0) cc_final: 0.7714 (tp30) REVERT: D 759 GLN cc_start: 0.8452 (mt0) cc_final: 0.8215 (mt0) REVERT: D 862 ASP cc_start: 0.8447 (t70) cc_final: 0.8202 (t0) REVERT: D 975 CYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7719 (p) REVERT: D 1112 MET cc_start: 0.8523 (tpp) cc_final: 0.8177 (tpp) REVERT: D 1139 GLN cc_start: 0.8643 (mm110) cc_final: 0.8277 (mm-40) REVERT: D 1235 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8100 (m-30) REVERT: E 88 GLN cc_start: 0.8227 (tp40) cc_final: 0.7939 (tp40) REVERT: F 220 GLU cc_start: 0.8066 (tt0) cc_final: 0.7537 (tp30) REVERT: F 257 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8889 (mp) REVERT: F 465 ASP cc_start: 0.8662 (m-30) cc_final: 0.8448 (m-30) REVERT: J 76 LYS cc_start: 0.7963 (pmtt) cc_final: 0.7551 (pttt) REVERT: M 4 LYS cc_start: 0.8144 (mtmm) cc_final: 0.7845 (mmtt) REVERT: M 41 GLN cc_start: 0.7293 (tt0) cc_final: 0.7074 (tm-30) REVERT: M 112 TRP cc_start: 0.8543 (t-100) cc_final: 0.8006 (t60) outliers start: 89 outliers final: 70 residues processed: 307 average time/residue: 0.3918 time to fit residues: 199.1319 Evaluate side-chains 302 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 224 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1235 ASP Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 437 ASP Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 21 ASN Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 71 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 313 optimal weight: 0.0170 chunk 330 optimal weight: 5.9990 chunk 301 optimal weight: 5.9990 chunk 321 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 98 optimal weight: 0.0010 chunk 290 optimal weight: 30.0000 chunk 304 optimal weight: 2.9990 chunk 320 optimal weight: 7.9990 overall best weight: 1.1828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN M 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 30661 Z= 0.195 Angle : 0.570 13.757 42076 Z= 0.296 Chirality : 0.040 0.206 4789 Planarity : 0.004 0.057 5084 Dihedral : 19.358 178.089 5267 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.56 % Favored : 94.41 % Rotamer: Outliers : 3.01 % Allowed : 14.79 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3488 helix: 1.33 (0.15), residues: 1369 sheet: -1.40 (0.26), residues: 386 loop : -1.41 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 656 HIS 0.007 0.001 HIS M 13 PHE 0.011 0.001 PHE C 430 TYR 0.032 0.001 TYR E 56 ARG 0.015 0.000 ARG D1143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 240 time to evaluate : 3.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8854 (pttt) cc_final: 0.8540 (ptmm) REVERT: B 123 MET cc_start: 0.8199 (tmm) cc_final: 0.7521 (tmm) REVERT: B 165 ASP cc_start: 0.8189 (m-30) cc_final: 0.7764 (m-30) REVERT: C 103 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8281 (ptt) REVERT: C 154 MET cc_start: 0.8524 (tpp) cc_final: 0.8061 (mpp) REVERT: C 191 ILE cc_start: 0.9029 (mt) cc_final: 0.8696 (tp) REVERT: C 394 SER cc_start: 0.9080 (m) cc_final: 0.8732 (p) REVERT: C 404 MET cc_start: 0.8382 (ttp) cc_final: 0.8029 (ttp) REVERT: C 441 ASP cc_start: 0.7876 (t70) cc_final: 0.7639 (t0) REVERT: C 463 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9030 (pt) REVERT: C 584 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8242 (ptp90) REVERT: C 586 MET cc_start: 0.9105 (ptm) cc_final: 0.8383 (ppp) REVERT: C 587 VAL cc_start: 0.9458 (OUTLIER) cc_final: 0.9185 (m) REVERT: C 661 MET cc_start: 0.8513 (tpt) cc_final: 0.8171 (tpt) REVERT: C 702 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8764 (tp) REVERT: C 779 GLU cc_start: 0.8227 (tt0) cc_final: 0.7724 (tp30) REVERT: D 759 GLN cc_start: 0.8449 (mt0) cc_final: 0.8219 (mt0) REVERT: D 862 ASP cc_start: 0.8417 (t70) cc_final: 0.8174 (t0) REVERT: D 975 CYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7704 (p) REVERT: D 1112 MET cc_start: 0.8519 (tpp) cc_final: 0.8183 (tpp) REVERT: D 1235 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8189 (m-30) REVERT: E 88 GLN cc_start: 0.8205 (tp40) cc_final: 0.7906 (tp40) REVERT: F 220 GLU cc_start: 0.8061 (tt0) cc_final: 0.7523 (tp30) REVERT: F 257 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8757 (mp) REVERT: F 465 ASP cc_start: 0.8624 (m-30) cc_final: 0.8419 (m-30) REVERT: J 76 LYS cc_start: 0.7959 (pmtt) cc_final: 0.7545 (pttt) REVERT: M 41 GLN cc_start: 0.7336 (tt0) cc_final: 0.7082 (tm-30) REVERT: M 112 TRP cc_start: 0.8580 (t-100) cc_final: 0.8101 (t60) outliers start: 88 outliers final: 70 residues processed: 306 average time/residue: 0.4195 time to fit residues: 212.4611 Evaluate side-chains 302 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 224 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 1143 ARG Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1235 ASP Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 437 ASP Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 21 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 71 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 211 optimal weight: 4.9990 chunk 340 optimal weight: 8.9990 chunk 207 optimal weight: 0.2980 chunk 161 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 356 optimal weight: 10.0000 chunk 328 optimal weight: 0.2980 chunk 284 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN E 70 GLN M 13 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30661 Z= 0.206 Angle : 0.578 13.602 42076 Z= 0.299 Chirality : 0.041 0.206 4789 Planarity : 0.004 0.070 5084 Dihedral : 19.333 177.874 5267 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.88 % Favored : 94.09 % Rotamer: Outliers : 3.01 % Allowed : 14.97 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3488 helix: 1.37 (0.15), residues: 1368 sheet: -1.37 (0.26), residues: 379 loop : -1.41 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 656 HIS 0.023 0.001 HIS M 13 PHE 0.011 0.001 PHE C 430 TYR 0.032 0.001 TYR E 56 ARG 0.027 0.000 ARG D1143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 231 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8849 (pttt) cc_final: 0.8569 (ptmm) REVERT: B 123 MET cc_start: 0.8196 (tmm) cc_final: 0.7519 (tmm) REVERT: B 165 ASP cc_start: 0.8176 (m-30) cc_final: 0.7709 (m-30) REVERT: C 103 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8289 (ptt) REVERT: C 154 MET cc_start: 0.8533 (tpp) cc_final: 0.8028 (mpp) REVERT: C 191 ILE cc_start: 0.9026 (mt) cc_final: 0.8686 (tp) REVERT: C 258 MET cc_start: 0.7648 (mmm) cc_final: 0.7411 (mtp) REVERT: C 394 SER cc_start: 0.9081 (m) cc_final: 0.8735 (p) REVERT: C 404 MET cc_start: 0.8371 (ttp) cc_final: 0.8034 (ttp) REVERT: C 441 ASP cc_start: 0.7831 (t70) cc_final: 0.7590 (t0) REVERT: C 463 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9034 (pt) REVERT: C 584 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8281 (ptp90) REVERT: C 586 MET cc_start: 0.9107 (ptm) cc_final: 0.8380 (ppp) REVERT: C 587 VAL cc_start: 0.9465 (OUTLIER) cc_final: 0.9191 (m) REVERT: C 661 MET cc_start: 0.8514 (tpt) cc_final: 0.8167 (tpt) REVERT: C 702 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8769 (tp) REVERT: C 779 GLU cc_start: 0.8233 (tt0) cc_final: 0.7731 (tp30) REVERT: D 37 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8808 (ptp-110) REVERT: D 124 ASP cc_start: 0.8331 (t0) cc_final: 0.7847 (t0) REVERT: D 759 GLN cc_start: 0.8416 (mt0) cc_final: 0.8202 (mt0) REVERT: D 862 ASP cc_start: 0.8408 (t70) cc_final: 0.8171 (t0) REVERT: D 975 CYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7702 (p) REVERT: D 1112 MET cc_start: 0.8449 (tpp) cc_final: 0.8116 (tpp) REVERT: D 1235 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8228 (m-30) REVERT: E 88 GLN cc_start: 0.8205 (tp40) cc_final: 0.7923 (tp40) REVERT: F 220 GLU cc_start: 0.8081 (tt0) cc_final: 0.7554 (tp30) REVERT: F 257 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8742 (mp) REVERT: J 76 LYS cc_start: 0.7961 (pmtt) cc_final: 0.7545 (pttt) REVERT: M 41 GLN cc_start: 0.7287 (tt0) cc_final: 0.7027 (tm-30) REVERT: M 112 TRP cc_start: 0.8582 (t-100) cc_final: 0.8107 (t60) outliers start: 88 outliers final: 74 residues processed: 298 average time/residue: 0.3869 time to fit residues: 190.4657 Evaluate side-chains 309 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 226 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 484 CYS Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 774 LEU Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 810 ASN Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1235 ASP Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 427 ILE Chi-restraints excluded: chain F residue 437 ASP Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 516 HIS Chi-restraints excluded: chain J residue 21 ASN Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain M residue 71 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 225 optimal weight: 3.9990 chunk 302 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 284 optimal weight: 0.8980 chunk 119 optimal weight: 0.1980 chunk 292 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 52 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D1139 GLN E 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.101128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.071191 restraints weight = 69504.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.073552 restraints weight = 33057.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.075029 restraints weight = 21235.935| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30661 Z= 0.185 Angle : 0.571 13.265 42076 Z= 0.295 Chirality : 0.040 0.199 4789 Planarity : 0.004 0.059 5084 Dihedral : 19.288 177.854 5267 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.65 % Favored : 94.32 % Rotamer: Outliers : 3.01 % Allowed : 14.97 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3488 helix: 1.43 (0.15), residues: 1366 sheet: -1.31 (0.26), residues: 379 loop : -1.37 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 656 HIS 0.024 0.001 HIS M 13 PHE 0.010 0.001 PHE C 430 TYR 0.030 0.001 TYR E 56 ARG 0.008 0.000 ARG D1143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5695.40 seconds wall clock time: 104 minutes 36.21 seconds (6276.21 seconds total)