Starting phenix.real_space_refine on Mon Feb 19 06:51:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e95_27956/02_2024/8e95_27956.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e95_27956/02_2024/8e95_27956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e95_27956/02_2024/8e95_27956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e95_27956/02_2024/8e95_27956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e95_27956/02_2024/8e95_27956.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e95_27956/02_2024/8e95_27956.pdb" } resolution = 2.9 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= 0.003 sd= 0.143 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 68 5.49 5 Mg 1 5.21 5 S 87 5.16 5 C 14792 2.51 5 N 4255 2.21 5 O 4738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 23943 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1769 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 221} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8485 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 60, 'TRANS': 1033} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 9916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 9916 Classifications: {'peptide': 1269} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1208} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 645 Classifications: {'peptide': 82} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 75} Chain: "P" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 666 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "Q" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 514 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} 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 12487 SG CYS D 60 109.325 75.054 111.808 1.00 59.49 S ATOM 12505 SG CYS D 62 111.304 75.898 112.270 1.00 67.74 S ATOM 12614 SG CYS D 75 110.872 72.803 114.866 1.00 67.04 S ATOM 12640 SG CYS D 78 109.341 75.116 114.388 1.00 66.98 S ATOM 19055 SG CYS D 891 70.397 22.954 88.079 1.00 31.73 S ATOM 19622 SG CYS D 968 69.866 26.822 89.590 1.00 9.65 S ATOM 19664 SG CYS D 975 70.676 25.954 86.115 1.00 14.23 S ATOM 19682 SG CYS D 978 67.693 25.179 86.622 1.00 17.04 S Time building chain proxies: 14.00, per 1000 atoms: 0.58 Number of scatterers: 23943 At special positions: 0 Unit cell: (127.735, 134.23, 198.097, 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 87 16.00 P 68 15.00 Mg 1 11.99 O 4738 8.00 N 4255 7.00 C 14792 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: 9.72 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 968 " Number of angles added : 12 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5346 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 38 sheets defined 39.2% alpha, 15.7% beta 29 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 8.90 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 203 through 219 Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.558A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 203 through 219 removed outlier: 3.690A pdb=" N ALA B 209 " --> pdb=" O ARG B 205 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.662A pdb=" N ARG B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 63 removed outlier: 3.900A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 62 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 removed outlier: 3.616A pdb=" N GLU C 76 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 233 through 241 removed outlier: 4.073A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 264 removed outlier: 3.520A pdb=" N ARG C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 262 " --> pdb=" O MET C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 300 Processing helix chain 'C' and resid 308 through 320 Processing helix chain 'C' and resid 334 through 349 removed outlier: 3.738A pdb=" N ILE C 342 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 404 Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.514A pdb=" N LEU C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.675A pdb=" N GLY C 448 " --> pdb=" O ASN C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 533 through 537 Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.715A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 631 through 639 removed outlier: 3.506A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 779 through 784 removed outlier: 4.561A pdb=" N ASP C 783 " --> pdb=" O VAL C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 921 through 926 removed outlier: 3.681A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1079 removed outlier: 3.642A pdb=" N CYS C1073 " --> pdb=" O GLY C1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1091 removed outlier: 3.671A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1108 removed outlier: 3.780A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1119 through 1131 removed outlier: 3.784A pdb=" N VAL C1123 " --> pdb=" O GLU C1119 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.541A pdb=" N GLY D 109 " --> pdb=" O TRP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 141 through 186 removed outlier: 4.404A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 229 Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.664A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.627A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 4.069A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.582A pdb=" N LYS D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.858A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 361 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 447 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 removed outlier: 3.513A pdb=" N ALA D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 491 removed outlier: 4.271A pdb=" N TRP D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 removed outlier: 4.146A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.634A pdb=" N ILE D 745 " --> pdb=" O ARG D 741 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 819 removed outlier: 3.654A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.846A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR D 872 " --> pdb=" O ALA D 868 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 873 " --> pdb=" O ASP D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.766A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1008 No H-bonds generated for 'chain 'D' and resid 1006 through 1008' Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1126 removed outlier: 3.729A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 4.033A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1160 removed outlier: 4.311A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1196 removed outlier: 3.628A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU D1196 " --> pdb=" O ARG D1192 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.507A pdb=" N ALA D1224 " --> pdb=" O TRP D1220 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1254 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 74 removed outlier: 3.830A pdb=" N GLY E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 73 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.508A pdb=" N ILE E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU E 96 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 6.614A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 189 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA A 180 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS A 191 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 178 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.451A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.772A pdb=" N GLY A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 15 removed outlier: 6.138A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.010A pdb=" N VAL B 111 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR B 96 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 99 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 134 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.670A pdb=" N GLY B 103 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.552A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.535A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA C 137 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR C 151 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE C 139 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N SER C 149 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ASN C 141 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE C 147 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.764A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 191 removed outlier: 3.912A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 505 through 506 removed outlier: 4.154A pdb=" N LYS C 518 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 removed outlier: 4.616A pdb=" N VAL C 541 " --> pdb=" O ARG C 562 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG C 562 " --> pdb=" O VAL C 541 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL C 559 " --> pdb=" O VAL C 571 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 571 " --> pdb=" O VAL C 559 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.439A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.952A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AC3, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC4, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 5.738A pdb=" N ILE C 735 " --> pdb=" O ILE C 895 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 749 through 756 removed outlier: 3.555A pdb=" N VAL C 873 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 759 through 760 removed outlier: 6.897A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 768 through 769 removed outlier: 3.653A pdb=" N GLU C 768 " --> pdb=" O VAL C 806 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AC9, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD1, first strand: chain 'C' and resid 1136 through 1138 Processing sheet with id=AD2, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.645A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.591A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 328 through 330 removed outlier: 4.247A pdb=" N VAL D 328 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 632 through 637 Processing sheet with id=AD6, first strand: chain 'D' and resid 822 through 825 removed outlier: 9.311A pdb=" N GLY D 822 " --> pdb=" O ARG D 834 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ARG D 834 " --> pdb=" O GLY D 822 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL D 824 " --> pdb=" O ILE D 832 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AD8, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.986A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1051 through 1053 removed outlier: 5.561A pdb=" N TYR D1062 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS D1079 " --> pdb=" O TYR D1062 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 4.879A pdb=" N ARG D1164 " --> pdb=" O VAL D1206 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL D1206 " --> pdb=" O ARG D1164 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1271 through 1274 932 hydrogen bonds defined for protein. 2589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 10.99 Time building geometry restraints manager: 10.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7802 1.34 - 1.46: 3305 1.46 - 1.58: 13099 1.58 - 1.70: 132 1.70 - 1.81: 153 Bond restraints: 24491 Sorted by residual: bond pdb=" N GLY D -1 " pdb=" CA GLY D -1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.18e+00 bond pdb=" P DG P 112 " pdb=" OP2 DG P 112 " ideal model delta sigma weight residual 1.480 1.520 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" P DT P 115 " pdb=" OP2 DT P 115 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" P DG P 114 " pdb=" OP2 DG P 114 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" P DT P 117 " pdb=" OP2 DT P 117 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.43e+00 ... (remaining 24486 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.08: 988 106.08 - 113.07: 13446 113.07 - 120.05: 8482 120.05 - 127.04: 10165 127.04 - 134.02: 394 Bond angle restraints: 33475 Sorted by residual: angle pdb=" C3' DA P 116 " pdb=" O3' DA P 116 " pdb=" P DT P 117 " ideal model delta sigma weight residual 120.20 106.47 13.73 1.50e+00 4.44e-01 8.38e+01 angle pdb=" C3' DG P 112 " pdb=" O3' DG P 112 " pdb=" P DG P 113 " ideal model delta sigma weight residual 120.20 111.03 9.17 1.50e+00 4.44e-01 3.73e+01 angle pdb=" C3' DT P 115 " pdb=" O3' DT P 115 " pdb=" P DA P 116 " ideal model delta sigma weight residual 120.20 112.08 8.12 1.50e+00 4.44e-01 2.93e+01 angle pdb=" N VAL B 183 " pdb=" CA VAL B 183 " pdb=" C VAL B 183 " ideal model delta sigma weight residual 113.71 109.62 4.09 9.50e-01 1.11e+00 1.86e+01 angle pdb=" N ARG C 584 " pdb=" CA ARG C 584 " pdb=" C ARG C 584 " ideal model delta sigma weight residual 111.71 106.56 5.15 1.34e+00 5.57e-01 1.48e+01 ... (remaining 33470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.36: 14350 33.36 - 66.72: 458 66.72 - 100.07: 5 100.07 - 133.43: 1 133.43 - 166.79: 1 Dihedral angle restraints: 14815 sinusoidal: 6497 harmonic: 8318 Sorted by residual: dihedral pdb=" O4' C R 11 " pdb=" C1' C R 11 " pdb=" N1 C R 11 " pdb=" C2 C R 11 " ideal model delta sinusoidal sigma weight residual 200.00 33.21 166.79 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" CA GLU E 77 " pdb=" C GLU E 77 " pdb=" N TYR E 78 " pdb=" CA TYR E 78 " ideal model delta harmonic sigma weight residual 180.00 -158.04 -21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ASN D 5 " pdb=" C ASN D 5 " pdb=" N PHE D 6 " pdb=" CA PHE D 6 " ideal model delta harmonic sigma weight residual -180.00 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 14812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3692 0.104 - 0.209: 127 0.209 - 0.313: 0 0.313 - 0.417: 0 0.417 - 0.522: 6 Chirality restraints: 3825 Sorted by residual: chirality pdb=" P DA P 116 " pdb=" OP1 DA P 116 " pdb=" OP2 DA P 116 " pdb=" O5' DA P 116 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.80e+00 chirality pdb=" P DG P 112 " pdb=" OP1 DG P 112 " pdb=" OP2 DG P 112 " pdb=" O5' DG P 112 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" P DG P 114 " pdb=" OP1 DG P 114 " pdb=" OP2 DG P 114 " pdb=" O5' DG P 114 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.44e+00 ... (remaining 3822 not shown) Planarity restraints: 4169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT P 117 " -0.004 2.00e-02 2.50e+03 2.11e-02 1.11e+01 pdb=" N1 DT P 117 " 0.011 2.00e-02 2.50e+03 pdb=" C2 DT P 117 " -0.013 2.00e-02 2.50e+03 pdb=" O2 DT P 117 " -0.019 2.00e-02 2.50e+03 pdb=" N3 DT P 117 " 0.056 2.00e-02 2.50e+03 pdb=" C4 DT P 117 " -0.006 2.00e-02 2.50e+03 pdb=" O4 DT P 117 " -0.024 2.00e-02 2.50e+03 pdb=" C5 DT P 117 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT P 117 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DT P 117 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT P 115 " 0.016 2.00e-02 2.50e+03 1.29e-02 4.17e+00 pdb=" N1 DT P 115 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DT P 115 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT P 115 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DT P 115 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT P 115 " -0.012 2.00e-02 2.50e+03 pdb=" O4 DT P 115 " 0.025 2.00e-02 2.50e+03 pdb=" C5 DT P 115 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT P 115 " -0.017 2.00e-02 2.50e+03 pdb=" C6 DT P 115 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 413 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO C 414 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 414 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 414 " -0.028 5.00e-02 4.00e+02 ... (remaining 4166 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 64 2.42 - 3.04: 15009 3.04 - 3.66: 33929 3.66 - 4.28: 52286 4.28 - 4.90: 88884 Nonbonded interactions: 190172 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 1.796 2.170 nonbonded pdb=" OE1 GLN C 150 " pdb=" OG1 THR C 413 " model vdw 1.992 2.440 nonbonded pdb=" O3' A R 20 " pdb="MG MG D2002 " model vdw 2.027 2.170 nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2002 " model vdw 2.097 2.170 nonbonded pdb=" O SER B 45 " pdb=" NH1 ARG B 144 " model vdw 2.099 2.520 ... (remaining 190167 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 1 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 through 226)) \ selection = (chain 'B' and resid 1 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.010 Extract box with map and model: 7.240 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 78.470 Find NCS groups from input model: 1.010 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: 0.010 Load rotamer database and sin/cos tables:15.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 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 : 0.003 0.040 24491 Z= 0.179 Angle : 0.592 13.728 33475 Z= 0.345 Chirality : 0.045 0.522 3825 Planarity : 0.004 0.050 4169 Dihedral : 14.082 166.790 9469 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.70 % Favored : 95.02 % Rotamer: Outliers : 4.39 % Allowed : 6.56 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 2893 helix: 0.83 (0.17), residues: 1011 sheet: -0.94 (0.29), residues: 316 loop : -1.40 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 938 HIS 0.003 0.001 HIS D 689 PHE 0.013 0.001 PHE C 439 TYR 0.010 0.001 TYR D 586 ARG 0.003 0.000 ARG C1067 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 496 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4486 (tpp) cc_final: 0.3594 (tmt) REVERT: A 221 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6877 (mt) REVERT: B 24 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6485 (mt-10) REVERT: B 55 ARG cc_start: 0.7583 (ptm160) cc_final: 0.7097 (ptp90) REVERT: C 160 MET cc_start: 0.9154 (ttm) cc_final: 0.8546 (ttp) REVERT: C 215 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6716 (m-30) REVERT: C 262 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5859 (pp) REVERT: C 302 LYS cc_start: 0.6580 (OUTLIER) cc_final: 0.6295 (mmtt) REVERT: C 419 ASN cc_start: 0.7166 (t0) cc_final: 0.6905 (t160) REVERT: C 483 MET cc_start: 0.9033 (ttp) cc_final: 0.8796 (ttt) REVERT: C 528 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8287 (pt) REVERT: C 673 ARG cc_start: 0.8101 (ptm160) cc_final: 0.7604 (ptm-80) REVERT: C 805 LYS cc_start: 0.6057 (OUTLIER) cc_final: 0.5803 (pttt) REVERT: C 901 VAL cc_start: 0.8765 (p) cc_final: 0.8466 (t) REVERT: C 952 VAL cc_start: 0.7953 (m) cc_final: 0.7715 (t) REVERT: C 1030 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8472 (mm) REVERT: C 1138 LEU cc_start: 0.8649 (mt) cc_final: 0.8382 (mt) REVERT: D 229 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6279 (tt) REVERT: D 403 SER cc_start: 0.8513 (t) cc_final: 0.8277 (m) REVERT: D 410 GLN cc_start: 0.8419 (mp10) cc_final: 0.8092 (mm-40) REVERT: D 423 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: D 496 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8133 (p) REVERT: D 672 MET cc_start: 0.8123 (mtt) cc_final: 0.7857 (mtt) REVERT: D 865 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7546 (mm) REVERT: D 1117 ASP cc_start: 0.7561 (p0) cc_final: 0.7325 (t0) REVERT: E 33 LEU cc_start: 0.8450 (pt) cc_final: 0.8159 (mt) REVERT: E 40 ILE cc_start: 0.8448 (tp) cc_final: 0.8076 (tp) REVERT: E 62 ARG cc_start: 0.8258 (mtt180) cc_final: 0.7787 (mmt-90) outliers start: 107 outliers final: 32 residues processed: 575 average time/residue: 1.2828 time to fit residues: 850.9350 Evaluate side-chains 335 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 291 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 805 LYS Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 947 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain E residue 79 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 230 optimal weight: 0.4980 chunk 89 optimal weight: 10.0000 chunk 140 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 chunk 266 optimal weight: 4.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 443 ASN ** C 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 HIS C 685 ASN C 739 ASN C 751 HIS C 755 HIS C1062 GLN D 564 ASN D 693 GLN D 748 HIS D 810 ASN D1032 GLN D1125 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 24491 Z= 0.445 Angle : 0.743 9.221 33475 Z= 0.390 Chirality : 0.050 0.207 3825 Planarity : 0.006 0.068 4169 Dihedral : 14.653 167.261 4018 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.53 % Favored : 93.16 % Rotamer: Outliers : 6.32 % Allowed : 13.62 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 2893 helix: 0.60 (0.16), residues: 1017 sheet: -0.59 (0.27), residues: 347 loop : -1.67 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 938 HIS 0.009 0.002 HIS D 689 PHE 0.026 0.003 PHE C 906 TYR 0.019 0.002 TYR A 168 ARG 0.008 0.001 ARG C 870 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 286 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4938 (tpp) cc_final: 0.3952 (tmt) REVERT: A 99 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7184 (tttt) REVERT: A 193 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8379 (mt) REVERT: A 202 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7919 (tp) REVERT: A 221 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7098 (mt) REVERT: B 6 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7352 (tmt170) REVERT: B 24 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6726 (mt-10) REVERT: B 55 ARG cc_start: 0.7637 (ptm160) cc_final: 0.7170 (ptp90) REVERT: B 75 GLU cc_start: 0.7008 (mp0) cc_final: 0.6757 (mp0) REVERT: B 123 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7487 (ttp) REVERT: B 150 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8003 (t) REVERT: B 217 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: C 454 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7886 (mtp180) REVERT: C 505 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7530 (ptp-170) REVERT: C 584 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7745 (ttt180) REVERT: C 673 ARG cc_start: 0.8223 (ptm160) cc_final: 0.7599 (ptm-80) REVERT: C 877 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8093 (mtm-85) REVERT: C 1028 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8008 (ttm) REVERT: C 1030 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8360 (mm) REVERT: C 1062 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8041 (pt0) REVERT: C 1119 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7357 (tm-30) REVERT: D 9 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6971 (mt-10) REVERT: D 30 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.6970 (tppp) REVERT: D 92 MET cc_start: 0.8451 (mtp) cc_final: 0.7981 (mtm) REVERT: D 126 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6712 (tt0) REVERT: D 410 GLN cc_start: 0.8396 (mp10) cc_final: 0.7950 (mm-40) REVERT: D 423 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7975 (m-30) REVERT: D 623 ASP cc_start: 0.7098 (m-30) cc_final: 0.6884 (m-30) REVERT: D 665 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7688 (pp20) REVERT: D 672 MET cc_start: 0.8520 (mtt) cc_final: 0.8262 (mtt) REVERT: D 824 VAL cc_start: 0.8504 (m) cc_final: 0.8020 (p) REVERT: D 865 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7419 (mm) REVERT: D 901 LEU cc_start: 0.7369 (tp) cc_final: 0.7140 (tt) REVERT: D 959 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7026 (pt0) REVERT: E 31 THR cc_start: 0.7965 (t) cc_final: 0.7754 (m) REVERT: E 62 ARG cc_start: 0.8319 (mtt180) cc_final: 0.7765 (mmt-90) outliers start: 154 outliers final: 73 residues processed: 399 average time/residue: 1.3350 time to fit residues: 614.2002 Evaluate side-chains 349 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 252 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain C residue 1106 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 423 ASP Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 665 GLU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 913 ASP Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1262 THR Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 105 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 222 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 267 optimal weight: 0.5980 chunk 288 optimal weight: 10.0000 chunk 238 optimal weight: 0.9980 chunk 265 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 214 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 GLN D 748 HIS D1145 GLN D1273 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24491 Z= 0.207 Angle : 0.575 7.897 33475 Z= 0.304 Chirality : 0.043 0.165 3825 Planarity : 0.005 0.060 4169 Dihedral : 14.312 159.450 3998 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.01 % Favored : 94.71 % Rotamer: Outliers : 5.46 % Allowed : 17.02 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 2893 helix: 0.89 (0.17), residues: 1031 sheet: -0.56 (0.27), residues: 366 loop : -1.51 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 70 HIS 0.005 0.001 HIS D 748 PHE 0.024 0.001 PHE C 214 TYR 0.013 0.001 TYR D 586 ARG 0.006 0.000 ARG D 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 290 time to evaluate : 2.658 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4751 (tpp) cc_final: 0.4026 (tmt) REVERT: A 22 VAL cc_start: 0.8130 (p) cc_final: 0.7723 (t) REVERT: A 221 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7065 (mt) REVERT: B 6 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7431 (tmt170) REVERT: B 24 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6420 (mt-10) REVERT: B 123 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7446 (ttt) REVERT: B 150 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.7965 (t) REVERT: B 186 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7251 (mtp180) REVERT: C 163 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7392 (mmpt) REVERT: C 396 MET cc_start: 0.7152 (ttp) cc_final: 0.6833 (ttp) REVERT: C 505 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7486 (ptp-170) REVERT: C 584 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7726 (ttt180) REVERT: C 673 ARG cc_start: 0.8189 (ptm160) cc_final: 0.7583 (ptm-80) REVERT: C 877 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8079 (mtm-85) REVERT: C 1028 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8157 (ttm) REVERT: C 1030 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8359 (mm) REVERT: C 1063 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: C 1119 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: D 1 MET cc_start: 0.5584 (OUTLIER) cc_final: 0.5379 (mtt) REVERT: D 92 MET cc_start: 0.8388 (mtp) cc_final: 0.7927 (mtm) REVERT: D 350 ARG cc_start: 0.7631 (tpp-160) cc_final: 0.7368 (mmt180) REVERT: D 623 ASP cc_start: 0.7188 (m-30) cc_final: 0.6953 (m-30) REVERT: D 672 MET cc_start: 0.8481 (mtt) cc_final: 0.8240 (mtt) REVERT: D 824 VAL cc_start: 0.8129 (m) cc_final: 0.7628 (p) REVERT: D 865 LEU cc_start: 0.7716 (tp) cc_final: 0.7398 (mm) REVERT: D 959 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6863 (pt0) REVERT: E 31 THR cc_start: 0.8084 (t) cc_final: 0.7837 (m) REVERT: E 62 ARG cc_start: 0.8212 (mtt180) cc_final: 0.7885 (mmt-90) REVERT: E 66 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7090 (t0) REVERT: E 92 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7496 (tt) outliers start: 133 outliers final: 59 residues processed: 385 average time/residue: 1.2914 time to fit residues: 575.5099 Evaluate side-chains 335 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 258 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 545 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1106 ILE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1272 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 chunk 138 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 284 optimal weight: 0.0980 chunk 140 optimal weight: 0.6980 chunk 254 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS D1227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24491 Z= 0.183 Angle : 0.549 7.670 33475 Z= 0.289 Chirality : 0.042 0.164 3825 Planarity : 0.005 0.059 4169 Dihedral : 14.157 162.466 3988 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.18 % Favored : 94.50 % Rotamer: Outliers : 5.37 % Allowed : 17.72 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 2893 helix: 1.08 (0.17), residues: 1030 sheet: -0.52 (0.27), residues: 372 loop : -1.39 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 70 HIS 0.005 0.001 HIS D 748 PHE 0.026 0.001 PHE C 214 TYR 0.011 0.001 TYR D 586 ARG 0.009 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 282 time to evaluate : 2.769 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4825 (tpp) cc_final: 0.4011 (tmt) REVERT: A 22 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7693 (t) REVERT: A 193 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8095 (mt) REVERT: A 221 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7025 (mt) REVERT: B 24 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6365 (mt-10) REVERT: B 150 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.7962 (t) REVERT: C 163 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7447 (mmpt) REVERT: C 421 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6018 (mmp-170) REVERT: C 505 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7491 (ptp-170) REVERT: C 673 ARG cc_start: 0.8181 (ptm160) cc_final: 0.7552 (ptm-80) REVERT: C 877 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8073 (mtm-85) REVERT: C 1028 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8150 (ttm) REVERT: C 1030 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8331 (mm) REVERT: C 1063 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: C 1119 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: D 92 MET cc_start: 0.8366 (mtp) cc_final: 0.7976 (mtm) REVERT: D 350 ARG cc_start: 0.7623 (tpp-160) cc_final: 0.7344 (mmt180) REVERT: D 420 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8905 (mmtm) REVERT: D 672 MET cc_start: 0.8492 (mtt) cc_final: 0.8253 (mtt) REVERT: D 865 LEU cc_start: 0.7679 (tp) cc_final: 0.7342 (mm) REVERT: D 959 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6862 (pt0) REVERT: E 31 THR cc_start: 0.8092 (t) cc_final: 0.7876 (m) REVERT: E 62 ARG cc_start: 0.8202 (mtt180) cc_final: 0.7728 (mmt-90) REVERT: E 92 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7377 (tt) outliers start: 131 outliers final: 61 residues processed: 373 average time/residue: 1.2557 time to fit residues: 544.7442 Evaluate side-chains 340 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 263 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 421 ARG Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 545 ASN Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 901 VAL Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 420 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 791 GLU Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 0.6980 chunk 161 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 145 optimal weight: 0.7980 chunk 255 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 443 ASN ** C 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24491 Z= 0.218 Angle : 0.561 7.207 33475 Z= 0.295 Chirality : 0.043 0.154 3825 Planarity : 0.005 0.060 4169 Dihedral : 14.099 161.273 3981 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.18 % Favored : 94.54 % Rotamer: Outliers : 5.66 % Allowed : 18.25 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 2893 helix: 1.13 (0.17), residues: 1032 sheet: -0.44 (0.26), residues: 385 loop : -1.36 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 778 HIS 0.006 0.001 HIS D 748 PHE 0.022 0.002 PHE C 214 TYR 0.013 0.001 TYR D 749 ARG 0.005 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 276 time to evaluate : 2.703 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5012 (tpp) cc_final: 0.4192 (tmt) REVERT: A 193 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8176 (mt) REVERT: A 221 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7009 (mt) REVERT: B 24 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6359 (mt-10) REVERT: B 123 MET cc_start: 0.7901 (ttt) cc_final: 0.7682 (ttt) REVERT: B 139 VAL cc_start: 0.7887 (OUTLIER) cc_final: 0.7552 (t) REVERT: B 150 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.7967 (t) REVERT: C 111 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7686 (mtm180) REVERT: C 163 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7529 (mmpt) REVERT: C 421 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6011 (mmp-170) REVERT: C 505 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7507 (ptp-170) REVERT: C 584 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7728 (ttt180) REVERT: C 673 ARG cc_start: 0.8202 (ptm160) cc_final: 0.7609 (ptm-80) REVERT: C 877 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8075 (mtm-85) REVERT: C 1028 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8151 (ttm) REVERT: C 1030 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8173 (mm) REVERT: C 1119 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: D 92 MET cc_start: 0.8385 (mtp) cc_final: 0.8031 (mtm) REVERT: D 420 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8891 (mttp) REVERT: D 437 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7035 (mttm) REVERT: D 672 MET cc_start: 0.8524 (mtt) cc_final: 0.8281 (mtt) REVERT: D 865 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7316 (mm) REVERT: D 959 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6899 (pt0) REVERT: D 1117 ASP cc_start: 0.7445 (p0) cc_final: 0.7156 (p0) REVERT: E 31 THR cc_start: 0.8094 (t) cc_final: 0.7863 (m) REVERT: E 62 ARG cc_start: 0.8208 (mtt180) cc_final: 0.7740 (mmt-90) REVERT: E 92 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7303 (tt) outliers start: 138 outliers final: 75 residues processed: 378 average time/residue: 1.2951 time to fit residues: 565.6302 Evaluate side-chains 343 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 250 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 421 ARG Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 443 ASN Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 545 ASN Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 803 VAL Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1028 MET Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1106 ILE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain C residue 1138 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 143 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 420 LYS Chi-restraints excluded: chain D residue 437 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 913 ASP Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 1012 MET Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 6.9990 chunk 255 optimal weight: 0.0670 chunk 56 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 284 optimal weight: 7.9990 chunk 236 optimal weight: 0.5980 chunk 131 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS D 759 GLN D1139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24491 Z= 0.148 Angle : 0.516 7.892 33475 Z= 0.272 Chirality : 0.041 0.158 3825 Planarity : 0.004 0.059 4169 Dihedral : 13.966 161.088 3976 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.80 % Favored : 94.92 % Rotamer: Outliers : 4.47 % Allowed : 19.48 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2893 helix: 1.35 (0.17), residues: 1033 sheet: -0.32 (0.27), residues: 362 loop : -1.24 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 656 HIS 0.005 0.001 HIS D 748 PHE 0.008 0.001 PHE C 439 TYR 0.014 0.001 TYR D 61 ARG 0.006 0.000 ARG B 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 272 time to evaluate : 2.776 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4995 (tpp) cc_final: 0.4195 (tmt) REVERT: A 78 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7689 (tt) REVERT: A 158 GLU cc_start: 0.6550 (tt0) cc_final: 0.6346 (tt0) REVERT: A 221 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7036 (mt) REVERT: B 24 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.6229 (mt-10) REVERT: B 123 MET cc_start: 0.7890 (ttt) cc_final: 0.7651 (ttt) REVERT: B 139 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7599 (t) REVERT: B 150 VAL cc_start: 0.8257 (OUTLIER) cc_final: 0.7928 (t) REVERT: B 213 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7005 (ttpt) REVERT: C 111 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7766 (mtm180) REVERT: C 163 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7549 (mmpt) REVERT: C 415 GLN cc_start: 0.7450 (tp-100) cc_final: 0.7246 (mm-40) REVERT: C 505 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7408 (ptp-170) REVERT: C 580 ASP cc_start: 0.8481 (m-30) cc_final: 0.8225 (m-30) REVERT: C 584 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7664 (ttt180) REVERT: C 673 ARG cc_start: 0.8146 (ptm160) cc_final: 0.7545 (ptm-80) REVERT: C 787 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7247 (ttm170) REVERT: C 952 VAL cc_start: 0.7864 (m) cc_final: 0.7558 (t) REVERT: C 1119 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: D 92 MET cc_start: 0.8295 (mtp) cc_final: 0.7919 (mtm) REVERT: D 117 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7969 (tp) REVERT: D 134 TYR cc_start: 0.8071 (m-80) cc_final: 0.7798 (m-80) REVERT: D 496 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8136 (p) REVERT: D 959 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6715 (pt0) REVERT: E 62 ARG cc_start: 0.8172 (mtt180) cc_final: 0.7725 (mmt-90) REVERT: E 92 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7188 (tt) outliers start: 109 outliers final: 56 residues processed: 355 average time/residue: 1.3155 time to fit residues: 539.9431 Evaluate side-chains 325 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 254 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 787 ARG Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 177 optimal weight: 0.7980 chunk 172 optimal weight: 30.0000 chunk 130 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 HIS D1246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24491 Z= 0.315 Angle : 0.616 9.626 33475 Z= 0.321 Chirality : 0.045 0.163 3825 Planarity : 0.005 0.061 4169 Dihedral : 14.058 159.925 3970 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.57 % Favored : 94.16 % Rotamer: Outliers : 4.84 % Allowed : 19.89 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 2893 helix: 1.10 (0.17), residues: 1038 sheet: -0.27 (0.26), residues: 375 loop : -1.38 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 938 HIS 0.007 0.001 HIS D 748 PHE 0.024 0.002 PHE A 219 TYR 0.015 0.002 TYR C1027 ARG 0.004 0.000 ARG C 505 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 266 time to evaluate : 2.532 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5096 (tpp) cc_final: 0.4310 (tmt) REVERT: A 193 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8306 (mt) REVERT: A 200 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8229 (t0) REVERT: A 221 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.6888 (mt) REVERT: B 24 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6453 (mt-10) REVERT: B 123 MET cc_start: 0.7953 (ttt) cc_final: 0.7720 (ttt) REVERT: B 139 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7595 (t) REVERT: B 150 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.7981 (t) REVERT: B 217 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: C 111 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7734 (mtm180) REVERT: C 163 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7586 (mmpt) REVERT: C 421 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6048 (mmp-170) REVERT: C 505 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7544 (ptp-170) REVERT: C 584 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7739 (ttt180) REVERT: C 673 ARG cc_start: 0.8242 (ptm160) cc_final: 0.7610 (ptm-80) REVERT: C 787 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7353 (ttm170) REVERT: C 877 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8135 (mtm-85) REVERT: C 1102 VAL cc_start: 0.7027 (t) cc_final: 0.6802 (t) REVERT: C 1119 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: D 92 MET cc_start: 0.8407 (mtp) cc_final: 0.8048 (mtm) REVERT: D 117 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7902 (tp) REVERT: D 437 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7203 (mttm) REVERT: D 688 MET cc_start: 0.7983 (mmt) cc_final: 0.7726 (mmp) REVERT: D 865 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7320 (mm) REVERT: D 959 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6937 (pt0) REVERT: E 62 ARG cc_start: 0.8195 (mtt180) cc_final: 0.7730 (mmt-90) REVERT: E 87 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7313 (tp) REVERT: E 92 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7333 (tt) outliers start: 118 outliers final: 70 residues processed: 356 average time/residue: 1.3291 time to fit residues: 547.7821 Evaluate side-chains 343 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 253 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 421 ARG Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 787 ARG Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain C residue 1138 LEU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 437 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 865 LEU Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 913 ASP Chi-restraints excluded: chain D residue 959 GLN Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1166 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1262 THR Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 7.9990 chunk 113 optimal weight: 0.4980 chunk 169 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 193 optimal weight: 0.3980 chunk 140 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 222 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 759 GLN D1246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24491 Z= 0.166 Angle : 0.532 7.319 33475 Z= 0.279 Chirality : 0.041 0.144 3825 Planarity : 0.004 0.060 4169 Dihedral : 13.963 160.216 3970 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.70 % Favored : 95.06 % Rotamer: Outliers : 4.02 % Allowed : 20.96 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2893 helix: 1.33 (0.17), residues: 1033 sheet: -0.29 (0.27), residues: 379 loop : -1.27 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 70 HIS 0.004 0.001 HIS D 94 PHE 0.010 0.001 PHE C 906 TYR 0.013 0.001 TYR D 61 ARG 0.005 0.000 ARG C 584 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 269 time to evaluate : 2.807 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5083 (tpp) cc_final: 0.4331 (tmt) REVERT: A 221 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.6896 (mt) REVERT: B 1 MET cc_start: 0.6391 (OUTLIER) cc_final: 0.5000 (mtt) REVERT: B 77 ILE cc_start: 0.8317 (mm) cc_final: 0.8102 (mt) REVERT: B 139 VAL cc_start: 0.7867 (OUTLIER) cc_final: 0.7601 (t) REVERT: B 150 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.7933 (t) REVERT: C 111 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7721 (mtm180) REVERT: C 163 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7576 (mmpt) REVERT: C 505 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7374 (ptp-170) REVERT: C 580 ASP cc_start: 0.8508 (m-30) cc_final: 0.8258 (m-30) REVERT: C 584 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7667 (ttt180) REVERT: C 673 ARG cc_start: 0.8188 (ptm160) cc_final: 0.7541 (ptm-80) REVERT: C 877 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8038 (mtm-85) REVERT: C 1119 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7413 (tm-30) REVERT: D 92 MET cc_start: 0.8329 (mtp) cc_final: 0.8037 (mtm) REVERT: D 117 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7878 (tp) REVERT: D 636 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8064 (ttt180) REVERT: D 688 MET cc_start: 0.7909 (mmt) cc_final: 0.7673 (mmt) REVERT: D 865 LEU cc_start: 0.7569 (tp) cc_final: 0.7221 (mm) REVERT: D 917 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: E 62 ARG cc_start: 0.8157 (mtt180) cc_final: 0.7710 (mmt-90) REVERT: E 92 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7170 (tt) outliers start: 98 outliers final: 60 residues processed: 347 average time/residue: 1.3389 time to fit residues: 535.4474 Evaluate side-chains 324 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 251 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain C residue 1138 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 714 ASP Chi-restraints excluded: chain D residue 805 SER Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 ASN Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 917 GLU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 0.2980 chunk 271 optimal weight: 5.9990 chunk 247 optimal weight: 0.1980 chunk 264 optimal weight: 0.9980 chunk 158 optimal weight: 0.0040 chunk 115 optimal weight: 0.8980 chunk 207 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 238 optimal weight: 0.6980 chunk 249 optimal weight: 0.8980 chunk 263 optimal weight: 0.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 759 GLN D1246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24491 Z= 0.144 Angle : 0.508 7.245 33475 Z= 0.267 Chirality : 0.041 0.150 3825 Planarity : 0.004 0.060 4169 Dihedral : 13.848 159.531 3967 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.32 % Favored : 95.44 % Rotamer: Outliers : 3.49 % Allowed : 21.49 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2893 helix: 1.51 (0.17), residues: 1035 sheet: -0.25 (0.27), residues: 384 loop : -1.17 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 656 HIS 0.004 0.000 HIS D 94 PHE 0.007 0.001 PHE D 268 TYR 0.012 0.001 TYR D 61 ARG 0.009 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 262 time to evaluate : 2.636 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5072 (tpp) cc_final: 0.4318 (tmt) REVERT: A 221 LEU cc_start: 0.7746 (pt) cc_final: 0.6923 (mt) REVERT: B 1 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.4965 (mtt) REVERT: B 123 MET cc_start: 0.7929 (ttt) cc_final: 0.7648 (ttt) REVERT: B 139 VAL cc_start: 0.7868 (OUTLIER) cc_final: 0.7623 (t) REVERT: B 150 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7862 (t) REVERT: C 163 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7560 (mmtt) REVERT: C 584 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7584 (ttt180) REVERT: C 673 ARG cc_start: 0.8159 (ptm160) cc_final: 0.7516 (ptm-80) REVERT: C 877 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8068 (mtm-85) REVERT: C 952 VAL cc_start: 0.7854 (m) cc_final: 0.7556 (t) REVERT: C 1119 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7387 (tm-30) REVERT: D 92 MET cc_start: 0.8241 (mtp) cc_final: 0.7977 (mtm) REVERT: D 117 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7890 (tp) REVERT: D 134 TYR cc_start: 0.7967 (m-80) cc_final: 0.7698 (m-80) REVERT: D 987 LYS cc_start: 0.8279 (mttp) cc_final: 0.8073 (mttp) REVERT: E 62 ARG cc_start: 0.8134 (mtt180) cc_final: 0.7693 (mmt-90) REVERT: E 92 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6988 (tt) outliers start: 85 outliers final: 54 residues processed: 333 average time/residue: 1.2878 time to fit residues: 497.0494 Evaluate side-chains 323 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 260 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain C residue 1138 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1166 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 8.9990 chunk 279 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 292 optimal weight: 10.0000 chunk 269 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 233 GLN D1246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24491 Z= 0.226 Angle : 0.565 7.966 33475 Z= 0.295 Chirality : 0.043 0.153 3825 Planarity : 0.005 0.060 4169 Dihedral : 13.919 157.937 3963 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.01 % Favored : 94.75 % Rotamer: Outliers : 3.36 % Allowed : 21.99 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2893 helix: 1.38 (0.17), residues: 1035 sheet: -0.29 (0.26), residues: 388 loop : -1.24 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 778 HIS 0.004 0.001 HIS D 689 PHE 0.018 0.002 PHE C 906 TYR 0.016 0.001 TYR D 130 ARG 0.005 0.000 ARG C 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5786 Ramachandran restraints generated. 2893 Oldfield, 0 Emsley, 2893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 263 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5101 (tpp) cc_final: 0.4345 (tmt) REVERT: A 221 LEU cc_start: 0.7819 (pt) cc_final: 0.6967 (mt) REVERT: B 1 MET cc_start: 0.6455 (OUTLIER) cc_final: 0.5142 (mtt) REVERT: B 123 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7654 (ttt) REVERT: B 139 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7596 (t) REVERT: B 150 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.7861 (t) REVERT: B 217 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: C 127 MET cc_start: 0.7895 (ptp) cc_final: 0.7605 (pmm) REVERT: C 163 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7605 (mmpt) REVERT: C 584 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7622 (ttt180) REVERT: C 673 ARG cc_start: 0.8216 (ptm160) cc_final: 0.7573 (ptm-80) REVERT: C 877 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8079 (mtm-85) REVERT: C 1119 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7358 (tm-30) REVERT: D 92 MET cc_start: 0.8322 (mtp) cc_final: 0.7976 (mtm) REVERT: D 117 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7879 (tp) REVERT: D 134 TYR cc_start: 0.7972 (m-80) cc_final: 0.7699 (m-80) REVERT: D 636 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8058 (ttt180) REVERT: D 865 LEU cc_start: 0.7431 (tp) cc_final: 0.7194 (mm) REVERT: D 987 LYS cc_start: 0.8239 (mttp) cc_final: 0.7980 (mttt) REVERT: E 62 ARG cc_start: 0.8133 (mtt180) cc_final: 0.7704 (mmt-90) REVERT: E 92 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7110 (tt) outliers start: 82 outliers final: 53 residues processed: 326 average time/residue: 1.3065 time to fit residues: 493.8152 Evaluate side-chains 315 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 250 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 758 ASP Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 869 VAL Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 877 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1076 MET Chi-restraints excluded: chain C residue 1117 ILE Chi-restraints excluded: chain C residue 1119 GLU Chi-restraints excluded: chain C residue 1138 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 636 ARG Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1166 THR Chi-restraints excluded: chain D residue 1181 ILE Chi-restraints excluded: chain D residue 1277 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 92 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 64 optimal weight: 9.9990 chunk 233 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 759 GLN D1246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.199743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.153364 restraints weight = 25755.502| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.59 r_work: 0.3423 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24491 Z= 0.235 Angle : 0.568 7.747 33475 Z= 0.297 Chirality : 0.043 0.161 3825 Planarity : 0.005 0.060 4169 Dihedral : 13.957 157.409 3963 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.77 % Favored : 94.99 % Rotamer: Outliers : 3.32 % Allowed : 22.27 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2893 helix: 1.30 (0.17), residues: 1035 sheet: -0.28 (0.26), residues: 382 loop : -1.26 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 778 HIS 0.005 0.001 HIS D 689 PHE 0.017 0.002 PHE C 906 TYR 0.013 0.001 TYR D 61 ARG 0.005 0.000 ARG C 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8975.41 seconds wall clock time: 159 minutes 53.09 seconds (9593.09 seconds total)