Starting phenix.real_space_refine on Mon Feb 19 22:31:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xln_22249/02_2024/6xln_22249_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xln_22249/02_2024/6xln_22249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xln_22249/02_2024/6xln_22249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xln_22249/02_2024/6xln_22249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xln_22249/02_2024/6xln_22249_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xln_22249/02_2024/6xln_22249_updated.pdb" } resolution = 2.8 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= 0.002 sd= 0.132 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 40 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16148 2.51 5 N 4582 2.21 5 O 5077 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 62": "OD1" <-> "OD2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B ASP 135": "OD1" <-> "OD2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B ASP 233": "OD1" <-> "OD2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C ASP 116": "OD1" <-> "OD2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ASP 281": "OD1" <-> "OD2" Residue "C GLU 290": "OE1" <-> "OE2" Residue "C ASP 320": "OD1" <-> "OD2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ASP 342": "OD1" <-> "OD2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 446": "OD1" <-> "OD2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C ASP 491": "OD1" <-> "OD2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C ASP 549": "OD1" <-> "OD2" Residue "C ASP 596": "OD1" <-> "OD2" Residue "C GLU 610": "OE1" <-> "OE2" Residue "C GLU 641": "OE1" <-> "OE2" Residue "C ASP 781": "OD1" <-> "OD2" Residue "C PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 930": "OD1" <-> "OD2" Residue "C ASP 959": "OD1" <-> "OD2" Residue "C ASP 1004": "OD1" <-> "OD2" Residue "C GLU 1012": "OE1" <-> "OE2" Residue "C TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1024": "OE1" <-> "OE2" Residue "C TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1059": "NH1" <-> "NH2" Residue "C GLU 1083": "OE1" <-> "OE2" Residue "C ASP 1126": "OD1" <-> "OD2" Residue "C ASP 1160": "OD1" <-> "OD2" Residue "C GLU 1192": "OE1" <-> "OE2" Residue "C TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D GLU 211": "OE1" <-> "OE2" Residue "D ASP 267": "OD1" <-> "OD2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D ARG 431": "NH1" <-> "NH2" Residue "D PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D ASP 505": "OD1" <-> "OD2" Residue "D GLU 532": "OE1" <-> "OE2" Residue "D GLU 660": "OE1" <-> "OE2" Residue "D GLU 663": "OE1" <-> "OE2" Residue "D PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 751": "OD1" <-> "OD2" Residue "D TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 830": "OD1" <-> "OD2" Residue "D ASP 902": "OD1" <-> "OD2" Residue "D PHE 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1015": "OE1" <-> "OE2" Residue "D PHE 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1042": "OD1" <-> "OD2" Residue "D ASP 1051": "OD1" <-> "OD2" Residue "D TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1110": "OE1" <-> "OE2" Residue "D ASP 1143": "OD1" <-> "OD2" Residue "D PHE 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1184": "OD1" <-> "OD2" Residue "D GLU 1200": "OE1" <-> "OE2" Residue "D GLU 1205": "OE1" <-> "OE2" Residue "D GLU 1278": "OE1" <-> "OE2" Residue "D PHE 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1327": "OE1" <-> "OE2" Residue "E ASP 18": "OD1" <-> "OD2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E ASP 44": "OD1" <-> "OD2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E GLU 79": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25956 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1793 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain: "B" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1711 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Chain: "C" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10560 Classifications: {'peptide': 1339} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1282} Chain: "D" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10381 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "N" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "R" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 193 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 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 14513 SG CYS D 70 100.483 41.374 69.547 1.00126.38 S ATOM 14527 SG CYS D 72 100.554 37.839 68.965 1.00129.54 S ATOM 14635 SG CYS D 85 102.971 39.790 67.518 1.00129.74 S ATOM 14659 SG CYS D 88 98.965 40.046 66.652 1.00129.43 S ATOM 20341 SG CYS D 814 88.381 106.087 73.943 1.00 89.97 S ATOM 20906 SG CYS D 888 86.529 103.030 73.832 1.00 91.64 S ATOM 20957 SG CYS D 895 87.888 104.356 76.782 1.00 82.79 S ATOM 20978 SG CYS D 898 85.411 106.176 75.448 1.00 85.12 S Time building chain proxies: 14.89, per 1000 atoms: 0.57 Number of scatterers: 25956 At special positions: 0 Unit cell: (138.632, 151.962, 163.959, 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 106 16.00 P 40 15.00 Mg 1 11.99 O 5077 8.00 N 4582 7.00 C 16148 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: 10.59 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " Number of angles added : 12 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 37 sheets defined 32.9% alpha, 14.3% beta 14 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 13.74 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 78 through 87 removed outlier: 4.071A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 155 through 160 removed outlier: 5.009A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 227 Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 78 through 86 removed outlier: 3.676A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 155 through 158 No H-bonds generated for 'chain 'B' and resid 155 through 158' Processing helix chain 'B' and resid 213 through 230 removed outlier: 3.670A pdb=" N GLU B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 243 through 246 Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 319 through 328 removed outlier: 3.700A pdb=" N SER C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.929A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 422 through 437 Processing helix chain 'C' and resid 456 through 480 removed outlier: 3.520A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 486 No H-bonds generated for 'chain 'C' and resid 484 through 486' Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 496 through 508 removed outlier: 4.034A pdb=" N LYS C 503 " --> pdb=" O SER C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 611 through 613 No H-bonds generated for 'chain 'C' and resid 611 through 613' Processing helix chain 'C' and resid 657 through 659 No H-bonds generated for 'chain 'C' and resid 657 through 659' Processing helix chain 'C' and resid 665 through 667 No H-bonds generated for 'chain 'C' and resid 665 through 667' Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 676 through 685 Processing helix chain 'C' and resid 705 through 711 Processing helix chain 'C' and resid 820 through 824 Processing helix chain 'C' and resid 897 through 906 removed outlier: 3.577A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 981 Processing helix chain 'C' and resid 986 through 989 No H-bonds generated for 'chain 'C' and resid 986 through 989' Processing helix chain 'C' and resid 994 through 999 removed outlier: 4.355A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU C 999 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1037 removed outlier: 3.597A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU C1030 " --> pdb=" O GLU C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1084 No H-bonds generated for 'chain 'C' and resid 1082 through 1084' Processing helix chain 'C' and resid 1100 through 1104 Proline residue: C1104 - end of helix Processing helix chain 'C' and resid 1109 through 1133 removed outlier: 3.907A pdb=" N LEU C1113 " --> pdb=" O GLY C1110 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU C1114 " --> pdb=" O GLN C1111 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY C1118 " --> pdb=" O THR C1115 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET C1119 " --> pdb=" O HIS C1116 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA C1121 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE C1124 " --> pdb=" O ALA C1121 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP C1126 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN C1129 " --> pdb=" O ASP C1126 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C1132 " --> pdb=" O ASN C1129 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1150 Processing helix chain 'C' and resid 1161 through 1163 No H-bonds generated for 'chain 'C' and resid 1161 through 1163' Processing helix chain 'C' and resid 1166 through 1176 Processing helix chain 'C' and resid 1192 through 1202 Processing helix chain 'C' and resid 1239 through 1242 No H-bonds generated for 'chain 'C' and resid 1239 through 1242' Processing helix chain 'C' and resid 1272 through 1280 Processing helix chain 'C' and resid 1284 through 1291 Processing helix chain 'C' and resid 1298 through 1309 removed outlier: 4.032A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1321 through 1331 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 59 through 62 No H-bonds generated for 'chain 'D' and resid 59 through 62' Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 115 through 118 No H-bonds generated for 'chain 'D' and resid 115 through 118' Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 132 through 139 removed outlier: 4.088A pdb=" N ARG D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 166 No H-bonds generated for 'chain 'D' and resid 163 through 166' Processing helix chain 'D' and resid 168 through 171 No H-bonds generated for 'chain 'D' and resid 168 through 171' Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 194 through 207 removed outlier: 3.725A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 229 removed outlier: 4.295A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 265 through 282 removed outlier: 3.527A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 307 Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 370 through 376 removed outlier: 3.702A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 387 Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 406 through 415 removed outlier: 3.884A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 451 through 457 removed outlier: 3.969A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 506 through 514 Processing helix chain 'D' and resid 530 through 538 Processing helix chain 'D' and resid 574 through 582 removed outlier: 3.893A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 591 No H-bonds generated for 'chain 'D' and resid 589 through 591' Processing helix chain 'D' and resid 598 through 611 Processing helix chain 'D' and resid 614 through 635 removed outlier: 3.773A pdb=" N ASP D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 668 removed outlier: 3.753A pdb=" N SER D 655 " --> pdb=" O HIS D 651 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA D 659 " --> pdb=" O SER D 655 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 701 Processing helix chain 'D' and resid 721 through 727 Processing helix chain 'D' and resid 734 through 741 removed outlier: 4.186A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 804 removed outlier: 3.701A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'D' and resid 866 through 874 Processing helix chain 'D' and resid 885 through 887 No H-bonds generated for 'chain 'D' and resid 885 through 887' Processing helix chain 'D' and resid 896 through 899 No H-bonds generated for 'chain 'D' and resid 896 through 899' Processing helix chain 'D' and resid 915 through 924 Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1138 through 1145 Processing helix chain 'D' and resid 1217 through 1244 removed outlier: 7.530A pdb=" N VAL D1226 " --> pdb=" O ARG D1222 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N HIS D1227 " --> pdb=" O LEU D1223 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA D1228 " --> pdb=" O ARG D1224 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D1243 " --> pdb=" O ASP D1239 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1260 removed outlier: 4.287A pdb=" N VAL D1255 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG D1258 " --> pdb=" O VAL D1255 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.943A pdb=" N ASN D1295 " --> pdb=" O GLU D1291 " (cutoff:3.500A) Processing helix chain 'D' and resid 1309 through 1314 Processing helix chain 'D' and resid 1320 through 1323 No H-bonds generated for 'chain 'D' and resid 1320 through 1323' Processing helix chain 'D' and resid 1328 through 1338 Processing helix chain 'D' and resid 1348 through 1352 Processing helix chain 'D' and resid 1360 through 1371 removed outlier: 4.459A pdb=" N ALA D1364 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN D1367 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG D1369 " --> pdb=" O HIS D1366 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 12 removed outlier: 3.637A pdb=" N GLU E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 7 through 12' Processing helix chain 'E' and resid 16 through 31 removed outlier: 4.093A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 61 through 77 Processing sheet with id= A, first strand: chain 'A' and resid 12 through 18 removed outlier: 6.666A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLN A 18 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N HIS A 23 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.714A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= D, first strand: chain 'A' and resid 108 through 111 Processing sheet with id= E, first strand: chain 'B' and resid 13 through 20 removed outlier: 6.382A pdb=" N HIS B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 90 through 92 Processing sheet with id= G, first strand: chain 'B' and resid 97 through 106 removed outlier: 4.319A pdb=" N ALA B 138 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.635A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= J, first strand: chain 'C' and resid 136 through 138 Processing sheet with id= K, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= L, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.581A pdb=" N ASP C 160 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 227 through 231 Processing sheet with id= N, first strand: chain 'C' and resid 529 through 531 Processing sheet with id= O, first strand: chain 'C' and resid 603 through 606 Processing sheet with id= P, first strand: chain 'C' and resid 633 through 638 Processing sheet with id= Q, first strand: chain 'C' and resid 748 through 752 removed outlier: 5.958A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 1226 through 1232 removed outlier: 4.343A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE C1096 " --> pdb=" O ALA C 803 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 887 through 889 Processing sheet with id= T, first strand: chain 'C' and resid 1065 through 1067 removed outlier: 7.378A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 66 through 75 removed outlier: 6.771A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.766A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= X, first strand: chain 'D' and resid 253 through 255 removed outlier: 3.658A pdb=" N ARG D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 350 through 354 Processing sheet with id= Z, first strand: chain 'D' and resid 547 through 557 Processing sheet with id= AA, first strand: chain 'D' and resid 703 through 707 Processing sheet with id= AB, first strand: chain 'D' and resid 820 through 823 Processing sheet with id= AC, first strand: chain 'D' and resid 957 through 961 removed outlier: 4.080A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= AE, first strand: chain 'D' and resid 1034 through 1038 Processing sheet with id= AF, first strand: chain 'D' and resid 1046 through 1050 Processing sheet with id= AG, first strand: chain 'D' and resid 1187 through 1191 removed outlier: 4.110A pdb=" N LYS D1167 " --> pdb=" O ARG D1174 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL D1176 " --> pdb=" O PHE D1165 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N PHE D1165 " --> pdb=" O VAL D1176 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N THR D1178 " --> pdb=" O VAL D1163 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL D1163 " --> pdb=" O THR D1178 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.701A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 145 through 148 removed outlier: 7.385A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'D' and resid 949 through 951 removed outlier: 4.105A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 3.818A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2310 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 10.87 Time building geometry restraints manager: 11.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7066 1.33 - 1.45: 4299 1.45 - 1.57: 14800 1.57 - 1.69: 77 1.69 - 1.81: 184 Bond restraints: 26426 Sorted by residual: bond pdb=" CA LEU C 351 " pdb=" C LEU C 351 " ideal model delta sigma weight residual 1.522 1.485 0.037 1.37e-02 5.33e+03 7.29e+00 bond pdb=" CG1 ILE C1076 " pdb=" CD1 ILE C1076 " ideal model delta sigma weight residual 1.513 1.416 0.097 3.90e-02 6.57e+02 6.19e+00 bond pdb=" CB THR D 890 " pdb=" OG1 THR D 890 " ideal model delta sigma weight residual 1.433 1.394 0.039 1.60e-02 3.91e+03 5.86e+00 bond pdb=" CB VAL D 548 " pdb=" CG2 VAL D 548 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.49e+00 bond pdb=" CB VAL D 507 " pdb=" CG2 VAL D 507 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.20e+00 ... (remaining 26421 not shown) Histogram of bond angle deviations from ideal: 96.71 - 104.19: 561 104.19 - 111.66: 12423 111.66 - 119.14: 9556 119.14 - 126.62: 13001 126.62 - 134.10: 337 Bond angle restraints: 35878 Sorted by residual: angle pdb=" N ASP C1296 " pdb=" CA ASP C1296 " pdb=" C ASP C1296 " ideal model delta sigma weight residual 111.28 123.15 -11.87 1.09e+00 8.42e-01 1.19e+02 angle pdb=" C CYS D 70 " pdb=" N LEU D 71 " pdb=" CA LEU D 71 " ideal model delta sigma weight residual 120.28 126.55 -6.27 1.44e+00 4.82e-01 1.90e+01 angle pdb=" C SER C 4 " pdb=" N TYR C 5 " pdb=" CA TYR C 5 " ideal model delta sigma weight residual 122.36 115.51 6.85 1.72e+00 3.38e-01 1.58e+01 angle pdb=" C ILE D 500 " pdb=" CA ILE D 500 " pdb=" CB ILE D 500 " ideal model delta sigma weight residual 112.68 108.20 4.48 1.14e+00 7.69e-01 1.55e+01 angle pdb=" N ILE D1253 " pdb=" CA ILE D1253 " pdb=" C ILE D1253 " ideal model delta sigma weight residual 111.81 108.51 3.30 8.60e-01 1.35e+00 1.47e+01 ... (remaining 35873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.32: 15261 24.32 - 48.64: 886 48.64 - 72.96: 130 72.96 - 97.27: 21 97.27 - 121.59: 4 Dihedral angle restraints: 16302 sinusoidal: 7098 harmonic: 9204 Sorted by residual: dihedral pdb=" CA PHE C1265 " pdb=" C PHE C1265 " pdb=" N GLY C1266 " pdb=" CA GLY C1266 " ideal model delta harmonic sigma weight residual 180.00 152.94 27.06 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA SER C1332 " pdb=" C SER C1332 " pdb=" N LEU C1333 " pdb=" CA LEU C1333 " ideal model delta harmonic sigma weight residual 180.00 153.58 26.42 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA PHE C 906 " pdb=" C PHE C 906 " pdb=" N GLY C 907 " pdb=" CA GLY C 907 " ideal model delta harmonic sigma weight residual 180.00 153.66 26.34 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 16299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3709 0.093 - 0.187: 384 0.187 - 0.280: 16 0.280 - 0.374: 4 0.374 - 0.467: 2 Chirality restraints: 4115 Sorted by residual: chirality pdb=" CA ASP C1296 " pdb=" N ASP C1296 " pdb=" C ASP C1296 " pdb=" CB ASP C1296 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CB VAL A 192 " pdb=" CA VAL A 192 " pdb=" CG1 VAL A 192 " pdb=" CG2 VAL A 192 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CG LEU C1101 " pdb=" CB LEU C1101 " pdb=" CD1 LEU C1101 " pdb=" CD2 LEU C1101 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.47e+00 ... (remaining 4112 not shown) Planarity restraints: 4552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 115 " 0.021 2.00e-02 2.50e+03 1.62e-02 6.55e+00 pdb=" CG TRP D 115 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP D 115 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP D 115 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 115 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 115 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 115 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 115 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 115 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 115 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 749 " 0.042 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO D 750 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 750 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 750 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 75 " -0.029 2.00e-02 2.50e+03 1.57e-02 4.93e+00 pdb=" CG TYR D 75 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR D 75 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR D 75 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR D 75 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 75 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 75 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 75 " -0.022 2.00e-02 2.50e+03 ... (remaining 4549 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 114 2.44 - 3.05: 16605 3.05 - 3.67: 39202 3.67 - 4.28: 60703 4.28 - 4.90: 102129 Nonbonded interactions: 218753 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 1.822 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1501 " model vdw 1.921 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 2.044 2.170 nonbonded pdb=" O PHE D 17 " pdb=" NH2 ARG D1355 " model vdw 2.196 2.520 nonbonded pdb=" OE1 GLU C 562 " pdb=" OG SER C 662 " model vdw 2.199 2.440 ... (remaining 218748 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 5 through 159 or resid 169 through 234)) selection = (chain 'B' and resid 5 through 234) } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.270 Check model and map are aligned: 0.420 Set scattering table: 0.280 Process input model: 85.570 Find NCS groups from input model: 1.060 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:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.097 26426 Z= 0.746 Angle : 0.926 11.875 35878 Z= 0.538 Chirality : 0.058 0.467 4115 Planarity : 0.005 0.063 4552 Dihedral : 15.283 121.593 10382 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 0.94 % Favored : 99.03 % Rotamer: Outliers : 0.22 % Allowed : 5.87 % Favored : 93.91 % 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: -2.97 (0.12), residues: 3191 helix: -2.38 (0.12), residues: 1107 sheet: -1.82 (0.22), residues: 424 loop : -1.64 (0.13), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP D 115 HIS 0.009 0.002 HIS B 23 PHE 0.020 0.003 PHE D 172 TYR 0.029 0.003 TYR D 75 ARG 0.008 0.001 ARG D1262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 316 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.8214 (mp10) cc_final: 0.7917 (pm20) REVERT: A 145 LYS cc_start: 0.8802 (tttt) cc_final: 0.8566 (ttpp) REVERT: A 194 GLN cc_start: 0.7790 (tp-100) cc_final: 0.7194 (tm-30) REVERT: A 205 MET cc_start: 0.8464 (mtp) cc_final: 0.7964 (mtp) REVERT: B 18 GLN cc_start: 0.8005 (mp10) cc_final: 0.7520 (mm-40) REVERT: B 95 LYS cc_start: 0.8695 (mttt) cc_final: 0.8417 (mttt) REVERT: B 127 GLN cc_start: 0.8162 (pm20) cc_final: 0.7919 (pm20) REVERT: B 145 LYS cc_start: 0.8566 (tttt) cc_final: 0.8326 (ttpt) REVERT: B 200 LYS cc_start: 0.8845 (tttt) cc_final: 0.8546 (tmmt) REVERT: C 70 TYR cc_start: 0.8350 (t80) cc_final: 0.8149 (t80) REVERT: C 115 LYS cc_start: 0.7751 (mttt) cc_final: 0.7512 (mttt) REVERT: C 142 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7807 (tt0) REVERT: C 158 ASP cc_start: 0.7224 (t70) cc_final: 0.6977 (t0) REVERT: C 191 LYS cc_start: 0.8693 (mmpt) cc_final: 0.8477 (mmtp) REVERT: C 200 ARG cc_start: 0.8123 (mmm160) cc_final: 0.7892 (mmm160) REVERT: C 222 ASP cc_start: 0.7713 (m-30) cc_final: 0.7365 (m-30) REVERT: C 230 PHE cc_start: 0.7440 (m-80) cc_final: 0.7206 (m-80) REVERT: C 335 THR cc_start: 0.7237 (m) cc_final: 0.6911 (p) REVERT: C 349 GLU cc_start: 0.7639 (mp0) cc_final: 0.6997 (mp0) REVERT: C 422 LYS cc_start: 0.8694 (mttt) cc_final: 0.8457 (mtpt) REVERT: C 439 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8480 (ttmt) REVERT: C 488 MET cc_start: 0.7483 (mmm) cc_final: 0.7122 (tpp) REVERT: C 503 LYS cc_start: 0.8648 (tptp) cc_final: 0.8271 (tttt) REVERT: C 516 ASP cc_start: 0.7825 (t70) cc_final: 0.7599 (t70) REVERT: C 653 MET cc_start: 0.8752 (ttt) cc_final: 0.8322 (ttm) REVERT: C 768 MET cc_start: 0.7797 (mtp) cc_final: 0.7523 (mtp) REVERT: C 943 LYS cc_start: 0.8541 (tppt) cc_final: 0.8321 (tppp) REVERT: C 950 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8129 (tm-30) REVERT: C 955 GLN cc_start: 0.8192 (tp40) cc_final: 0.7527 (tp-100) REVERT: C 965 GLN cc_start: 0.7591 (mt0) cc_final: 0.7353 (mt0) REVERT: C 1025 PHE cc_start: 0.7170 (t80) cc_final: 0.6844 (t80) REVERT: C 1027 LYS cc_start: 0.8831 (tptp) cc_final: 0.8518 (pttt) REVERT: C 1032 LYS cc_start: 0.8025 (ptpp) cc_final: 0.7790 (ptpp) REVERT: C 1167 GLU cc_start: 0.7926 (tp30) cc_final: 0.7357 (tm-30) REVERT: D 74 LYS cc_start: 0.9152 (tttt) cc_final: 0.8891 (ttmm) REVERT: D 151 MET cc_start: 0.6986 (mpp) cc_final: 0.5935 (pp-130) REVERT: D 200 GLN cc_start: 0.8434 (tt0) cc_final: 0.8197 (mt0) REVERT: D 289 ASP cc_start: 0.6950 (m-30) cc_final: 0.6588 (t0) REVERT: D 398 LYS cc_start: 0.8222 (tttm) cc_final: 0.7731 (ttmm) REVERT: D 402 GLU cc_start: 0.8269 (pp20) cc_final: 0.7978 (pp20) REVERT: D 603 LYS cc_start: 0.7844 (tttt) cc_final: 0.7609 (ttpt) REVERT: D 781 LYS cc_start: 0.7792 (tttt) cc_final: 0.7370 (ttpt) REVERT: D 955 LYS cc_start: 0.8569 (pttt) cc_final: 0.8295 (pptt) REVERT: D 1190 ILE cc_start: 0.7765 (mt) cc_final: 0.7540 (mp) REVERT: E 8 ASP cc_start: 0.8413 (m-30) cc_final: 0.7925 (m-30) REVERT: E 11 GLU cc_start: 0.8050 (mp0) cc_final: 0.7644 (mp0) REVERT: E 41 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7183 (tm-30) REVERT: E 42 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7995 (mt-10) REVERT: E 68 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7331 (tm-30) REVERT: E 72 GLN cc_start: 0.8441 (tt0) cc_final: 0.8013 (tm-30) outliers start: 6 outliers final: 3 residues processed: 322 average time/residue: 1.7166 time to fit residues: 626.7435 Evaluate side-chains 228 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 225 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 1186 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 6.9990 chunk 242 optimal weight: 7.9990 chunk 134 optimal weight: 0.0020 chunk 82 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 250 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 290 optimal weight: 6.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 160 HIS A 194 GLN B 137 ASN C 46 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN C 518 ASN C 582 ASN C 620 ASN C 628 HIS C 649 GLN C 673 HIS C 798 GLN C 955 GLN C1017 GLN C1061 GLN C1134 GLN C1244 HIS C1268 GLN D 80 HIS D 157 GLN D 158 GLN D 209 ASN D 274 ASN D 817 HIS D 910 ASN D1244 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26426 Z= 0.188 Angle : 0.540 9.041 35878 Z= 0.284 Chirality : 0.043 0.177 4115 Planarity : 0.004 0.061 4552 Dihedral : 10.842 81.208 4118 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.61 % Allowed : 11.73 % Favored : 86.66 % 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: -1.65 (0.14), residues: 3191 helix: -0.95 (0.15), residues: 1103 sheet: -1.27 (0.23), residues: 437 loop : -1.04 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 115 HIS 0.006 0.001 HIS C1237 PHE 0.020 0.001 PHE C 337 TYR 0.017 0.001 TYR D 679 ARG 0.007 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 272 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.7878 (tpp80) REVERT: A 127 GLN cc_start: 0.8148 (mp10) cc_final: 0.7864 (pm20) REVERT: A 145 LYS cc_start: 0.8682 (tttt) cc_final: 0.8462 (ttpp) REVERT: A 194 GLN cc_start: 0.7889 (tp40) cc_final: 0.7614 (tm-30) REVERT: A 205 MET cc_start: 0.8290 (mtp) cc_final: 0.7841 (mtp) REVERT: B 18 GLN cc_start: 0.8014 (mp10) cc_final: 0.7591 (mm-40) REVERT: B 95 LYS cc_start: 0.8530 (mttt) cc_final: 0.8233 (mttt) REVERT: B 127 GLN cc_start: 0.8101 (pm20) cc_final: 0.7859 (pm20) REVERT: B 145 LYS cc_start: 0.8540 (tttt) cc_final: 0.8303 (ttpt) REVERT: B 200 LYS cc_start: 0.8639 (tttt) cc_final: 0.8350 (tmmt) REVERT: C 46 GLN cc_start: 0.8537 (mt0) cc_final: 0.8325 (mt0) REVERT: C 70 TYR cc_start: 0.8310 (t80) cc_final: 0.7926 (t80) REVERT: C 222 ASP cc_start: 0.7529 (m-30) cc_final: 0.7113 (m-30) REVERT: C 230 PHE cc_start: 0.7369 (m-80) cc_final: 0.6743 (m-80) REVERT: C 370 MET cc_start: 0.8199 (mmm) cc_final: 0.7978 (mmm) REVERT: C 422 LYS cc_start: 0.8638 (mttt) cc_final: 0.8415 (mtpt) REVERT: C 439 LYS cc_start: 0.8716 (ttpt) cc_final: 0.8361 (ttmt) REVERT: C 503 LYS cc_start: 0.8481 (tptp) cc_final: 0.8026 (tttt) REVERT: C 600 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8338 (p) REVERT: C 633 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7744 (tp) REVERT: C 694 ARG cc_start: 0.7850 (mmt90) cc_final: 0.7531 (mtm-85) REVERT: C 738 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.8009 (tp30) REVERT: C 768 MET cc_start: 0.7659 (mtp) cc_final: 0.7378 (mtp) REVERT: C 876 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7514 (tm-30) REVERT: C 955 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7670 (tp-100) REVERT: C 1025 PHE cc_start: 0.7145 (t80) cc_final: 0.6797 (t80) REVERT: C 1027 LYS cc_start: 0.8812 (tptp) cc_final: 0.8509 (pttt) REVERT: C 1163 THR cc_start: 0.8679 (m) cc_final: 0.8433 (p) REVERT: C 1167 GLU cc_start: 0.7688 (tp30) cc_final: 0.7367 (tm-30) REVERT: D 80 HIS cc_start: 0.7535 (OUTLIER) cc_final: 0.6756 (p-80) REVERT: D 151 MET cc_start: 0.6604 (mpp) cc_final: 0.5732 (ppp) REVERT: D 159 ILE cc_start: 0.8792 (pp) cc_final: 0.8589 (tp) REVERT: D 200 GLN cc_start: 0.8557 (tt0) cc_final: 0.8272 (mt0) REVERT: D 217 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8055 (tp) REVERT: D 312 ARG cc_start: 0.7228 (mmm160) cc_final: 0.7028 (mmm160) REVERT: D 375 GLU cc_start: 0.8063 (tp30) cc_final: 0.7798 (mm-30) REVERT: D 398 LYS cc_start: 0.8174 (tttm) cc_final: 0.7750 (ttmm) REVERT: D 603 LYS cc_start: 0.7741 (tttt) cc_final: 0.7514 (ttmt) REVERT: D 738 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6976 (mtt180) REVERT: D 781 LYS cc_start: 0.7898 (tttt) cc_final: 0.7483 (ttpt) REVERT: D 955 LYS cc_start: 0.8846 (pttt) cc_final: 0.8498 (pptt) REVERT: D 993 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6621 (pp20) REVERT: D 1189 MET cc_start: 0.8584 (mtt) cc_final: 0.8348 (mmm) REVERT: D 1195 GLN cc_start: 0.7101 (pm20) cc_final: 0.6339 (pp30) REVERT: E 8 ASP cc_start: 0.8329 (m-30) cc_final: 0.7858 (m-30) REVERT: E 11 GLU cc_start: 0.7984 (mp0) cc_final: 0.7512 (mp0) REVERT: E 35 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.6779 (mptt) REVERT: E 41 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6874 (tm-30) REVERT: E 68 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7243 (tm-30) REVERT: E 72 GLN cc_start: 0.8457 (tt0) cc_final: 0.7932 (tm-30) REVERT: E 76 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7503 (mt-10) outliers start: 44 outliers final: 10 residues processed: 299 average time/residue: 1.5714 time to fit residues: 537.6552 Evaluate side-chains 239 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 221 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 738 GLU Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 35 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 241 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 291 optimal weight: 7.9990 chunk 314 optimal weight: 7.9990 chunk 259 optimal weight: 6.9990 chunk 288 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 233 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26426 Z= 0.252 Angle : 0.540 9.998 35878 Z= 0.280 Chirality : 0.043 0.176 4115 Planarity : 0.004 0.062 4552 Dihedral : 10.464 80.929 4117 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.53 % Allowed : 13.45 % Favored : 84.02 % 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: -1.15 (0.14), residues: 3191 helix: -0.48 (0.15), residues: 1122 sheet: -0.94 (0.24), residues: 425 loop : -0.81 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 115 HIS 0.005 0.001 HIS D 80 PHE 0.020 0.001 PHE C 906 TYR 0.015 0.001 TYR D 679 ARG 0.009 0.000 ARG D 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 240 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.8001 (tpp80) REVERT: A 127 GLN cc_start: 0.8076 (mp10) cc_final: 0.7807 (pm20) REVERT: A 145 LYS cc_start: 0.8691 (tttt) cc_final: 0.8471 (ttpp) REVERT: A 194 GLN cc_start: 0.7893 (tp40) cc_final: 0.7502 (tm-30) REVERT: A 205 MET cc_start: 0.8216 (mtp) cc_final: 0.7757 (mtp) REVERT: B 18 GLN cc_start: 0.8018 (mp10) cc_final: 0.7592 (mm-40) REVERT: B 95 LYS cc_start: 0.8502 (mttt) cc_final: 0.8225 (mttt) REVERT: B 127 GLN cc_start: 0.8117 (pm20) cc_final: 0.7890 (pm20) REVERT: B 145 LYS cc_start: 0.8601 (tttt) cc_final: 0.8350 (ttpt) REVERT: B 200 LYS cc_start: 0.8663 (tttt) cc_final: 0.8393 (tmmt) REVERT: C 70 TYR cc_start: 0.8318 (t80) cc_final: 0.7915 (t80) REVERT: C 222 ASP cc_start: 0.7574 (m-30) cc_final: 0.7125 (m-30) REVERT: C 230 PHE cc_start: 0.7409 (m-80) cc_final: 0.7037 (m-80) REVERT: C 360 LEU cc_start: 0.8617 (tp) cc_final: 0.8376 (mm) REVERT: C 422 LYS cc_start: 0.8643 (mttt) cc_final: 0.8432 (mtpt) REVERT: C 503 LYS cc_start: 0.8409 (tptp) cc_final: 0.7976 (tttt) REVERT: C 600 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8301 (p) REVERT: C 694 ARG cc_start: 0.7948 (mmt90) cc_final: 0.7547 (mtm-85) REVERT: C 768 MET cc_start: 0.7696 (mtp) cc_final: 0.7415 (mtp) REVERT: C 876 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7412 (tm-30) REVERT: C 955 GLN cc_start: 0.8230 (tp-100) cc_final: 0.7698 (tp-100) REVERT: C 1025 PHE cc_start: 0.7119 (t80) cc_final: 0.6795 (t80) REVERT: C 1027 LYS cc_start: 0.8816 (tptp) cc_final: 0.8505 (pttt) REVERT: C 1163 THR cc_start: 0.8696 (m) cc_final: 0.8431 (p) REVERT: C 1167 GLU cc_start: 0.7702 (tp30) cc_final: 0.7265 (tm-30) REVERT: C 1232 MET cc_start: 0.8665 (mmm) cc_final: 0.8451 (tpp) REVERT: D 129 ASP cc_start: 0.7768 (t0) cc_final: 0.7393 (t0) REVERT: D 151 MET cc_start: 0.6552 (mpp) cc_final: 0.5629 (ppp) REVERT: D 200 GLN cc_start: 0.8594 (tt0) cc_final: 0.8287 (mt0) REVERT: D 291 ILE cc_start: 0.8271 (tp) cc_final: 0.8071 (pt) REVERT: D 312 ARG cc_start: 0.7260 (mmm160) cc_final: 0.6799 (mmm160) REVERT: D 347 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7835 (m) REVERT: D 375 GLU cc_start: 0.8065 (tp30) cc_final: 0.7792 (mm-30) REVERT: D 398 LYS cc_start: 0.8239 (tttm) cc_final: 0.7766 (ttmm) REVERT: D 603 LYS cc_start: 0.7970 (tttt) cc_final: 0.7579 (ttmt) REVERT: D 649 LYS cc_start: 0.7989 (mmmt) cc_final: 0.7776 (mtmm) REVERT: D 703 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8696 (t) REVERT: D 738 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6963 (mtt180) REVERT: D 781 LYS cc_start: 0.7867 (tttt) cc_final: 0.7524 (ttmt) REVERT: D 955 LYS cc_start: 0.8761 (pttt) cc_final: 0.8468 (pptt) REVERT: D 993 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6248 (pp20) REVERT: D 1021 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6364 (t0) REVERT: D 1189 MET cc_start: 0.8501 (mtt) cc_final: 0.8295 (mmm) REVERT: D 1195 GLN cc_start: 0.6996 (pm20) cc_final: 0.6424 (pp30) REVERT: E 8 ASP cc_start: 0.8380 (m-30) cc_final: 0.7836 (m-30) REVERT: E 11 GLU cc_start: 0.8033 (mp0) cc_final: 0.7452 (mp0) REVERT: E 41 GLU cc_start: 0.7231 (tm-30) cc_final: 0.7002 (tm-30) REVERT: E 68 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7308 (tm-30) REVERT: E 72 GLN cc_start: 0.8426 (tt0) cc_final: 0.7960 (tm-30) REVERT: E 76 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7524 (mt-10) outliers start: 69 outliers final: 21 residues processed: 288 average time/residue: 1.5612 time to fit residues: 515.5760 Evaluate side-chains 248 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 221 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1021 ASP Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 0.9990 chunk 218 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 195 optimal weight: 6.9990 chunk 292 optimal weight: 8.9990 chunk 309 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 276 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN D 80 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26426 Z= 0.214 Angle : 0.517 10.467 35878 Z= 0.267 Chirality : 0.043 0.184 4115 Planarity : 0.004 0.056 4552 Dihedral : 10.294 81.503 4117 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.75 % Allowed : 14.30 % Favored : 82.95 % 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 (0.14), residues: 3191 helix: -0.12 (0.16), residues: 1126 sheet: -0.79 (0.24), residues: 425 loop : -0.67 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 115 HIS 0.003 0.001 HIS B 66 PHE 0.020 0.001 PHE C 906 TYR 0.015 0.001 TYR D 679 ARG 0.008 0.000 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 239 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.8001 (tpp80) REVERT: A 127 GLN cc_start: 0.8064 (mp10) cc_final: 0.7806 (pm20) REVERT: A 194 GLN cc_start: 0.7875 (tp40) cc_final: 0.7583 (tm-30) REVERT: A 205 MET cc_start: 0.8165 (mtp) cc_final: 0.7736 (mtp) REVERT: B 12 ARG cc_start: 0.7600 (ttm110) cc_final: 0.7185 (ptt180) REVERT: B 18 GLN cc_start: 0.8008 (mp10) cc_final: 0.7590 (mm-40) REVERT: B 95 LYS cc_start: 0.8487 (mttt) cc_final: 0.8225 (mttt) REVERT: B 127 GLN cc_start: 0.8116 (pm20) cc_final: 0.7884 (pm20) REVERT: B 188 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7457 (pm20) REVERT: B 200 LYS cc_start: 0.8669 (tttt) cc_final: 0.8392 (tmmt) REVERT: C 70 TYR cc_start: 0.8327 (t80) cc_final: 0.7892 (t80) REVERT: C 222 ASP cc_start: 0.7608 (m-30) cc_final: 0.7168 (m-30) REVERT: C 230 PHE cc_start: 0.7450 (m-80) cc_final: 0.7123 (m-80) REVERT: C 284 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7250 (tm) REVERT: C 349 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7159 (mt-10) REVERT: C 360 LEU cc_start: 0.8612 (tp) cc_final: 0.8407 (mm) REVERT: C 370 MET cc_start: 0.7982 (mmm) cc_final: 0.7763 (mmm) REVERT: C 422 LYS cc_start: 0.8654 (mttt) cc_final: 0.8435 (mtpt) REVERT: C 503 LYS cc_start: 0.8348 (tptp) cc_final: 0.7943 (tttt) REVERT: C 600 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8267 (p) REVERT: C 694 ARG cc_start: 0.7945 (mmt90) cc_final: 0.7557 (mtm-85) REVERT: C 768 MET cc_start: 0.7735 (mtp) cc_final: 0.7409 (mtp) REVERT: C 876 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7434 (tm-30) REVERT: C 955 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7801 (tp-100) REVERT: C 1025 PHE cc_start: 0.7056 (t80) cc_final: 0.6740 (t80) REVERT: C 1027 LYS cc_start: 0.8787 (tptp) cc_final: 0.8475 (pttm) REVERT: C 1163 THR cc_start: 0.8802 (m) cc_final: 0.8563 (p) REVERT: D 29 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6610 (ttp) REVERT: D 129 ASP cc_start: 0.7880 (t0) cc_final: 0.7464 (t0) REVERT: D 151 MET cc_start: 0.6558 (mpp) cc_final: 0.5629 (ppp) REVERT: D 237 MET cc_start: 0.9032 (mtp) cc_final: 0.8716 (mtp) REVERT: D 291 ILE cc_start: 0.8293 (tp) cc_final: 0.8034 (pt) REVERT: D 312 ARG cc_start: 0.7363 (mmm160) cc_final: 0.6815 (mmm-85) REVERT: D 330 MET cc_start: 0.8075 (mtm) cc_final: 0.7731 (mtp) REVERT: D 375 GLU cc_start: 0.8072 (tp30) cc_final: 0.7799 (mm-30) REVERT: D 398 LYS cc_start: 0.8238 (tttm) cc_final: 0.7816 (ttmm) REVERT: D 603 LYS cc_start: 0.7974 (tttt) cc_final: 0.7577 (ttmt) REVERT: D 703 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8693 (t) REVERT: D 738 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6993 (mtt180) REVERT: D 781 LYS cc_start: 0.7845 (tttt) cc_final: 0.7464 (ttpt) REVERT: D 805 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7183 (pm20) REVERT: D 955 LYS cc_start: 0.8759 (pttt) cc_final: 0.8481 (pptt) REVERT: D 993 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6348 (pp20) REVERT: D 1021 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6350 (t0) REVERT: E 8 ASP cc_start: 0.8348 (m-30) cc_final: 0.7836 (m-30) REVERT: E 11 GLU cc_start: 0.8031 (mp0) cc_final: 0.7475 (mp0) REVERT: E 41 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6958 (tm-30) REVERT: E 68 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7383 (tm-30) REVERT: E 72 GLN cc_start: 0.8392 (tt0) cc_final: 0.7966 (tm-30) outliers start: 75 outliers final: 29 residues processed: 291 average time/residue: 1.6104 time to fit residues: 537.8206 Evaluate side-chains 257 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 218 time to evaluate : 5.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1021 ASP Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 257 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 230 optimal weight: 3.9990 chunk 127 optimal weight: 0.1980 chunk 263 optimal weight: 0.1980 chunk 213 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 277 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN C 69 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 26426 Z= 0.156 Angle : 0.491 9.808 35878 Z= 0.253 Chirality : 0.042 0.173 4115 Planarity : 0.003 0.056 4552 Dihedral : 10.144 82.394 4117 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.49 % Allowed : 15.62 % Favored : 81.89 % 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: -0.44 (0.15), residues: 3191 helix: 0.31 (0.16), residues: 1111 sheet: -0.65 (0.24), residues: 446 loop : -0.52 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 115 HIS 0.003 0.001 HIS B 66 PHE 0.022 0.001 PHE C 906 TYR 0.015 0.001 TYR D 679 ARG 0.008 0.000 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 239 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.7919 (tpp80) REVERT: A 127 GLN cc_start: 0.8039 (mp10) cc_final: 0.7832 (pm20) REVERT: A 194 GLN cc_start: 0.7900 (tp40) cc_final: 0.7605 (tm-30) REVERT: A 205 MET cc_start: 0.8094 (mtp) cc_final: 0.7689 (mtp) REVERT: B 12 ARG cc_start: 0.7501 (ttm110) cc_final: 0.7184 (ptt180) REVERT: B 18 GLN cc_start: 0.7967 (mp10) cc_final: 0.7548 (mm-40) REVERT: B 127 GLN cc_start: 0.8115 (pm20) cc_final: 0.7877 (pm20) REVERT: B 142 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8060 (ptm) REVERT: B 200 LYS cc_start: 0.8661 (tttt) cc_final: 0.8414 (tmmt) REVERT: C 70 TYR cc_start: 0.8328 (t80) cc_final: 0.7809 (t80) REVERT: C 284 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7187 (tm) REVERT: C 349 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7036 (mt-10) REVERT: C 371 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6988 (mtm110) REVERT: C 422 LYS cc_start: 0.8652 (mttt) cc_final: 0.8426 (mtpt) REVERT: C 439 LYS cc_start: 0.8406 (ttmm) cc_final: 0.8044 (ttmt) REVERT: C 503 LYS cc_start: 0.8368 (tptp) cc_final: 0.8004 (tttt) REVERT: C 600 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8256 (p) REVERT: C 694 ARG cc_start: 0.7922 (mmt90) cc_final: 0.7563 (mtm-85) REVERT: C 768 MET cc_start: 0.7690 (mtp) cc_final: 0.7367 (mtp) REVERT: C 813 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8195 (tp30) REVERT: C 876 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7427 (tm-30) REVERT: C 950 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8027 (tm-30) REVERT: C 955 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7816 (tp-100) REVERT: C 1025 PHE cc_start: 0.7004 (t80) cc_final: 0.6716 (t80) REVERT: C 1027 LYS cc_start: 0.8766 (tptp) cc_final: 0.8446 (pttm) REVERT: D 129 ASP cc_start: 0.7885 (t0) cc_final: 0.7474 (t0) REVERT: D 151 MET cc_start: 0.6637 (mpp) cc_final: 0.5712 (ppp) REVERT: D 237 MET cc_start: 0.8956 (mtp) cc_final: 0.8626 (mtp) REVERT: D 291 ILE cc_start: 0.8349 (tp) cc_final: 0.8098 (pt) REVERT: D 375 GLU cc_start: 0.8093 (tp30) cc_final: 0.7799 (mm-30) REVERT: D 398 LYS cc_start: 0.8216 (tttm) cc_final: 0.7800 (ttmm) REVERT: D 414 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7158 (tp30) REVERT: D 525 MET cc_start: 0.8465 (ptp) cc_final: 0.8219 (ptp) REVERT: D 603 LYS cc_start: 0.7898 (tttt) cc_final: 0.7522 (ttmt) REVERT: D 703 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8686 (t) REVERT: D 738 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6935 (mtt180) REVERT: D 754 ILE cc_start: 0.7901 (pt) cc_final: 0.7699 (pp) REVERT: D 781 LYS cc_start: 0.7812 (tttt) cc_final: 0.7431 (ttpt) REVERT: D 805 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7017 (pm20) REVERT: D 955 LYS cc_start: 0.8594 (pttt) cc_final: 0.8322 (pptt) REVERT: D 1021 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.6434 (t0) REVERT: D 1040 MET cc_start: 0.4199 (mmm) cc_final: 0.3969 (tmm) REVERT: E 8 ASP cc_start: 0.8350 (m-30) cc_final: 0.7822 (m-30) REVERT: E 11 GLU cc_start: 0.8023 (mp0) cc_final: 0.7451 (mp0) REVERT: E 41 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6878 (tm-30) REVERT: E 68 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7382 (tm-30) REVERT: E 69 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7877 (ttm-80) REVERT: E 72 GLN cc_start: 0.8415 (tt0) cc_final: 0.7983 (tm-30) outliers start: 68 outliers final: 21 residues processed: 291 average time/residue: 1.5575 time to fit residues: 519.6614 Evaluate side-chains 243 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 211 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1021 ASP Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 0.9990 chunk 278 optimal weight: 40.0000 chunk 61 optimal weight: 0.0870 chunk 181 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 309 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 143 optimal weight: 0.0060 chunk 25 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 overall best weight: 0.9978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 227 GLN C 618 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26426 Z= 0.199 Angle : 0.505 9.689 35878 Z= 0.258 Chirality : 0.042 0.171 4115 Planarity : 0.004 0.055 4552 Dihedral : 10.128 82.266 4117 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.57 % Allowed : 16.35 % Favored : 81.09 % 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: -0.29 (0.15), residues: 3191 helix: 0.40 (0.16), residues: 1118 sheet: -0.40 (0.24), residues: 437 loop : -0.45 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 115 HIS 0.003 0.001 HIS B 66 PHE 0.021 0.001 PHE C 906 TYR 0.013 0.001 TYR D 679 ARG 0.011 0.000 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 232 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7897 (tpp80) REVERT: A 127 GLN cc_start: 0.8052 (mp10) cc_final: 0.7832 (pm20) REVERT: A 194 GLN cc_start: 0.7957 (tp40) cc_final: 0.7646 (tm-30) REVERT: A 205 MET cc_start: 0.8246 (mtp) cc_final: 0.7830 (mtp) REVERT: B 12 ARG cc_start: 0.7455 (ttm110) cc_final: 0.7237 (ptt180) REVERT: B 18 GLN cc_start: 0.7966 (mp10) cc_final: 0.7400 (tp40) REVERT: B 95 LYS cc_start: 0.8598 (mtpp) cc_final: 0.8297 (mttt) REVERT: B 127 GLN cc_start: 0.8150 (pm20) cc_final: 0.7899 (pm20) REVERT: B 142 MET cc_start: 0.8507 (ptm) cc_final: 0.8191 (ptm) REVERT: B 200 LYS cc_start: 0.8682 (tttt) cc_final: 0.8422 (tmmt) REVERT: C 70 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7835 (t80) REVERT: C 222 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7418 (m-30) REVERT: C 284 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7227 (tm) REVERT: C 333 ILE cc_start: 0.7925 (pt) cc_final: 0.7658 (pp) REVERT: C 349 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7004 (mt-10) REVERT: C 371 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7006 (mtm110) REVERT: C 439 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8170 (ttmt) REVERT: C 503 LYS cc_start: 0.8372 (tptp) cc_final: 0.7975 (tttt) REVERT: C 600 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8219 (p) REVERT: C 694 ARG cc_start: 0.7928 (mmt90) cc_final: 0.7569 (mtm-85) REVERT: C 768 MET cc_start: 0.7720 (mtp) cc_final: 0.7393 (mtp) REVERT: C 876 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7437 (tm-30) REVERT: C 950 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8120 (tm-30) REVERT: C 955 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7749 (tp-100) REVERT: C 1025 PHE cc_start: 0.6924 (t80) cc_final: 0.6655 (t80) REVERT: C 1027 LYS cc_start: 0.8777 (tptp) cc_final: 0.8442 (pttm) REVERT: D 80 HIS cc_start: 0.6904 (OUTLIER) cc_final: 0.6197 (p90) REVERT: D 129 ASP cc_start: 0.7858 (t0) cc_final: 0.7421 (t0) REVERT: D 151 MET cc_start: 0.6673 (mpp) cc_final: 0.5705 (ppp) REVERT: D 237 MET cc_start: 0.8961 (mtp) cc_final: 0.8696 (mtp) REVERT: D 291 ILE cc_start: 0.8343 (tp) cc_final: 0.8080 (pt) REVERT: D 312 ARG cc_start: 0.7250 (mmm160) cc_final: 0.6774 (mmm-85) REVERT: D 375 GLU cc_start: 0.8098 (tp30) cc_final: 0.7795 (mm-30) REVERT: D 398 LYS cc_start: 0.8232 (tttm) cc_final: 0.7814 (ttmm) REVERT: D 547 ARG cc_start: 0.8283 (mtt90) cc_final: 0.7814 (mtt90) REVERT: D 603 LYS cc_start: 0.7916 (tttt) cc_final: 0.7535 (ttmt) REVERT: D 703 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8695 (t) REVERT: D 738 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6841 (mtt180) REVERT: D 754 ILE cc_start: 0.7925 (pt) cc_final: 0.7716 (pp) REVERT: D 781 LYS cc_start: 0.7831 (tttt) cc_final: 0.7444 (ttpt) REVERT: D 805 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.6984 (pm20) REVERT: D 955 LYS cc_start: 0.8653 (pttt) cc_final: 0.8271 (pptt) REVERT: D 1021 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6467 (t0) REVERT: E 8 ASP cc_start: 0.8385 (m-30) cc_final: 0.7837 (m-30) REVERT: E 11 GLU cc_start: 0.8038 (mp0) cc_final: 0.7481 (mp0) REVERT: E 41 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6886 (tm-30) REVERT: E 68 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7337 (tm-30) REVERT: E 71 GLU cc_start: 0.7630 (pp20) cc_final: 0.7426 (pp20) REVERT: E 72 GLN cc_start: 0.8437 (tt0) cc_final: 0.8013 (tm-30) outliers start: 70 outliers final: 30 residues processed: 282 average time/residue: 1.5694 time to fit residues: 506.8988 Evaluate side-chains 254 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 213 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 70 TYR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 834 GLN Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1021 ASP Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1329 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 226 optimal weight: 0.0570 chunk 175 optimal weight: 0.7980 chunk 260 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 308 optimal weight: 4.9990 chunk 193 optimal weight: 10.0000 chunk 188 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN C 618 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26426 Z= 0.214 Angle : 0.516 10.277 35878 Z= 0.262 Chirality : 0.042 0.169 4115 Planarity : 0.004 0.055 4552 Dihedral : 10.121 82.458 4117 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.53 % Allowed : 17.30 % Favored : 80.17 % 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: -0.22 (0.15), residues: 3191 helix: 0.51 (0.16), residues: 1112 sheet: -0.41 (0.24), residues: 447 loop : -0.43 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 115 HIS 0.003 0.001 HIS B 66 PHE 0.020 0.001 PHE C 906 TYR 0.013 0.001 TYR C1018 ARG 0.012 0.000 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 218 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.7905 (tpp80) REVERT: A 127 GLN cc_start: 0.8060 (mp10) cc_final: 0.7835 (pm20) REVERT: A 194 GLN cc_start: 0.7976 (tp40) cc_final: 0.7663 (tm-30) REVERT: A 205 MET cc_start: 0.8250 (mtp) cc_final: 0.7817 (mtp) REVERT: B 12 ARG cc_start: 0.7469 (ttm110) cc_final: 0.7229 (ptt180) REVERT: B 18 GLN cc_start: 0.7926 (mp10) cc_final: 0.7482 (mm-40) REVERT: B 95 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8126 (ptpt) REVERT: B 127 GLN cc_start: 0.8155 (pm20) cc_final: 0.7901 (pm20) REVERT: B 142 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8200 (ptm) REVERT: B 200 LYS cc_start: 0.8812 (tttt) cc_final: 0.8598 (tmmt) REVERT: C 222 ASP cc_start: 0.7712 (m-30) cc_final: 0.7328 (m-30) REVERT: C 284 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7202 (tm) REVERT: C 503 LYS cc_start: 0.8425 (tptp) cc_final: 0.8124 (tttt) REVERT: C 600 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8260 (p) REVERT: C 694 ARG cc_start: 0.7928 (mmt90) cc_final: 0.7578 (mtm-85) REVERT: C 768 MET cc_start: 0.7733 (mtp) cc_final: 0.7412 (mtp) REVERT: C 876 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7458 (tm-30) REVERT: C 950 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8123 (tm-30) REVERT: C 955 GLN cc_start: 0.8235 (tp-100) cc_final: 0.7745 (tp-100) REVERT: C 1025 PHE cc_start: 0.6926 (t80) cc_final: 0.6690 (t80) REVERT: C 1027 LYS cc_start: 0.8781 (tptp) cc_final: 0.8450 (pttm) REVERT: D 80 HIS cc_start: 0.6794 (OUTLIER) cc_final: 0.6184 (p90) REVERT: D 129 ASP cc_start: 0.7815 (t0) cc_final: 0.7386 (t0) REVERT: D 151 MET cc_start: 0.6684 (mpp) cc_final: 0.5726 (ppp) REVERT: D 237 MET cc_start: 0.9008 (mtp) cc_final: 0.8745 (mtp) REVERT: D 291 ILE cc_start: 0.8315 (tp) cc_final: 0.8034 (pt) REVERT: D 312 ARG cc_start: 0.7083 (mmm160) cc_final: 0.6639 (mmm-85) REVERT: D 375 GLU cc_start: 0.8102 (tp30) cc_final: 0.7794 (mm-30) REVERT: D 398 LYS cc_start: 0.8238 (tttm) cc_final: 0.7821 (ttmm) REVERT: D 414 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7195 (tp30) REVERT: D 547 ARG cc_start: 0.8293 (mtt90) cc_final: 0.7815 (mtt90) REVERT: D 603 LYS cc_start: 0.7920 (tttt) cc_final: 0.7538 (ttmt) REVERT: D 703 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8634 (t) REVERT: D 738 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6801 (mtt180) REVERT: D 781 LYS cc_start: 0.7854 (tttt) cc_final: 0.7471 (ttpt) REVERT: D 805 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.6985 (pm20) REVERT: D 955 LYS cc_start: 0.8639 (pttt) cc_final: 0.8255 (pptt) REVERT: D 1174 ARG cc_start: 0.3755 (mpp80) cc_final: 0.3517 (mpp80) REVERT: E 8 ASP cc_start: 0.8393 (m-30) cc_final: 0.7850 (m-30) REVERT: E 11 GLU cc_start: 0.8019 (mp0) cc_final: 0.7457 (mp0) REVERT: E 41 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6869 (tm-30) REVERT: E 68 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7269 (tm-30) REVERT: E 71 GLU cc_start: 0.7401 (pp20) cc_final: 0.7081 (pp20) REVERT: E 72 GLN cc_start: 0.8416 (tt0) cc_final: 0.7965 (tm-30) REVERT: E 74 GLU cc_start: 0.7950 (pp20) cc_final: 0.7717 (pp20) outliers start: 69 outliers final: 34 residues processed: 269 average time/residue: 1.5947 time to fit residues: 492.2687 Evaluate side-chains 251 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 209 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 738 ARG Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1208 ASP Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1329 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 190 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 184 optimal weight: 0.0050 chunk 92 optimal weight: 0.1980 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 210 optimal weight: 0.5980 chunk 152 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 242 optimal weight: 0.7980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN C 618 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 26426 Z= 0.150 Angle : 0.500 10.817 35878 Z= 0.255 Chirality : 0.041 0.172 4115 Planarity : 0.003 0.061 4552 Dihedral : 10.039 83.410 4117 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.20 % Allowed : 17.93 % Favored : 79.88 % 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: -0.03 (0.15), residues: 3191 helix: 0.74 (0.16), residues: 1105 sheet: -0.33 (0.24), residues: 456 loop : -0.37 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 115 HIS 0.003 0.001 HIS B 66 PHE 0.021 0.001 PHE C 906 TYR 0.016 0.001 TYR D 679 ARG 0.012 0.000 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 224 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.7928 (tpp80) REVERT: A 127 GLN cc_start: 0.8045 (mp10) cc_final: 0.7803 (pm20) REVERT: A 194 GLN cc_start: 0.7933 (tp40) cc_final: 0.7613 (tm-30) REVERT: A 205 MET cc_start: 0.8186 (mtp) cc_final: 0.7749 (mtp) REVERT: B 18 GLN cc_start: 0.7956 (mp10) cc_final: 0.7405 (tp40) REVERT: B 95 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8089 (ptpt) REVERT: B 127 GLN cc_start: 0.8156 (pm20) cc_final: 0.7903 (pm20) REVERT: B 142 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8132 (ptm) REVERT: B 200 LYS cc_start: 0.8706 (tttt) cc_final: 0.8475 (tmmt) REVERT: C 222 ASP cc_start: 0.7569 (m-30) cc_final: 0.7109 (m-30) REVERT: C 239 MET cc_start: 0.5107 (tmm) cc_final: 0.4762 (tmm) REVERT: C 284 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.6881 (tm) REVERT: C 349 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6991 (mt-10) REVERT: C 503 LYS cc_start: 0.8362 (tptp) cc_final: 0.8050 (tttt) REVERT: C 600 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8222 (p) REVERT: C 694 ARG cc_start: 0.7903 (mmt90) cc_final: 0.7569 (mtm-85) REVERT: C 768 MET cc_start: 0.7695 (mtp) cc_final: 0.7378 (mtp) REVERT: C 813 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8179 (tp30) REVERT: C 814 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.7059 (t0) REVERT: C 876 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7430 (tm-30) REVERT: C 950 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8132 (tm-30) REVERT: C 955 GLN cc_start: 0.8240 (tp-100) cc_final: 0.7763 (tp-100) REVERT: C 1025 PHE cc_start: 0.6941 (t80) cc_final: 0.6694 (t80) REVERT: C 1027 LYS cc_start: 0.8811 (tptp) cc_final: 0.8507 (pttm) REVERT: D 80 HIS cc_start: 0.6689 (OUTLIER) cc_final: 0.6101 (p90) REVERT: D 129 ASP cc_start: 0.7804 (t0) cc_final: 0.7343 (t0) REVERT: D 151 MET cc_start: 0.6642 (mpp) cc_final: 0.5699 (ppp) REVERT: D 237 MET cc_start: 0.8942 (mtp) cc_final: 0.8680 (mtp) REVERT: D 291 ILE cc_start: 0.8341 (tp) cc_final: 0.8087 (pt) REVERT: D 312 ARG cc_start: 0.7064 (mmm160) cc_final: 0.6621 (mmm-85) REVERT: D 375 GLU cc_start: 0.8045 (tp30) cc_final: 0.7763 (mm-30) REVERT: D 398 LYS cc_start: 0.8220 (tttm) cc_final: 0.7805 (ttmm) REVERT: D 414 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7135 (tp30) REVERT: D 525 MET cc_start: 0.8542 (ptp) cc_final: 0.8299 (ptp) REVERT: D 603 LYS cc_start: 0.8030 (tttt) cc_final: 0.7694 (ttmt) REVERT: D 703 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8679 (t) REVERT: D 781 LYS cc_start: 0.7817 (tttt) cc_final: 0.7445 (ttpt) REVERT: D 805 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.6966 (pm20) REVERT: D 955 LYS cc_start: 0.8613 (pttt) cc_final: 0.8238 (pptt) REVERT: D 1021 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6444 (t0) REVERT: E 11 GLU cc_start: 0.8046 (mp0) cc_final: 0.7669 (mp0) REVERT: E 41 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6796 (tm-30) REVERT: E 68 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7327 (tm-30) REVERT: E 72 GLN cc_start: 0.8357 (tt0) cc_final: 0.7977 (tm-30) outliers start: 60 outliers final: 24 residues processed: 269 average time/residue: 1.6391 time to fit residues: 504.5056 Evaluate side-chains 242 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 207 time to evaluate : 3.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1021 ASP Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1208 ASP Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 280 optimal weight: 40.0000 chunk 295 optimal weight: 5.9990 chunk 269 optimal weight: 0.5980 chunk 287 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 259 optimal weight: 0.8980 chunk 271 optimal weight: 20.0000 chunk 286 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN C 618 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 26426 Z= 0.314 Angle : 0.568 11.060 35878 Z= 0.289 Chirality : 0.044 0.192 4115 Planarity : 0.004 0.066 4552 Dihedral : 10.115 82.429 4117 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.20 % Allowed : 18.26 % Favored : 79.55 % 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: -0.16 (0.15), residues: 3191 helix: 0.53 (0.16), residues: 1105 sheet: -0.28 (0.25), residues: 438 loop : -0.41 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 115 HIS 0.004 0.001 HIS D 430 PHE 0.019 0.002 PHE C 906 TYR 0.016 0.001 TYR D 679 ARG 0.013 0.000 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 215 time to evaluate : 3.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.7960 (tpp80) REVERT: A 127 GLN cc_start: 0.8088 (mp10) cc_final: 0.7839 (pm20) REVERT: A 194 GLN cc_start: 0.8019 (tp40) cc_final: 0.7582 (tm-30) REVERT: A 205 MET cc_start: 0.8292 (mtp) cc_final: 0.7899 (mtp) REVERT: B 18 GLN cc_start: 0.7944 (mp10) cc_final: 0.7481 (mm-40) REVERT: B 95 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8174 (ptpt) REVERT: B 127 GLN cc_start: 0.8168 (pm20) cc_final: 0.7911 (pm20) REVERT: B 142 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8227 (ptm) REVERT: B 200 LYS cc_start: 0.8821 (tttt) cc_final: 0.8609 (tmmt) REVERT: C 70 TYR cc_start: 0.8414 (t80) cc_final: 0.7458 (t80) REVERT: C 222 ASP cc_start: 0.7576 (m-30) cc_final: 0.7040 (m-30) REVERT: C 284 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.6921 (tm) REVERT: C 439 LYS cc_start: 0.8667 (ttmt) cc_final: 0.8210 (tmmt) REVERT: C 503 LYS cc_start: 0.8410 (tptp) cc_final: 0.8110 (tttt) REVERT: C 600 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8278 (p) REVERT: C 694 ARG cc_start: 0.7944 (mmt90) cc_final: 0.7595 (mtm-85) REVERT: C 768 MET cc_start: 0.7779 (mtp) cc_final: 0.7453 (mtp) REVERT: C 813 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8252 (tp30) REVERT: C 876 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7389 (tm-30) REVERT: C 950 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8131 (tm-30) REVERT: C 955 GLN cc_start: 0.8240 (tp-100) cc_final: 0.7752 (tp-100) REVERT: C 1025 PHE cc_start: 0.6912 (t80) cc_final: 0.6669 (t80) REVERT: C 1027 LYS cc_start: 0.8749 (tptp) cc_final: 0.8394 (pttm) REVERT: C 1032 LYS cc_start: 0.8087 (mppt) cc_final: 0.7854 (mppt) REVERT: C 1230 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8536 (ttp) REVERT: D 80 HIS cc_start: 0.6798 (OUTLIER) cc_final: 0.6225 (p90) REVERT: D 129 ASP cc_start: 0.7953 (t0) cc_final: 0.7384 (t0) REVERT: D 151 MET cc_start: 0.6734 (mpp) cc_final: 0.5758 (ppp) REVERT: D 237 MET cc_start: 0.8941 (mtp) cc_final: 0.8676 (mtp) REVERT: D 291 ILE cc_start: 0.8325 (tp) cc_final: 0.8022 (pt) REVERT: D 312 ARG cc_start: 0.7265 (mmm160) cc_final: 0.6845 (mmm-85) REVERT: D 375 GLU cc_start: 0.8148 (tp30) cc_final: 0.7838 (mm-30) REVERT: D 398 LYS cc_start: 0.8259 (tttm) cc_final: 0.7840 (ttmm) REVERT: D 414 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7200 (tp30) REVERT: D 603 LYS cc_start: 0.7932 (tttt) cc_final: 0.7566 (ttmt) REVERT: D 703 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8644 (t) REVERT: D 781 LYS cc_start: 0.7885 (tttt) cc_final: 0.7508 (ttpt) REVERT: D 805 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7014 (pm20) REVERT: D 832 LYS cc_start: 0.6972 (mtpt) cc_final: 0.6638 (mtpt) REVERT: D 853 THR cc_start: 0.7384 (OUTLIER) cc_final: 0.7048 (t) REVERT: D 955 LYS cc_start: 0.8591 (pttt) cc_final: 0.8225 (pptt) REVERT: D 1021 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6442 (t0) REVERT: D 1195 GLN cc_start: 0.6468 (tm-30) cc_final: 0.6251 (tm130) REVERT: E 11 GLU cc_start: 0.8011 (mp0) cc_final: 0.7654 (mp0) REVERT: E 41 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6948 (tm-30) REVERT: E 68 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7304 (tm-30) REVERT: E 72 GLN cc_start: 0.8402 (tt0) cc_final: 0.8013 (tm-30) REVERT: E 74 GLU cc_start: 0.7843 (pp20) cc_final: 0.7397 (pp20) outliers start: 60 outliers final: 30 residues processed: 264 average time/residue: 1.6085 time to fit residues: 487.0479 Evaluate side-chains 249 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 208 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 387 ASN Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1021 ASP Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1208 ASP Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 188 optimal weight: 1.9990 chunk 303 optimal weight: 0.5980 chunk 185 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 318 optimal weight: 10.0000 chunk 293 optimal weight: 7.9990 chunk 253 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN C 69 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26426 Z= 0.181 Angle : 0.533 12.922 35878 Z= 0.270 Chirality : 0.042 0.180 4115 Planarity : 0.004 0.076 4552 Dihedral : 10.034 83.776 4117 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.65 % Allowed : 18.88 % Favored : 79.47 % 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: -0.02 (0.15), residues: 3191 helix: 0.73 (0.16), residues: 1099 sheet: -0.23 (0.24), residues: 453 loop : -0.39 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 115 HIS 0.003 0.001 HIS B 66 PHE 0.020 0.001 PHE C 906 TYR 0.016 0.001 TYR C1018 ARG 0.017 0.000 ARG D 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6382 Ramachandran restraints generated. 3191 Oldfield, 0 Emsley, 3191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 210 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7919 (tpp80) REVERT: A 127 GLN cc_start: 0.8063 (mp10) cc_final: 0.7835 (pm20) REVERT: A 145 LYS cc_start: 0.8866 (ttpp) cc_final: 0.8563 (ttmm) REVERT: A 194 GLN cc_start: 0.8012 (tp40) cc_final: 0.7543 (tm-30) REVERT: A 205 MET cc_start: 0.8187 (mtp) cc_final: 0.7745 (mtp) REVERT: B 18 GLN cc_start: 0.8081 (mp10) cc_final: 0.7563 (tp40) REVERT: B 95 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8135 (ptpt) REVERT: B 127 GLN cc_start: 0.8162 (pm20) cc_final: 0.7911 (pm20) REVERT: B 142 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8105 (ptm) REVERT: B 200 LYS cc_start: 0.8724 (tttt) cc_final: 0.8486 (tmmt) REVERT: C 69 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8471 (pt0) REVERT: C 284 LEU cc_start: 0.7517 (tt) cc_final: 0.7005 (mp) REVERT: C 368 ARG cc_start: 0.8768 (ttm110) cc_final: 0.8399 (mtp-110) REVERT: C 439 LYS cc_start: 0.8697 (ttmt) cc_final: 0.8213 (tmmt) REVERT: C 503 LYS cc_start: 0.8418 (tptp) cc_final: 0.8119 (tttt) REVERT: C 600 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8321 (t) REVERT: C 694 ARG cc_start: 0.7927 (mmt90) cc_final: 0.7599 (mtm-85) REVERT: C 768 MET cc_start: 0.7718 (mtp) cc_final: 0.7398 (mtp) REVERT: C 791 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8425 (tp) REVERT: C 813 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8187 (tp30) REVERT: C 876 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7497 (tm-30) REVERT: C 950 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8131 (tm-30) REVERT: C 955 GLN cc_start: 0.8245 (tp-100) cc_final: 0.7769 (tp-100) REVERT: C 1013 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7663 (tm-30) REVERT: C 1025 PHE cc_start: 0.6894 (t80) cc_final: 0.6669 (t80) REVERT: C 1027 LYS cc_start: 0.8739 (tptp) cc_final: 0.8406 (pttm) REVERT: D 80 HIS cc_start: 0.6714 (OUTLIER) cc_final: 0.6204 (p90) REVERT: D 129 ASP cc_start: 0.7927 (t0) cc_final: 0.7354 (t0) REVERT: D 151 MET cc_start: 0.6682 (mpp) cc_final: 0.5669 (ppp) REVERT: D 237 MET cc_start: 0.8961 (mtp) cc_final: 0.8698 (mtp) REVERT: D 291 ILE cc_start: 0.8352 (tp) cc_final: 0.8092 (pt) REVERT: D 312 ARG cc_start: 0.7088 (mmm160) cc_final: 0.6653 (mmm-85) REVERT: D 375 GLU cc_start: 0.8094 (tp30) cc_final: 0.7787 (mm-30) REVERT: D 398 LYS cc_start: 0.8239 (tttm) cc_final: 0.7818 (ttmm) REVERT: D 414 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7177 (tp30) REVERT: D 603 LYS cc_start: 0.7997 (tttt) cc_final: 0.7635 (ttmt) REVERT: D 703 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8630 (t) REVERT: D 781 LYS cc_start: 0.7871 (tttt) cc_final: 0.7486 (ttpt) REVERT: D 805 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.6947 (pm20) REVERT: D 832 LYS cc_start: 0.6897 (mtpt) cc_final: 0.6564 (mtpt) REVERT: D 853 THR cc_start: 0.7209 (OUTLIER) cc_final: 0.6868 (t) REVERT: D 955 LYS cc_start: 0.8538 (pttt) cc_final: 0.8096 (pptt) REVERT: D 980 THR cc_start: 0.7770 (OUTLIER) cc_final: 0.7223 (m) REVERT: D 1189 MET cc_start: 0.7580 (mmm) cc_final: 0.7320 (mmp) REVERT: D 1195 GLN cc_start: 0.6542 (tm-30) cc_final: 0.6300 (tm130) REVERT: E 11 GLU cc_start: 0.8087 (mp0) cc_final: 0.7720 (mp0) REVERT: E 41 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6835 (tm-30) REVERT: E 68 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7349 (tm-30) REVERT: E 72 GLN cc_start: 0.8346 (tt0) cc_final: 0.7971 (tm-30) REVERT: E 74 GLU cc_start: 0.7874 (pp20) cc_final: 0.7440 (pp20) outliers start: 45 outliers final: 25 residues processed: 247 average time/residue: 1.6157 time to fit residues: 455.6893 Evaluate side-chains 245 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 209 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 813 GLU Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1296 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 PHE Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 980 THR Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1194 ARG Chi-restraints excluded: chain D residue 1208 ASP Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 201 optimal weight: 0.0020 chunk 270 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 254 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN C 69 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.140252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092620 restraints weight = 35721.735| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.47 r_work: 0.3112 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.217 26426 Z= 0.253 Angle : 0.659 59.199 35878 Z= 0.367 Chirality : 0.042 0.400 4115 Planarity : 0.004 0.072 4552 Dihedral : 10.033 83.768 4117 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.54 % Allowed : 18.99 % Favored : 79.47 % 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: -0.03 (0.15), residues: 3191 helix: 0.73 (0.16), residues: 1099 sheet: -0.25 (0.24), residues: 453 loop : -0.39 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 115 HIS 0.003 0.001 HIS B 66 PHE 0.020 0.001 PHE C 906 TYR 0.015 0.001 TYR D 679 ARG 0.015 0.000 ARG D 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9054.70 seconds wall clock time: 161 minutes 55.60 seconds (9715.60 seconds total)