Starting phenix.real_space_refine on Mon May 26 14:44:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rea_19080/05_2025/8rea_19080.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rea_19080/05_2025/8rea_19080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rea_19080/05_2025/8rea_19080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rea_19080/05_2025/8rea_19080.map" model { file = "/net/cci-nas-00/data/ceres_data/8rea_19080/05_2025/8rea_19080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rea_19080/05_2025/8rea_19080.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 100 5.49 5 Mg 1 5.21 5 S 98 5.16 5 C 17773 2.51 5 N 5123 2.21 5 O 5724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.28s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28821 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2365 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1735 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 10080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10080 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 619 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 22, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 338 Chain: "D" Number of atoms: 9682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 9682 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PTRANS': 53, 'TRANS': 1276} Chain breaks: 5 Unresolved non-hydrogen bonds: 691 Unresolved non-hydrogen angles: 840 Unresolved non-hydrogen dihedrals: 585 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 9, 'GLU:plan': 31, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 441 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "M" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2354 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 196} Link IDs: {'PTRANS': 16, 'TRANS': 363} Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 832 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 12, 'ARG:plan': 13, 'TYR:plan': 3, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 3, 'GLU:plan': 25, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 395 Chain: "N" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 899 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "R" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 106 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} Chain: "T" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1051 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} 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 14703 SG CYS D 70 105.384 115.698 91.370 1.00 25.43 S ATOM 14832 SG CYS D 88 103.734 115.861 95.297 1.00 28.14 S ATOM 20325 SG CYS D 814 101.741 47.710 89.204 1.00 22.49 S ATOM 20945 SG CYS D 898 98.843 47.324 88.719 1.00 14.48 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 166 " occ=0.98 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.98 Time building chain proxies: 15.33, per 1000 atoms: 0.53 Number of scatterers: 28821 At special positions: 0 Unit cell: (144.1, 172.7, 165, 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 98 16.00 P 100 15.00 Mg 1 11.99 O 5724 8.00 N 5123 7.00 C 17773 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.92 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6804 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 44 sheets defined 39.6% alpha, 13.6% beta 38 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 11.10 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.848A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.849A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.934A pdb=" N ASP A 164 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.696A pdb=" N CYS A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.585A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 282' Processing helix chain 'A' and resid 285 through 291 removed outlier: 3.914A pdb=" N LYS A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.521A pdb=" N GLU A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.737A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.703A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.825A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.880A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.564A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.693A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.564A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.629A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 389 removed outlier: 3.571A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 422 through 438 removed outlier: 3.811A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 479 removed outlier: 3.520A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.230A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 528 removed outlier: 3.735A pdb=" N SER C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.772A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 713 removed outlier: 3.988A pdb=" N GLY C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.806A pdb=" N GLU C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.696A pdb=" N LEU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.771A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1009 Processing helix chain 'C' and resid 1009 through 1037 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.655A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 4.374A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.640A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1175 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.503A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1311 removed outlier: 3.808A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.719A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 14 removed outlier: 3.524A pdb=" N THR D 14 " --> pdb=" O GLN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 70 through 74 removed outlier: 4.040A pdb=" N LYS D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 removed outlier: 3.850A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.537A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.631A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 212 through 231 removed outlier: 4.191A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.807A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.641A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.758A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.731A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.045A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.889A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.518A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.882A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.636A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.749A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1260 removed outlier: 3.937A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1295 through 1299 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.740A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1353 removed outlier: 3.798A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1376 removed outlier: 3.590A pdb=" N MET D1370 " --> pdb=" O HIS D1366 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D1371 " --> pdb=" O GLN D1367 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.611A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.892A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 119 through 129 Processing helix chain 'M' and resid 134 through 147 removed outlier: 3.769A pdb=" N ALA M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 166 Processing helix chain 'M' and resid 171 through 184 removed outlier: 3.561A pdb=" N VAL M 175 " --> pdb=" O GLY M 171 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG M 184 " --> pdb=" O LYS M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 205 Processing helix chain 'M' and resid 212 through 218 removed outlier: 3.600A pdb=" N ALA M 216 " --> pdb=" O TRP M 212 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU M 218 " --> pdb=" O GLU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 230 Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.574A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN M 251 " --> pdb=" O LYS M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 311 removed outlier: 3.840A pdb=" N GLY M 307 " --> pdb=" O TYR M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 322 through 351 removed outlier: 3.886A pdb=" N ALA M 326 " --> pdb=" O ASN M 322 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG M 327 " --> pdb=" O LEU M 323 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TRP M 328 " --> pdb=" O GLN M 324 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 356 removed outlier: 3.983A pdb=" N PHE M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 375 removed outlier: 3.617A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 removed outlier: 3.535A pdb=" N ILE M 381 " --> pdb=" O HIS M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 430 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 454 through 466 removed outlier: 3.602A pdb=" N VAL M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA M 459 " --> pdb=" O ARG M 455 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU M 465 " --> pdb=" O TYR M 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 31 removed outlier: 6.658A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.408A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.679A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 19 removed outlier: 5.323A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 61 removed outlier: 3.537A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.860A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.816A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 99 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.816A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 99 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB6, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.043A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.507A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.154A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'C' and resid 634 through 636 Processing sheet with id=AC3, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.563A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET C 768 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 723 through 727 removed outlier: 6.745A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.403A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.539A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.539A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD2, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.609A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1338 Processing sheet with id=AD5, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.871A pdb=" N LYS D 50 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 104 through 112 removed outlier: 8.477A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.895A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.902A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD9, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AE1, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.046A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.822A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 957 through 961 Processing sheet with id=AE5, first strand: chain 'D' and resid 966 through 967 removed outlier: 5.080A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU D1003 " --> pdb=" O LEU D 973 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA D1001 " --> pdb=" O ILE D 975 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1059 through 1062 removed outlier: 3.764A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AE8, first strand: chain 'M' and resid 277 through 278 removed outlier: 7.361A pdb=" N LEU M 277 " --> pdb=" O HIS M 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 1140 hydrogen bonds defined for protein. 3195 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 97 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 14.89 Time building geometry restraints manager: 8.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9540 1.34 - 1.46: 5442 1.46 - 1.58: 14094 1.58 - 1.70: 196 1.70 - 1.82: 170 Bond restraints: 29442 Sorted by residual: bond pdb=" C3' DA N -2 " pdb=" O3' DA N -2 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.84e+00 bond pdb=" C ASP C1084 " pdb=" N MET C1085 " ideal model delta sigma weight residual 1.331 1.367 -0.036 2.83e-02 1.25e+03 1.59e+00 bond pdb=" CB ASN D 45 " pdb=" CG ASN D 45 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.45e+00 bond pdb=" CB PRO C 567 " pdb=" CG PRO C 567 " ideal model delta sigma weight residual 1.492 1.551 -0.059 5.00e-02 4.00e+02 1.42e+00 bond pdb=" CA ILE D 646 " pdb=" CB ILE D 646 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.23e-02 6.61e+03 1.41e+00 ... (remaining 29437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 40049 2.55 - 5.09: 356 5.09 - 7.64: 30 7.64 - 10.19: 6 10.19 - 12.73: 3 Bond angle restraints: 40444 Sorted by residual: angle pdb=" CB MET C 800 " pdb=" CG MET C 800 " pdb=" SD MET C 800 " ideal model delta sigma weight residual 112.70 125.43 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" N GLU M 325 " pdb=" CA GLU M 325 " pdb=" C GLU M 325 " ideal model delta sigma weight residual 113.18 108.29 4.89 1.33e+00 5.65e-01 1.35e+01 angle pdb=" CA PRO C 567 " pdb=" N PRO C 567 " pdb=" CD PRO C 567 " ideal model delta sigma weight residual 112.00 107.24 4.76 1.40e+00 5.10e-01 1.16e+01 angle pdb=" N GLY D 613 " pdb=" CA GLY D 613 " pdb=" C GLY D 613 " ideal model delta sigma weight residual 110.29 114.47 -4.18 1.28e+00 6.10e-01 1.07e+01 angle pdb=" N VAL C 114 " pdb=" CA VAL C 114 " pdb=" C VAL C 114 " ideal model delta sigma weight residual 113.53 110.34 3.19 9.80e-01 1.04e+00 1.06e+01 ... (remaining 40439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 16774 35.50 - 71.00: 872 71.00 - 106.49: 37 106.49 - 141.99: 2 141.99 - 177.49: 1 Dihedral angle restraints: 17686 sinusoidal: 7140 harmonic: 10546 Sorted by residual: dihedral pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " pdb=" CA PRO D1139 " ideal model delta harmonic sigma weight residual 180.00 140.76 39.24 0 5.00e+00 4.00e-02 6.16e+01 dihedral pdb=" C4' DG N 4 " pdb=" C3' DG N 4 " pdb=" O3' DG N 4 " pdb=" P DA N 5 " ideal model delta sinusoidal sigma weight residual -140.00 37.49 -177.49 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA PHE D 338 " pdb=" C PHE D 338 " pdb=" N ARG D 339 " pdb=" CA ARG D 339 " ideal model delta harmonic sigma weight residual 180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 17683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3909 0.050 - 0.099: 720 0.099 - 0.149: 178 0.149 - 0.199: 5 0.199 - 0.249: 1 Chirality restraints: 4813 Sorted by residual: chirality pdb=" CB ILE M 170 " pdb=" CA ILE M 170 " pdb=" CG1 ILE M 170 " pdb=" CG2 ILE M 170 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB THR M 386 " pdb=" CA THR M 386 " pdb=" OG1 THR M 386 " pdb=" CG2 THR M 386 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CG LEU C 210 " pdb=" CB LEU C 210 " pdb=" CD1 LEU C 210 " pdb=" CD2 LEU C 210 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 4810 not shown) Planarity restraints: 4961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 566 " 0.102 5.00e-02 4.00e+02 1.54e-01 3.78e+01 pdb=" N PRO C 567 " -0.266 5.00e-02 4.00e+02 pdb=" CA PRO C 567 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO C 567 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 273 " -0.065 5.00e-02 4.00e+02 9.92e-02 1.57e+01 pdb=" N PRO M 274 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO M 274 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO M 274 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D1138 " 0.047 5.00e-02 4.00e+02 7.18e-02 8.24e+00 pdb=" N PRO D1139 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO D1139 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D1139 " 0.040 5.00e-02 4.00e+02 ... (remaining 4958 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 459 2.67 - 3.22: 26848 3.22 - 3.78: 43599 3.78 - 4.34: 57204 4.34 - 4.90: 95113 Nonbonded interactions: 223223 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.108 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb=" O2' C R 3 " model vdw 2.173 3.040 nonbonded pdb=" OG SER C 421 " pdb=" OD1 ASP C 423 " model vdw 2.183 3.040 nonbonded pdb=" O LEU D1356 " pdb=" NE2 HIS D1366 " model vdw 2.209 3.120 nonbonded pdb=" OG1 THR D 262 " pdb=" OD1 ASP D 267 " model vdw 2.220 3.040 ... (remaining 223218 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.450 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: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 79.740 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29446 Z= 0.124 Angle : 0.604 12.733 40444 Z= 0.326 Chirality : 0.041 0.249 4813 Planarity : 0.005 0.154 4961 Dihedral : 18.952 177.491 10882 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 0.23 % Allowed : 27.79 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3644 helix: 1.10 (0.15), residues: 1312 sheet: 0.10 (0.27), residues: 386 loop : -1.43 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 33 HIS 0.011 0.001 HIS B 128 PHE 0.021 0.001 PHE M 354 TYR 0.016 0.001 TYR M 112 ARG 0.013 0.001 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.17658 ( 1221) hydrogen bonds : angle 5.94507 ( 3389) metal coordination : bond 0.00046 ( 4) covalent geometry : bond 0.00258 (29442) covalent geometry : angle 0.60433 (40444) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 223 time to evaluate : 3.081 Fit side-chains revert: symmetry clash REVERT: D 1040 MET cc_start: 0.0469 (tpt) cc_final: -0.0453 (mmp) REVERT: M 280 LYS cc_start: 0.7138 (mmmm) cc_final: 0.6461 (pttt) REVERT: M 365 MET cc_start: 0.7370 (ppp) cc_final: 0.6985 (ptp) REVERT: M 460 LYS cc_start: 0.7757 (ttmt) cc_final: 0.7305 (mmtt) outliers start: 6 outliers final: 3 residues processed: 228 average time/residue: 0.4081 time to fit residues: 148.9713 Evaluate side-chains 157 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 154 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain D residue 221 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 315 optimal weight: 8.9990 chunk 283 optimal weight: 30.0000 chunk 157 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 151 optimal weight: 40.0000 chunk 293 optimal weight: 50.0000 chunk 113 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 chunk 339 optimal weight: 20.0000 overall best weight: 11.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C1236 ASN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1249 ASN D1268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.072691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.047796 restraints weight = 114283.484| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.35 r_work: 0.2718 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 29446 Z= 0.367 Angle : 0.746 11.025 40444 Z= 0.394 Chirality : 0.047 0.210 4813 Planarity : 0.006 0.114 4961 Dihedral : 15.987 176.753 5071 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.05 % Favored : 92.89 % Rotamer: Outliers : 5.51 % Allowed : 23.74 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.60 (0.14), residues: 3644 helix: 1.01 (0.14), residues: 1345 sheet: -0.02 (0.27), residues: 393 loop : -1.58 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 115 HIS 0.008 0.002 HIS C1237 PHE 0.019 0.002 PHE D 7 TYR 0.025 0.002 TYR M 461 ARG 0.007 0.001 ARG D 220 Details of bonding type rmsd hydrogen bonds : bond 0.05538 ( 1221) hydrogen bonds : angle 4.83414 ( 3389) metal coordination : bond 0.00294 ( 4) covalent geometry : bond 0.00839 (29442) covalent geometry : angle 0.74633 (40444) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 156 time to evaluate : 3.287 Fit side-chains revert: symmetry clash REVERT: C 131 THR cc_start: 0.9466 (OUTLIER) cc_final: 0.9255 (p) REVERT: C 796 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.8932 (pp) REVERT: C 972 PHE cc_start: 0.3929 (OUTLIER) cc_final: 0.3465 (m-10) REVERT: C 1207 SER cc_start: 0.9571 (OUTLIER) cc_final: 0.9336 (p) REVERT: D 9 LYS cc_start: 0.7849 (pttm) cc_final: 0.6907 (ptpt) REVERT: D 308 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8456 (t0) REVERT: D 478 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9294 (mm) REVERT: D 644 MET cc_start: 0.8787 (mtm) cc_final: 0.8535 (mtm) REVERT: D 883 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.6479 (ptm160) REVERT: D 932 MET cc_start: 0.6599 (ptp) cc_final: 0.6242 (ptm) REVERT: D 1040 MET cc_start: 0.2998 (tpt) cc_final: 0.1796 (mmm) REVERT: M 206 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7658 (m-10) REVERT: M 280 LYS cc_start: 0.7339 (mmmm) cc_final: 0.6648 (pttt) REVERT: M 365 MET cc_start: 0.7349 (ppp) cc_final: 0.7012 (ptp) REVERT: M 460 LYS cc_start: 0.8007 (tttt) cc_final: 0.7486 (mmtt) outliers start: 144 outliers final: 74 residues processed: 285 average time/residue: 0.4052 time to fit residues: 192.8240 Evaluate side-chains 224 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 142 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1172 LEU Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 278 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 99 optimal weight: 9.9990 chunk 72 optimal weight: 0.0770 chunk 213 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 286 optimal weight: 0.3980 chunk 356 optimal weight: 6.9990 chunk 310 optimal weight: 5.9990 chunk 88 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 overall best weight: 3.8944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 ASN D 294 ASN D 488 ASN M 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.074549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.049672 restraints weight = 113063.840| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.42 r_work: 0.2763 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29446 Z= 0.151 Angle : 0.573 11.102 40444 Z= 0.300 Chirality : 0.042 0.172 4813 Planarity : 0.004 0.087 4961 Dihedral : 15.870 176.569 5069 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer: Outliers : 4.17 % Allowed : 24.92 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3644 helix: 1.45 (0.15), residues: 1333 sheet: 0.16 (0.27), residues: 399 loop : -1.50 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.003 0.001 HIS D1366 PHE 0.012 0.001 PHE C 405 TYR 0.017 0.001 TYR M 112 ARG 0.006 0.000 ARG D 337 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 1221) hydrogen bonds : angle 4.32208 ( 3389) metal coordination : bond 0.00126 ( 4) covalent geometry : bond 0.00345 (29442) covalent geometry : angle 0.57350 (40444) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 151 time to evaluate : 2.956 Fit side-chains revert: symmetry clash REVERT: B 61 ILE cc_start: 0.9245 (mt) cc_final: 0.9013 (mm) REVERT: B 214 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8054 (pm20) REVERT: C 36 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8482 (tm-30) REVERT: C 131 THR cc_start: 0.9425 (OUTLIER) cc_final: 0.9161 (p) REVERT: C 359 ARG cc_start: 0.6016 (OUTLIER) cc_final: 0.5327 (tmt90) REVERT: C 378 ARG cc_start: 0.7304 (mmp80) cc_final: 0.7065 (mmp80) REVERT: C 461 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8913 (tt0) REVERT: C 796 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9201 (pp) REVERT: C 946 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9216 (mm) REVERT: C 972 PHE cc_start: 0.3851 (OUTLIER) cc_final: 0.3220 (m-10) REVERT: D 160 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8731 (pp) REVERT: D 298 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8645 (mpp) REVERT: D 308 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8118 (t0) REVERT: D 312 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7345 (mmm-85) REVERT: D 478 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9154 (mm) REVERT: D 644 MET cc_start: 0.8801 (mtm) cc_final: 0.8449 (mtm) REVERT: D 883 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.6153 (ptm160) REVERT: D 1040 MET cc_start: 0.3310 (tpt) cc_final: 0.2044 (mmm) REVERT: E 69 ARG cc_start: 0.9124 (ptm-80) cc_final: 0.8877 (ttp80) REVERT: M 206 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7666 (m-10) REVERT: M 217 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7266 (ttm110) REVERT: M 279 ARG cc_start: 0.6585 (ptm-80) cc_final: 0.5727 (ptm-80) REVERT: M 280 LYS cc_start: 0.7131 (mmmm) cc_final: 0.6820 (pttt) REVERT: M 365 MET cc_start: 0.7307 (ppp) cc_final: 0.6953 (ptp) outliers start: 109 outliers final: 51 residues processed: 247 average time/residue: 0.3743 time to fit residues: 153.3975 Evaluate side-chains 208 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 142 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 297 LEU Chi-restraints excluded: chain M residue 333 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 85 optimal weight: 30.0000 chunk 361 optimal weight: 50.0000 chunk 336 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 135 optimal weight: 0.0770 chunk 23 optimal weight: 20.0000 chunk 290 optimal weight: 50.0000 chunk 372 optimal weight: 30.0000 chunk 236 optimal weight: 9.9990 chunk 45 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.073970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.049196 restraints weight = 113057.210| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.41 r_work: 0.2748 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29446 Z= 0.182 Angle : 0.580 11.487 40444 Z= 0.302 Chirality : 0.042 0.271 4813 Planarity : 0.004 0.070 4961 Dihedral : 15.825 176.839 5069 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.53 % Favored : 93.44 % Rotamer: Outliers : 4.67 % Allowed : 24.23 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.18 (0.14), residues: 3644 helix: 1.53 (0.15), residues: 1338 sheet: 0.16 (0.27), residues: 392 loop : -1.46 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 115 HIS 0.003 0.001 HIS D 364 PHE 0.011 0.001 PHE C 405 TYR 0.021 0.001 TYR M 461 ARG 0.006 0.000 ARG D 47 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 1221) hydrogen bonds : angle 4.23678 ( 3389) metal coordination : bond 0.00156 ( 4) covalent geometry : bond 0.00418 (29442) covalent geometry : angle 0.58010 (40444) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 154 time to evaluate : 3.012 Fit side-chains revert: symmetry clash REVERT: B 61 ILE cc_start: 0.9299 (mt) cc_final: 0.9069 (mm) REVERT: C 131 THR cc_start: 0.9448 (OUTLIER) cc_final: 0.9234 (p) REVERT: C 325 LEU cc_start: 0.7867 (pp) cc_final: 0.7627 (tt) REVERT: C 461 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8845 (tt0) REVERT: C 542 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7669 (mmp80) REVERT: C 946 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9233 (mm) REVERT: C 972 PHE cc_start: 0.3694 (OUTLIER) cc_final: 0.3321 (m-10) REVERT: C 1265 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8793 (t80) REVERT: D 160 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8759 (pp) REVERT: D 308 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8379 (t0) REVERT: D 312 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7379 (mmm-85) REVERT: D 330 MET cc_start: 0.8879 (ppp) cc_final: 0.8589 (ppp) REVERT: D 478 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9197 (mm) REVERT: D 644 MET cc_start: 0.8794 (mtm) cc_final: 0.8428 (mtm) REVERT: D 883 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.6221 (ptm160) REVERT: D 1040 MET cc_start: 0.2936 (tpt) cc_final: 0.1829 (mmm) REVERT: E 69 ARG cc_start: 0.9123 (ptm-80) cc_final: 0.8917 (ttp80) REVERT: M 206 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7643 (m-10) REVERT: M 217 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.7370 (ttm110) REVERT: M 270 GLU cc_start: 0.7802 (tp30) cc_final: 0.7544 (tp30) REVERT: M 279 ARG cc_start: 0.6429 (ptm-80) cc_final: 0.5628 (ptm-80) REVERT: M 365 MET cc_start: 0.7303 (ppp) cc_final: 0.7000 (ptp) REVERT: M 460 LYS cc_start: 0.8211 (tppt) cc_final: 0.7474 (mmmt) REVERT: M 461 TYR cc_start: 0.8197 (m-80) cc_final: 0.7945 (m-80) outliers start: 122 outliers final: 75 residues processed: 262 average time/residue: 0.4017 time to fit residues: 172.6958 Evaluate side-chains 233 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 146 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 972 PHE Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1182 ILE Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 333 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 258 optimal weight: 9.9990 chunk 279 optimal weight: 0.9990 chunk 291 optimal weight: 0.9990 chunk 222 optimal weight: 9.9990 chunk 156 optimal weight: 30.0000 chunk 29 optimal weight: 8.9990 chunk 309 optimal weight: 7.9990 chunk 353 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 294 ASN B 41 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.073594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.048981 restraints weight = 113795.913| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.38 r_work: 0.2759 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29446 Z= 0.168 Angle : 0.564 12.208 40444 Z= 0.294 Chirality : 0.041 0.171 4813 Planarity : 0.004 0.064 4961 Dihedral : 15.781 176.364 5069 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.23 % Favored : 93.74 % Rotamer: Outliers : 4.94 % Allowed : 24.31 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.11 (0.14), residues: 3644 helix: 1.64 (0.15), residues: 1336 sheet: 0.19 (0.26), residues: 405 loop : -1.47 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 115 HIS 0.003 0.001 HIS D1366 PHE 0.010 0.001 PHE C 405 TYR 0.016 0.001 TYR M 461 ARG 0.005 0.000 ARG D 47 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 1221) hydrogen bonds : angle 4.12636 ( 3389) metal coordination : bond 0.00154 ( 4) covalent geometry : bond 0.00385 (29442) covalent geometry : angle 0.56438 (40444) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 149 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 ILE cc_start: 0.9317 (mt) cc_final: 0.9096 (mm) REVERT: C 325 LEU cc_start: 0.7894 (pp) cc_final: 0.7608 (tt) REVERT: C 461 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8896 (tt0) REVERT: C 542 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7794 (mmp80) REVERT: C 946 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9235 (mm) REVERT: C 1207 SER cc_start: 0.9559 (OUTLIER) cc_final: 0.9310 (p) REVERT: C 1265 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.8830 (t80) REVERT: D 160 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8779 (pp) REVERT: D 308 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8189 (t0) REVERT: D 312 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7444 (mmm-85) REVERT: D 478 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9197 (mm) REVERT: D 644 MET cc_start: 0.8644 (mtm) cc_final: 0.8290 (mtm) REVERT: D 883 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.6296 (ptm160) REVERT: D 1040 MET cc_start: 0.2955 (tpt) cc_final: 0.1878 (mmm) REVERT: M 206 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7586 (m-10) REVERT: M 217 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.7371 (ttm110) REVERT: M 279 ARG cc_start: 0.6485 (ptm-80) cc_final: 0.5711 (ptm-80) REVERT: M 280 LYS cc_start: 0.7217 (mmmm) cc_final: 0.6795 (pttt) REVERT: M 365 MET cc_start: 0.7362 (ppp) cc_final: 0.7089 (ptp) REVERT: M 460 LYS cc_start: 0.8275 (tppt) cc_final: 0.7578 (mmmt) REVERT: M 461 TYR cc_start: 0.8447 (m-80) cc_final: 0.8208 (m-80) outliers start: 129 outliers final: 82 residues processed: 265 average time/residue: 0.3711 time to fit residues: 163.5502 Evaluate side-chains 234 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 141 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1182 ILE Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 297 LEU Chi-restraints excluded: chain M residue 333 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 225 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 257 optimal weight: 30.0000 chunk 3 optimal weight: 9.9990 chunk 284 optimal weight: 30.0000 chunk 313 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 321 optimal weight: 9.9990 chunk 301 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.072028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.047504 restraints weight = 115041.562| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.32 r_work: 0.2719 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 29446 Z= 0.259 Angle : 0.643 16.682 40444 Z= 0.334 Chirality : 0.044 0.188 4813 Planarity : 0.005 0.065 4961 Dihedral : 15.903 176.099 5069 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.44 % Favored : 92.54 % Rotamer: Outliers : 5.13 % Allowed : 23.97 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.28 (0.14), residues: 3644 helix: 1.48 (0.15), residues: 1341 sheet: 0.15 (0.27), residues: 399 loop : -1.57 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 115 HIS 0.004 0.001 HIS D 469 PHE 0.013 0.001 PHE D 7 TYR 0.016 0.001 TYR M 461 ARG 0.007 0.000 ARG C 378 Details of bonding type rmsd hydrogen bonds : bond 0.04422 ( 1221) hydrogen bonds : angle 4.31300 ( 3389) metal coordination : bond 0.00284 ( 4) covalent geometry : bond 0.00596 (29442) covalent geometry : angle 0.64348 (40444) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 142 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 194 GLN cc_start: 0.8551 (mp10) cc_final: 0.8332 (mp10) REVERT: B 214 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8256 (pm20) REVERT: C 325 LEU cc_start: 0.7995 (pp) cc_final: 0.7541 (tt) REVERT: C 461 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8879 (tt0) REVERT: C 946 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9233 (mm) REVERT: C 1207 SER cc_start: 0.9540 (OUTLIER) cc_final: 0.9302 (p) REVERT: C 1265 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8851 (t80) REVERT: D 160 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8785 (pp) REVERT: D 298 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8594 (mpp) REVERT: D 308 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8388 (t0) REVERT: D 312 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7490 (mmm-85) REVERT: D 644 MET cc_start: 0.8568 (mtm) cc_final: 0.8243 (mtm) REVERT: D 883 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.6394 (ptm160) REVERT: D 1040 MET cc_start: 0.2990 (tpt) cc_final: 0.2067 (mmm) REVERT: E 67 ARG cc_start: 0.8657 (tpp80) cc_final: 0.8456 (tpp80) REVERT: M 206 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7691 (m-10) REVERT: M 279 ARG cc_start: 0.6563 (ptm-80) cc_final: 0.5718 (ptm-80) REVERT: M 365 MET cc_start: 0.7411 (ppp) cc_final: 0.7041 (ptp) outliers start: 134 outliers final: 91 residues processed: 263 average time/residue: 0.3764 time to fit residues: 164.6235 Evaluate side-chains 239 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 137 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1172 LEU Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1190 ILE Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1340 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 333 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 300 optimal weight: 20.0000 chunk 323 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 272 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 chunk 341 optimal weight: 40.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.073278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.048987 restraints weight = 113066.022| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.31 r_work: 0.2762 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29446 Z= 0.140 Angle : 0.561 15.181 40444 Z= 0.291 Chirality : 0.041 0.184 4813 Planarity : 0.004 0.062 4961 Dihedral : 15.812 175.972 5069 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.13 % Rotamer: Outliers : 4.06 % Allowed : 24.96 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.11 (0.14), residues: 3644 helix: 1.71 (0.15), residues: 1339 sheet: 0.19 (0.27), residues: 399 loop : -1.52 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 285 HIS 0.003 0.001 HIS D 777 PHE 0.010 0.001 PHE C 405 TYR 0.013 0.001 TYR M 112 ARG 0.004 0.000 ARG D 47 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 1221) hydrogen bonds : angle 4.04395 ( 3389) metal coordination : bond 0.00172 ( 4) covalent geometry : bond 0.00321 (29442) covalent geometry : angle 0.56098 (40444) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 143 time to evaluate : 3.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8628 (t) REVERT: A 268 ASN cc_start: 0.8722 (m-40) cc_final: 0.8450 (m110) REVERT: B 194 GLN cc_start: 0.8491 (mp10) cc_final: 0.8262 (mp10) REVERT: C 325 LEU cc_start: 0.7971 (pp) cc_final: 0.7644 (tt) REVERT: C 461 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8820 (tt0) REVERT: C 946 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9150 (mm) REVERT: C 1265 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8739 (t80) REVERT: D 160 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8757 (pp) REVERT: D 253 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.8956 (p) REVERT: D 308 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8193 (t0) REVERT: D 312 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7428 (mmm-85) REVERT: D 330 MET cc_start: 0.8800 (ppp) cc_final: 0.8555 (ppp) REVERT: D 644 MET cc_start: 0.8568 (mtm) cc_final: 0.8203 (mtm) REVERT: D 747 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7556 (pmm) REVERT: D 883 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.6287 (ptm160) REVERT: D 1040 MET cc_start: 0.2946 (tpt) cc_final: 0.1848 (mmm) REVERT: M 279 ARG cc_start: 0.6211 (ptm-80) cc_final: 0.5193 (ptm-80) REVERT: M 280 LYS cc_start: 0.7261 (mmmm) cc_final: 0.6776 (pttt) REVERT: M 365 MET cc_start: 0.7420 (ppp) cc_final: 0.7059 (ptp) REVERT: M 460 LYS cc_start: 0.8249 (tppt) cc_final: 0.7559 (mmmt) outliers start: 106 outliers final: 74 residues processed: 241 average time/residue: 0.3767 time to fit residues: 150.8005 Evaluate side-chains 221 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 137 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1340 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 333 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 170 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 365 optimal weight: 30.0000 chunk 323 optimal weight: 7.9990 chunk 300 optimal weight: 0.0070 chunk 192 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 185 optimal weight: 6.9990 chunk 345 optimal weight: 1.9990 chunk 267 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 overall best weight: 2.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.073994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.049729 restraints weight = 114054.596| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.35 r_work: 0.2790 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29446 Z= 0.116 Angle : 0.548 14.924 40444 Z= 0.282 Chirality : 0.041 0.172 4813 Planarity : 0.004 0.061 4961 Dihedral : 15.691 175.960 5069 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.94 % Rotamer: Outliers : 3.48 % Allowed : 25.34 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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 (0.14), residues: 3644 helix: 1.81 (0.15), residues: 1346 sheet: 0.30 (0.26), residues: 410 loop : -1.48 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 33 HIS 0.003 0.001 HIS C 551 PHE 0.010 0.001 PHE C 405 TYR 0.011 0.001 TYR M 112 ARG 0.005 0.000 ARG E 69 Details of bonding type rmsd hydrogen bonds : bond 0.03098 ( 1221) hydrogen bonds : angle 3.90069 ( 3389) metal coordination : bond 0.00104 ( 4) covalent geometry : bond 0.00260 (29442) covalent geometry : angle 0.54818 (40444) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 150 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ASN cc_start: 0.8651 (m-40) cc_final: 0.8341 (m110) REVERT: B 194 GLN cc_start: 0.8491 (mp10) cc_final: 0.8255 (mp10) REVERT: C 325 LEU cc_start: 0.8042 (pp) cc_final: 0.7731 (tt) REVERT: C 461 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8763 (tt0) REVERT: C 946 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9155 (mm) REVERT: C 1207 SER cc_start: 0.9503 (OUTLIER) cc_final: 0.9258 (p) REVERT: D 21 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8617 (ttmm) REVERT: D 160 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8825 (pp) REVERT: D 253 VAL cc_start: 0.9266 (OUTLIER) cc_final: 0.8985 (p) REVERT: D 308 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8114 (t0) REVERT: D 312 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7382 (mmm-85) REVERT: D 330 MET cc_start: 0.8766 (ppp) cc_final: 0.8525 (ppp) REVERT: D 747 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7471 (pmm) REVERT: D 883 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.6245 (ptm160) REVERT: D 1040 MET cc_start: 0.2911 (tpt) cc_final: 0.1847 (mmm) REVERT: M 206 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7362 (m-10) REVERT: M 217 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.7408 (ttm110) REVERT: M 279 ARG cc_start: 0.6087 (ptm-80) cc_final: 0.5163 (ptm-80) REVERT: M 280 LYS cc_start: 0.7225 (mmmm) cc_final: 0.6752 (pttt) REVERT: M 365 MET cc_start: 0.7389 (ppp) cc_final: 0.7003 (ptp) REVERT: M 460 LYS cc_start: 0.8316 (tppt) cc_final: 0.7630 (mmtt) outliers start: 91 outliers final: 64 residues processed: 230 average time/residue: 0.3524 time to fit residues: 136.4725 Evaluate side-chains 212 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 137 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1340 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 333 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 155 optimal weight: 10.0000 chunk 201 optimal weight: 40.0000 chunk 77 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 285 optimal weight: 0.0050 chunk 343 optimal weight: 4.9990 chunk 355 optimal weight: 0.0980 chunk 368 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 230 optimal weight: 0.5980 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.074410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.050171 restraints weight = 113522.498| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.36 r_work: 0.2804 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29446 Z= 0.106 Angle : 0.547 14.527 40444 Z= 0.280 Chirality : 0.041 0.233 4813 Planarity : 0.004 0.061 4961 Dihedral : 15.626 175.644 5069 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.90 % Favored : 94.07 % Rotamer: Outliers : 3.41 % Allowed : 25.73 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 0.10 (0.14), residues: 3644 helix: 1.87 (0.15), residues: 1345 sheet: 0.34 (0.27), residues: 408 loop : -1.41 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 33 HIS 0.009 0.001 HIS A 117 PHE 0.011 0.001 PHE M 185 TYR 0.010 0.001 TYR M 112 ARG 0.011 0.000 ARG M 184 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 1221) hydrogen bonds : angle 3.82341 ( 3389) metal coordination : bond 0.00078 ( 4) covalent geometry : bond 0.00237 (29442) covalent geometry : angle 0.54742 (40444) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 139 time to evaluate : 3.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 ASN cc_start: 0.8692 (m-40) cc_final: 0.8369 (m110) REVERT: B 194 GLN cc_start: 0.8525 (mp10) cc_final: 0.8275 (mp10) REVERT: C 325 LEU cc_start: 0.8051 (pp) cc_final: 0.7742 (tt) REVERT: C 461 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8731 (tt0) REVERT: C 946 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9156 (mm) REVERT: C 1207 SER cc_start: 0.9489 (OUTLIER) cc_final: 0.9244 (p) REVERT: C 1265 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8751 (t80) REVERT: D 9 LYS cc_start: 0.8008 (pttm) cc_final: 0.7718 (pttp) REVERT: D 21 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8618 (ttmm) REVERT: D 160 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8861 (pp) REVERT: D 253 VAL cc_start: 0.9176 (OUTLIER) cc_final: 0.8898 (p) REVERT: D 298 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8602 (mpp) REVERT: D 312 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7398 (mmm-85) REVERT: D 330 MET cc_start: 0.8732 (ppp) cc_final: 0.8490 (ppp) REVERT: D 644 MET cc_start: 0.8433 (mtm) cc_final: 0.8015 (mtm) REVERT: D 747 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7447 (pmm) REVERT: D 883 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.6204 (ptm160) REVERT: D 1040 MET cc_start: 0.2953 (tpt) cc_final: 0.1835 (mmm) REVERT: M 206 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7447 (m-10) REVERT: M 217 ARG cc_start: 0.8274 (ttm-80) cc_final: 0.7383 (ttm110) REVERT: M 279 ARG cc_start: 0.5975 (ptm-80) cc_final: 0.5165 (ptm-80) REVERT: M 280 LYS cc_start: 0.7213 (mmmm) cc_final: 0.6753 (pttt) REVERT: M 365 MET cc_start: 0.7427 (ppp) cc_final: 0.7104 (ptp) REVERT: M 460 LYS cc_start: 0.8303 (tppt) cc_final: 0.7615 (mmtt) outliers start: 89 outliers final: 63 residues processed: 215 average time/residue: 0.3728 time to fit residues: 133.8290 Evaluate side-chains 212 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 137 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1340 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 204 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 231 optimal weight: 9.9990 chunk 185 optimal weight: 0.9980 chunk 300 optimal weight: 8.9990 chunk 259 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 194 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.073661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.049357 restraints weight = 114251.457| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.35 r_work: 0.2777 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29446 Z= 0.145 Angle : 0.562 14.402 40444 Z= 0.288 Chirality : 0.041 0.246 4813 Planarity : 0.004 0.063 4961 Dihedral : 15.625 175.641 5069 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.45 % Favored : 93.52 % Rotamer: Outliers : 3.29 % Allowed : 25.96 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 0.10 (0.14), residues: 3644 helix: 1.90 (0.15), residues: 1343 sheet: 0.32 (0.26), residues: 411 loop : -1.43 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 115 HIS 0.003 0.001 HIS D 777 PHE 0.009 0.001 PHE C 405 TYR 0.011 0.001 TYR M 461 ARG 0.007 0.000 ARG D 425 Details of bonding type rmsd hydrogen bonds : bond 0.03262 ( 1221) hydrogen bonds : angle 3.86403 ( 3389) metal coordination : bond 0.00158 ( 4) covalent geometry : bond 0.00336 (29442) covalent geometry : angle 0.56242 (40444) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7288 Ramachandran restraints generated. 3644 Oldfield, 0 Emsley, 3644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 136 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 125 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8639 (ttmm) REVERT: B 194 GLN cc_start: 0.8553 (mp10) cc_final: 0.8301 (mp10) REVERT: C 325 LEU cc_start: 0.8057 (pp) cc_final: 0.7741 (tt) REVERT: C 461 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8834 (tt0) REVERT: C 946 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9144 (mm) REVERT: C 1207 SER cc_start: 0.9511 (OUTLIER) cc_final: 0.9270 (p) REVERT: C 1265 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8741 (t80) REVERT: D 21 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8650 (ttmm) REVERT: D 160 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8826 (pp) REVERT: D 253 VAL cc_start: 0.9255 (OUTLIER) cc_final: 0.8968 (p) REVERT: D 298 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8575 (mpp) REVERT: D 312 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7449 (mmm-85) REVERT: D 330 MET cc_start: 0.8756 (ppp) cc_final: 0.8496 (ppp) REVERT: D 644 MET cc_start: 0.8448 (mtm) cc_final: 0.8010 (mtm) REVERT: D 747 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7531 (pmm) REVERT: D 883 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.6339 (ptm160) REVERT: D 1040 MET cc_start: 0.3048 (tpt) cc_final: 0.1906 (mmm) REVERT: M 206 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7414 (m-10) REVERT: M 217 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.7414 (ttm110) REVERT: M 279 ARG cc_start: 0.5925 (ptm-80) cc_final: 0.5100 (ptm-80) REVERT: M 280 LYS cc_start: 0.7199 (mmmm) cc_final: 0.6730 (pttt) REVERT: M 365 MET cc_start: 0.7420 (ppp) cc_final: 0.7104 (ptp) REVERT: M 460 LYS cc_start: 0.8321 (tppt) cc_final: 0.7639 (mmtt) outliers start: 86 outliers final: 68 residues processed: 211 average time/residue: 0.3711 time to fit residues: 130.9845 Evaluate side-chains 216 residues out of total 3137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 136 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 951 MET Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1170 MET Chi-restraints excluded: chain C residue 1207 SER Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 21 LYS Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 312 ARG Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 883 ARG Chi-restraints excluded: chain D residue 889 ASP Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1340 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 68 optimal weight: 9.9990 chunk 354 optimal weight: 0.0040 chunk 152 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 chunk 234 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 205 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 268 optimal weight: 0.0970 chunk 64 optimal weight: 3.9990 overall best weight: 2.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN M 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.074362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.050178 restraints weight = 113235.450| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.36 r_work: 0.2803 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29446 Z= 0.110 Angle : 0.545 14.277 40444 Z= 0.278 Chirality : 0.040 0.232 4813 Planarity : 0.004 0.061 4961 Dihedral : 15.573 175.247 5069 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.98 % Favored : 93.99 % Rotamer: Outliers : 2.99 % Allowed : 26.26 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 0.18 (0.14), residues: 3644 helix: 1.95 (0.15), residues: 1342 sheet: 0.40 (0.27), residues: 409 loop : -1.38 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 33 HIS 0.002 0.000 HIS D1366 PHE 0.010 0.001 PHE M 185 TYR 0.009 0.001 TYR M 112 ARG 0.005 0.000 ARG M 184 Details of bonding type rmsd hydrogen bonds : bond 0.02939 ( 1221) hydrogen bonds : angle 3.77996 ( 3389) metal coordination : bond 0.00072 ( 4) covalent geometry : bond 0.00249 (29442) covalent geometry : angle 0.54467 (40444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13845.64 seconds wall clock time: 239 minutes 44.15 seconds (14384.15 seconds total)