Starting phenix.real_space_refine on Mon Feb 19 18:00:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nsr_3695/02_2024/5nsr_3695_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nsr_3695/02_2024/5nsr_3695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nsr_3695/02_2024/5nsr_3695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nsr_3695/02_2024/5nsr_3695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nsr_3695/02_2024/5nsr_3695_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nsr_3695/02_2024/5nsr_3695_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 5 Type Number sf(0) Gaussians P 54 5.49 5 S 83 5.16 5 C 15673 2.51 5 N 4552 2.21 5 O 5001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 473": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 540": "NH1" <-> "NH2" Residue "C ARG 647": "NH1" <-> "NH2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C ARG 919": "NH1" <-> "NH2" Residue "C ARG 974": "NH1" <-> "NH2" Residue "C ARG 1034": "NH1" <-> "NH2" Residue "C ARG 1059": "NH1" <-> "NH2" Residue "C ARG 1106": "NH1" <-> "NH2" Residue "C ARG 1211": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 515": "NH1" <-> "NH2" Residue "D ARG 798": "NH1" <-> "NH2" Residue "D ARG 838": "NH1" <-> "NH2" Residue "D ARG 860": "NH1" <-> "NH2" Residue "D ARG 883": "NH1" <-> "NH2" Residue "D ARG 1148": "NH1" <-> "NH2" Residue "D ARG 1149": "NH1" <-> "NH2" Residue "D ARG 1242": "NH1" <-> "NH2" Residue "D ARG 1258": "NH1" <-> "NH2" Residue "D ARG 1341": "NH1" <-> "NH2" Residue "D ARG 1355": "NH1" <-> "NH2" Residue "D ARG 1372": "NH1" <-> "NH2" Residue "E ARG 16": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25363 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1694 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 102 Chain: "B" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1606 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 9472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 9472 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 264} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1138 Unresolved non-hydrogen angles: 1396 Unresolved non-hydrogen dihedrals: 965 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 6, 'TYR:plan': 13, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 32, 'PHE:plan': 13, 'GLU:plan': 48, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 779 Chain: "D" Number of atoms: 8969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1320, 8969 Classifications: {'peptide': 1320} Incomplete info: {'truncation_to_alanine': 348} Link IDs: {'PTRANS': 53, 'TRANS': 1266} Chain breaks: 6 Unresolved non-hydrogen bonds: 1364 Unresolved non-hydrogen angles: 1689 Unresolved non-hydrogen dihedrals: 1131 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 34, 'TYR:plan': 8, 'ASN:plan1': 13, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 19, 'GLU:plan': 52, 'ARG:plan': 40} Unresolved non-hydrogen planarities: 857 Chain: "E" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "M" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 1983 Classifications: {'peptide': 386} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 322} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 375} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1015 Unresolved non-hydrogen angles: 1333 Unresolved non-hydrogen dihedrals: 759 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 4, 'ASN:plan1': 8, 'TYR:plan': 5, 'UNK:plan-1': 96, 'TRP:plan': 3, 'ASP:plan': 20, 'PHE:plan': 7, 'GLU:plan': 23, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 569 Chain: "F" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 511 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "G" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 596 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N GLY M 166 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.20 residue: pdb=" N ASP M 167 " occ=0.20 ... (3 atoms not shown) pdb=" CB ASP M 167 " occ=0.20 residue: pdb=" N ASP M 168 " occ=0.20 ... (3 atoms not shown) pdb=" CB ASP M 168 " occ=0.20 residue: pdb=" N GLU M 169 " occ=0.20 ... (3 atoms not shown) pdb=" CB GLU M 169 " occ=0.20 residue: pdb=" N ILE M 170 " occ=0.20 ... (3 atoms not shown) pdb=" CB ILE M 170 " occ=0.20 residue: pdb=" N GLY M 171 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 171 " occ=0.20 residue: pdb=" N ARG M 311 " occ=0.00 ... (3 atoms not shown) pdb=" CB ARG M 311 " occ=0.00 Time building chain proxies: 13.63, per 1000 atoms: 0.54 Number of scatterers: 25363 At special positions: 0 Unit cell: (150.52, 169.6, 164.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 83 16.00 P 54 15.00 O 5001 8.00 N 4552 7.00 C 15673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.92 Conformation dependent library (CDL) restraints added in 5.2 seconds 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6652 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 41 sheets defined 39.2% alpha, 8.6% beta 20 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 8.19 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.652A pdb=" N GLY A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 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 154 through 163 removed outlier: 3.757A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.493A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.538A pdb=" N LEU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B 40 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 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 212 through 229 Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.767A pdb=" N GLN C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 277 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 removed outlier: 4.113A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN C 327 " --> pdb=" O ALA C 323 " (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 380 through 389 Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.759A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.516A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 528 removed outlier: 3.645A pdb=" N SER C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.512A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 4.081A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.960A pdb=" N GLN C 659 " --> pdb=" O SER C 656 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 703 through 712 removed outlier: 4.285A pdb=" N ALA C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 865 removed outlier: 4.156A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 907 removed outlier: 3.742A pdb=" N GLU C 899 " --> pdb=" O LEU C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 979 removed outlier: 3.802A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 990 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 4.467A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1039 removed outlier: 3.548A pdb=" N LYS C1035 " --> pdb=" O ALA C1031 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY C1039 " --> pdb=" O LYS C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 Processing helix chain 'C' and resid 1109 through 1135 removed outlier: 4.124A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.794A pdb=" N PHE C1144 " --> pdb=" O LYS C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1168 through 1176 removed outlier: 4.045A pdb=" N GLU C1174 " --> pdb=" O MET C1170 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1297 through 1311 removed outlier: 3.709A pdb=" N ARG C1301 " --> pdb=" O ASP C1297 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.738A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.571A pdb=" N LEU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 182 through 192 removed outlier: 4.047A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.853A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 removed outlier: 3.754A pdb=" N ILE D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 265 through 286 removed outlier: 3.648A pdb=" N ARG D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.518A pdb=" N LYS D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 406 through 419 removed outlier: 4.153A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.907A pdb=" N ILE D 434 " --> pdb=" O ARG D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.941A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.924A pdb=" N ALA D 476 " --> pdb=" O LEU D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 530 through 538 removed outlier: 4.151A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 581 removed outlier: 3.955A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.839A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 613 removed outlier: 3.745A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET D 604 " --> pdb=" O ALA D 600 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 605 " --> pdb=" O ILE D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.778A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 671 removed outlier: 4.391A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.129A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 807 No H-bonds generated for 'chain 'D' and resid 805 through 807' Processing helix chain 'D' and resid 834 through 840 removed outlier: 4.212A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 874 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.948A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 895 through 900' Processing helix chain 'D' and resid 914 through 919 removed outlier: 3.781A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 936 removed outlier: 3.751A pdb=" N THR D 934 " --> pdb=" O THR D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 1139 through 1147 removed outlier: 3.670A pdb=" N GLU D1146 " --> pdb=" O ALA D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1223 Processing helix chain 'D' and resid 1225 through 1245 Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.166A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.607A pdb=" N VAL D1337 " --> pdb=" O THR D1333 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1362 through 1371 Processing helix chain 'D' and resid 1372 through 1375 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 18 through 33 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 17 through 22 Processing helix chain 'M' and resid 29 through 40 Processing helix chain 'M' and resid 121 through 130 Processing helix chain 'M' and resid 135 through 146 removed outlier: 3.925A pdb=" N ASP M 146 " --> pdb=" O THR M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 166 removed outlier: 3.993A pdb=" N GLY M 166 " --> pdb=" O VAL M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 184 removed outlier: 4.180A pdb=" N ARG M 181 " --> pdb=" O ALA M 177 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG M 184 " --> pdb=" O LYS M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 205 removed outlier: 3.528A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 223 Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 242 through 245 Processing helix chain 'M' and resid 246 through 254 Processing helix chain 'M' and resid 303 through 304 No H-bonds generated for 'chain 'M' and resid 303 through 304' Processing helix chain 'M' and resid 306 through 309 removed outlier: 3.673A pdb=" N SER M 309 " --> pdb=" O MET M 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 306 through 309' Processing helix chain 'M' and resid 318 through 355 removed outlier: 3.683A pdb=" N PHE M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 368 through 375 removed outlier: 3.670A pdb=" N VAL M 374 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 386 removed outlier: 3.809A pdb=" N THR M 386 " --> pdb=" O SER M 382 " (cutoff:3.500A) Processing helix chain 'M' and resid 418 through 428 Processing helix chain 'M' and resid 438 through 449 Processing helix chain 'M' and resid 457 through 462 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 3.905A pdb=" N LEU A 198 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 184 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.554A pdb=" N GLY A 53 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 105 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.469A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 17 removed outlier: 5.316A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 61 removed outlier: 5.459A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.018A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AB2, first strand: chain 'C' and resid 93 through 94 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 removed outlier: 3.642A pdb=" N GLY C 154 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE C 177 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 175 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C 174 " --> pdb=" O PHE C 186 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.487A 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: 4.496A pdb=" N VAL C 296 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.203A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (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 616 through 617 Processing sheet with id=AC3, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 Processing sheet with id=AC5, first strand: chain 'C' and resid 722 through 724 removed outlier: 3.803A pdb=" N ASP C 749 " --> pdb=" O ILE C 734 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.634A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1073 through 1074 removed outlier: 4.654A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET C1230 " --> pdb=" O MET C 800 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1073 through 1074 removed outlier: 3.915A pdb=" N VAL C1225 " --> pdb=" O ILE C1210 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 830 through 838 removed outlier: 4.215A pdb=" N VAL C1050 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 849 through 850 removed outlier: 3.693A pdb=" N GLU C 849 " --> pdb=" O VAL C 887 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1335 through 1337 Processing sheet with id=AD4, first strand: chain 'D' and resid 104 through 105 Processing sheet with id=AD5, first strand: chain 'D' and resid 145 through 147 removed outlier: 4.523A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 435 through 437 removed outlier: 3.527A pdb=" N LEU D 422 " --> pdb=" O HIS D 469 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 551 through 556 Processing sheet with id=AD8, first strand: chain 'D' and resid 820 through 822 removed outlier: 4.350A pdb=" N VAL D 843 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 960 through 961 Processing sheet with id=AE1, first strand: chain 'D' and resid 966 through 967 Processing sheet with id=AE2, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AE3, first strand: chain 'D' and resid 1059 through 1060 Processing sheet with id=AE4, first strand: chain 'D' and resid 1165 through 1166 removed outlier: 3.638A pdb=" N GLY D1166 " --> pdb=" O VAL D1176 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL D1176 " --> pdb=" O GLY D1166 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 279 through 280 removed outlier: 4.168A pdb=" N UNK M 287 " --> pdb=" O UNK M 280 " (cutoff:3.500A) 1003 hydrogen bonds defined for protein. 2841 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 10.69 Time building geometry restraints manager: 10.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.53: 22505 1.53 - 1.84: 3271 1.84 - 2.15: 0 2.15 - 2.46: 0 2.46 - 2.76: 1 Bond restraints: 25777 Sorted by residual: bond pdb=" C UNK M 304 " pdb=" N MET M 306 " ideal model delta sigma weight residual 1.329 2.765 -1.436 1.40e-02 5.10e+03 1.05e+04 bond pdb=" O3' DG G -10 " pdb=" P DA G -9 " ideal model delta sigma weight residual 1.607 1.317 0.290 1.50e-02 4.44e+03 3.73e+02 bond pdb=" O3' DA G -11 " pdb=" P DG G -10 " ideal model delta sigma weight residual 1.607 1.461 0.146 1.50e-02 4.44e+03 9.52e+01 bond pdb=" O3' DA G -9 " pdb=" P DT G -8 " ideal model delta sigma weight residual 1.607 1.464 0.143 1.50e-02 4.44e+03 9.09e+01 bond pdb=" O3' DC G -7 " pdb=" P DA G -6 " ideal model delta sigma weight residual 1.607 1.472 0.135 1.50e-02 4.44e+03 8.05e+01 ... (remaining 25772 not shown) Histogram of bond angle deviations from ideal: 75.20 - 92.04: 4 92.04 - 108.89: 1801 108.89 - 125.74: 33214 125.74 - 142.59: 421 142.59 - 159.44: 1 Bond angle restraints: 35441 Sorted by residual: angle pdb=" O UNK M 304 " pdb=" C UNK M 304 " pdb=" N MET M 306 " ideal model delta sigma weight residual 123.00 75.20 47.80 1.60e+00 3.91e-01 8.93e+02 angle pdb=" C3' DT F 71 " pdb=" O3' DT F 71 " pdb=" P DC F 72 " ideal model delta sigma weight residual 120.20 159.44 -39.24 1.50e+00 4.44e-01 6.84e+02 angle pdb=" O3' DT F 71 " pdb=" P DC F 72 " pdb=" OP1 DC F 72 " ideal model delta sigma weight residual 108.00 141.52 -33.52 3.00e+00 1.11e-01 1.25e+02 angle pdb=" O3' DT F 71 " pdb=" P DC F 72 " pdb=" O5' DC F 72 " ideal model delta sigma weight residual 104.00 89.70 14.30 1.50e+00 4.44e-01 9.09e+01 angle pdb=" C3' DA G -11 " pdb=" O3' DA G -11 " pdb=" P DG G -10 " ideal model delta sigma weight residual 120.20 107.10 13.10 1.50e+00 4.44e-01 7.63e+01 ... (remaining 35436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.69: 15068 31.69 - 63.39: 378 63.39 - 95.08: 16 95.08 - 126.78: 2 126.78 - 158.47: 2 Dihedral angle restraints: 15466 sinusoidal: 5193 harmonic: 10273 Sorted by residual: dihedral pdb=" CA UNK M 304 " pdb=" C UNK M 304 " pdb=" N MET M 306 " pdb=" CA MET M 306 " ideal model delta harmonic sigma weight residual -180.00 -68.20 -111.80 0 5.00e+00 4.00e-02 5.00e+02 dihedral pdb=" CA PHE M 133 " pdb=" C PHE M 133 " pdb=" N THR M 134 " pdb=" CA THR M 134 " ideal model delta harmonic sigma weight residual 180.00 149.52 30.48 0 5.00e+00 4.00e-02 3.72e+01 dihedral pdb=" CA THR D 473 " pdb=" C THR D 473 " pdb=" N LEU D 474 " pdb=" CA LEU D 474 " ideal model delta harmonic sigma weight residual 180.00 -152.30 -27.70 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 15463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 4308 0.120 - 0.240: 77 0.240 - 0.361: 10 0.361 - 0.481: 2 0.481 - 0.601: 1 Chirality restraints: 4398 Sorted by residual: chirality pdb=" C1' DC G -7 " pdb=" O4' DC G -7 " pdb=" C2' DC G -7 " pdb=" N1 DC G -7 " both_signs ideal model delta sigma weight residual False 2.47 3.07 -0.60 2.00e-01 2.50e+01 9.03e+00 chirality pdb=" C3' DC G -12 " pdb=" C4' DC G -12 " pdb=" O3' DC G -12 " pdb=" C2' DC G -12 " both_signs ideal model delta sigma weight residual False -2.66 -2.25 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" C4' DA G -6 " pdb=" C5' DA G -6 " pdb=" O4' DA G -6 " pdb=" C3' DA G -6 " both_signs ideal model delta sigma weight residual False -2.53 -2.13 -0.40 2.00e-01 2.50e+01 3.98e+00 ... (remaining 4395 not shown) Planarity restraints: 4505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK M 304 " 0.177 2.00e-02 2.50e+03 2.27e-01 5.16e+02 pdb=" C UNK M 304 " -0.386 2.00e-02 2.50e+03 pdb=" O UNK M 304 " 0.153 2.00e-02 2.50e+03 pdb=" N MET M 306 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER M 221 " 0.026 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C SER M 221 " -0.092 2.00e-02 2.50e+03 pdb=" O SER M 221 " 0.035 2.00e-02 2.50e+03 pdb=" N ASP M 222 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT F 82 " 0.067 2.00e-02 2.50e+03 2.98e-02 2.22e+01 pdb=" N1 DT F 82 " -0.020 2.00e-02 2.50e+03 pdb=" C2 DT F 82 " -0.016 2.00e-02 2.50e+03 pdb=" O2 DT F 82 " -0.025 2.00e-02 2.50e+03 pdb=" N3 DT F 82 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT F 82 " 0.011 2.00e-02 2.50e+03 pdb=" O4 DT F 82 " 0.038 2.00e-02 2.50e+03 pdb=" C5 DT F 82 " -0.013 2.00e-02 2.50e+03 pdb=" C7 DT F 82 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DT F 82 " -0.035 2.00e-02 2.50e+03 ... (remaining 4502 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 6 2.02 - 2.74: 2295 2.74 - 3.46: 35591 3.46 - 4.18: 54389 4.18 - 4.90: 94215 Nonbonded interactions: 186496 Sorted by model distance: nonbonded pdb=" O UNK M 289 " pdb=" N UNK M 291 " model vdw 1.302 2.520 nonbonded pdb=" C UNK M 289 " pdb=" N UNK M 291 " model vdw 1.446 3.350 nonbonded pdb=" O UNK M 303 " pdb=" N GLY M 307 " model vdw 1.559 2.520 nonbonded pdb=" O2 DC F 83 " pdb=" N2 DG G -21 " model vdw 1.832 2.520 nonbonded pdb=" O VAL A 192 " pdb=" N GLN A 194 " model vdw 1.985 2.520 ... (remaining 186491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O or name CB )) or resid 25 through 64 or (resi \ d 65 through 67 and (name N or name CA or name C or name O or name CB )) or resi \ d 68 through 70 or (resid 71 through 72 and (name N or name CA or name C or name \ O or name CB )) or resid 73 or (resid 74 and (name N or name CA or name C or na \ me O or name CB )) or resid 75 through 79 or (resid 80 and (name N or name CA or \ name C or name O or name CB )) or resid 81 through 95 or (resid 96 and (name N \ or name CA or name C or name O or name CB )) or resid 97 through 102 or (resid 1 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 104 through \ 127 or (resid 128 and (name N or name CA or name C or name O or name CB )) or r \ esid 129 through 141 or (resid 142 and (name N or name CA or name C or name O or \ name CB )) or resid 143 through 157 or (resid 158 and (name N or name CA or nam \ e C or name O or name CB )) or resid 159 or resid 172 through 193 or (resid 194 \ through 195 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 6 or (resid 197 and (name N or name CA or name C or name O or name CB )) or resi \ d 198 through 226 or (resid 227 and (name N or name CA or name C or name O or na \ me CB )) or resid 228 through 230 or (resid 231 and (name N or name CA or name C \ or name O or name CB )) or resid 232 or (resid 233 through 235 and (name N or n \ ame CA or name C or name O or name CB )) or resid 236 through 237)) selection = (chain 'B' and (resid 5 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 32 or (resid 33 and (name N or name CA \ or name C or name O or name CB )) or resid 34 through 40 or (resid 41 through 4 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 43 through 7 \ 6 or (resid 77 and (name N or name CA or name C or name O or name CB )) or resid \ 78 through 135 or (resid 136 and (name N or name CA or name C or name O or name \ CB )) or resid 137 through 184 or (resid 185 and (name N or name CA or name C o \ r name O or name CB )) or resid 186 through 190 or (resid 191 and (name N or nam \ e CA or name C or name O or name CB )) or resid 192 through 194 or (resid 195 an \ d (name N or name CA or name C or name O or name CB )) or resid 196 through 203 \ or (resid 204 and (name N or name CA or name C or name O or name CB )) or resid \ 205 through 211 or (resid 212 and (name N or name CA or name C or name O or name \ CB )) or resid 213 through 216 or (resid 217 and (name N or name CA or name C o \ r name O or name CB )) or resid 218 through 225 or (resid 226 through 227 and (n \ ame N or name CA or name C or name O or name CB )) or resid 228 or (resid 229 th \ rough 231 and (name N or name CA or name C or name O or name CB )) or resid 232 \ through 237)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 4.790 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 73.270 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.100 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.436 25777 Z= 0.735 Angle : 0.902 47.804 35441 Z= 0.523 Chirality : 0.049 0.601 4398 Planarity : 0.005 0.227 4505 Dihedral : 12.710 158.471 8814 Min Nonbonded Distance : 1.302 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.96 % Allowed : 8.78 % Favored : 90.26 % Rotamer: Outliers : 0.19 % Allowed : 1.35 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.11), residues: 3451 helix: -2.95 (0.10), residues: 1161 sheet: -1.12 (0.28), residues: 258 loop : -2.25 (0.11), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 686 HIS 0.003 0.000 HIS D 419 PHE 0.023 0.001 PHE D 620 TYR 0.030 0.001 TYR D 140 ARG 0.008 0.000 ARG D 610 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 718 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8622 (tt0) cc_final: 0.8237 (pm20) REVERT: A 65 LEU cc_start: 0.8967 (tp) cc_final: 0.8764 (tp) REVERT: A 133 LEU cc_start: 0.7995 (mt) cc_final: 0.7775 (mm) REVERT: A 139 SER cc_start: 0.7804 (p) cc_final: 0.7343 (m) REVERT: A 143 ARG cc_start: 0.8757 (mtm-85) cc_final: 0.8520 (mtm-85) REVERT: A 174 ASP cc_start: 0.7878 (m-30) cc_final: 0.6286 (p0) REVERT: A 197 ASP cc_start: 0.7864 (p0) cc_final: 0.6929 (p0) REVERT: A 231 PHE cc_start: 0.8314 (m-10) cc_final: 0.7993 (m-10) REVERT: B 57 THR cc_start: 0.4906 (t) cc_final: 0.4228 (m) REVERT: B 137 ASN cc_start: 0.8450 (m-40) cc_final: 0.8170 (p0) REVERT: B 212 ASP cc_start: 0.6979 (t0) cc_final: 0.6431 (t70) REVERT: C 79 VAL cc_start: 0.8358 (m) cc_final: 0.7552 (p) REVERT: C 183 TRP cc_start: 0.6609 (m-10) cc_final: 0.5977 (m-10) REVERT: C 195 PHE cc_start: 0.7406 (m-10) cc_final: 0.7183 (m-80) REVERT: C 201 ARG cc_start: 0.8719 (mmt-90) cc_final: 0.8477 (mmt90) REVERT: C 357 ASN cc_start: 0.8728 (t0) cc_final: 0.8395 (p0) REVERT: C 419 ILE cc_start: 0.9141 (pt) cc_final: 0.8751 (mp) REVERT: C 445 ILE cc_start: 0.8432 (mt) cc_final: 0.8007 (pt) REVERT: C 450 ASN cc_start: 0.7684 (m-40) cc_final: 0.7437 (p0) REVERT: C 575 LEU cc_start: 0.8867 (mt) cc_final: 0.8661 (mp) REVERT: C 629 PHE cc_start: 0.8508 (m-10) cc_final: 0.7838 (m-80) REVERT: C 660 VAL cc_start: 0.8572 (m) cc_final: 0.8362 (t) REVERT: C 726 TYR cc_start: 0.9138 (t80) cc_final: 0.8458 (t80) REVERT: C 752 ASN cc_start: 0.8965 (m-40) cc_final: 0.8724 (t0) REVERT: C 950 GLU cc_start: 0.9331 (mm-30) cc_final: 0.9036 (pp20) REVERT: C 952 GLN cc_start: 0.9239 (mm110) cc_final: 0.8999 (tp-100) REVERT: C 954 LYS cc_start: 0.9503 (mmtp) cc_final: 0.9191 (mtmm) REVERT: C 1019 ASP cc_start: 0.9538 (m-30) cc_final: 0.9116 (t0) REVERT: C 1033 ARG cc_start: 0.8865 (ttt-90) cc_final: 0.8604 (ttp80) REVERT: C 1036 ILE cc_start: 0.9417 (mm) cc_final: 0.9131 (mm) REVERT: C 1076 ILE cc_start: 0.8349 (mp) cc_final: 0.7890 (mt) REVERT: C 1106 ARG cc_start: 0.8465 (mtt180) cc_final: 0.8076 (mpt180) REVERT: C 1109 ILE cc_start: 0.8533 (mm) cc_final: 0.8271 (mm) REVERT: C 1194 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7548 (mm-30) REVERT: C 1214 ASP cc_start: 0.9281 (t0) cc_final: 0.8989 (t0) REVERT: C 1219 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8460 (pp20) REVERT: C 1254 VAL cc_start: 0.7005 (t) cc_final: 0.6240 (m) REVERT: D 53 ARG cc_start: 0.7402 (ttt180) cc_final: 0.7037 (tpm170) REVERT: D 298 MET cc_start: 0.6799 (mmt) cc_final: 0.6395 (mmp) REVERT: D 353 SER cc_start: 0.9026 (p) cc_final: 0.8820 (p) REVERT: D 485 MET cc_start: 0.8601 (mmm) cc_final: 0.8123 (mmm) REVERT: D 568 SER cc_start: 0.7028 (t) cc_final: 0.6745 (m) REVERT: D 603 LYS cc_start: 0.8450 (pttt) cc_final: 0.8196 (tptp) REVERT: D 886 VAL cc_start: 0.8598 (p) cc_final: 0.8373 (p) REVERT: D 1040 MET cc_start: 0.3078 (mtp) cc_final: 0.1716 (mmt) REVERT: D 1256 ILE cc_start: 0.8680 (mt) cc_final: 0.8380 (pt) REVERT: D 1361 THR cc_start: 0.8858 (p) cc_final: 0.8416 (t) REVERT: D 1363 TYR cc_start: 0.8358 (t80) cc_final: 0.8038 (t80) REVERT: E 41 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7304 (mp0) REVERT: E 51 LEU cc_start: 0.6328 (mp) cc_final: 0.5900 (tt) outliers start: 4 outliers final: 2 residues processed: 719 average time/residue: 0.3998 time to fit residues: 443.0100 Evaluate side-chains 368 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 366 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain D residue 366 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 83 optimal weight: 0.0020 chunk 164 optimal weight: 8.9990 chunk 130 optimal weight: 0.0070 chunk 252 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 153 optimal weight: 0.0030 chunk 187 optimal weight: 2.9990 chunk 292 optimal weight: 9.9990 overall best weight: 1.4020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN C 41 GLN C 86 GLN C 139 ASN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 ASN C 604 HIS C 808 ASN C 832 HIS C1070 HIS C1146 GLN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 519 ASN D 897 HIS D1367 GLN E 15 ASN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 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 0.046 25777 Z= 0.212 Angle : 0.679 13.270 35441 Z= 0.347 Chirality : 0.044 0.224 4398 Planarity : 0.005 0.056 4505 Dihedral : 13.593 156.905 4345 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.17 % Favored : 93.25 % Rotamer: Outliers : 4.01 % Allowed : 13.48 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.13), residues: 3451 helix: -0.73 (0.14), residues: 1189 sheet: -0.85 (0.28), residues: 294 loop : -2.01 (0.12), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 115 HIS 0.005 0.001 HIS D 469 PHE 0.018 0.002 PHE D 57 TYR 0.022 0.002 TYR B 185 ARG 0.006 0.001 ARG D 838 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 382 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.8093 (pp) cc_final: 0.7838 (pt) REVERT: A 58 GLU cc_start: 0.7617 (pt0) cc_final: 0.7246 (pp20) REVERT: A 60 GLU cc_start: 0.8763 (tt0) cc_final: 0.8268 (pm20) REVERT: A 139 SER cc_start: 0.7748 (p) cc_final: 0.7461 (m) REVERT: A 143 ARG cc_start: 0.8733 (mtm-85) cc_final: 0.8522 (mtm-85) REVERT: A 194 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.8035 (pp30) REVERT: B 81 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8399 (tp) REVERT: B 85 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8705 (mt) REVERT: B 137 ASN cc_start: 0.8403 (m-40) cc_final: 0.8056 (p0) REVERT: B 147 GLN cc_start: 0.6685 (OUTLIER) cc_final: 0.6407 (mp10) REVERT: B 212 ASP cc_start: 0.7210 (t0) cc_final: 0.6480 (t0) REVERT: C 79 VAL cc_start: 0.8386 (m) cc_final: 0.7571 (p) REVERT: C 195 PHE cc_start: 0.7554 (m-10) cc_final: 0.7196 (m-80) REVERT: C 357 ASN cc_start: 0.8695 (t0) cc_final: 0.8391 (p0) REVERT: C 445 ILE cc_start: 0.8580 (mt) cc_final: 0.7777 (pt) REVERT: C 450 ASN cc_start: 0.7936 (m-40) cc_final: 0.7576 (p0) REVERT: C 653 MET cc_start: 0.8090 (tpt) cc_final: 0.6870 (mtt) REVERT: C 871 VAL cc_start: 0.7064 (m) cc_final: 0.6688 (p) REVERT: C 1033 ARG cc_start: 0.8870 (ttt-90) cc_final: 0.8650 (ttp80) REVERT: C 1036 ILE cc_start: 0.9259 (mm) cc_final: 0.9012 (mm) REVERT: C 1076 ILE cc_start: 0.8142 (mp) cc_final: 0.7920 (mt) REVERT: C 1085 MET cc_start: 0.9074 (mmt) cc_final: 0.8801 (mmp) REVERT: C 1194 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7730 (mm-30) REVERT: C 1254 VAL cc_start: 0.7616 (t) cc_final: 0.7031 (m) REVERT: C 1259 LEU cc_start: 0.8374 (mp) cc_final: 0.7823 (tt) REVERT: D 53 ARG cc_start: 0.7311 (ttt180) cc_final: 0.6921 (tpm170) REVERT: D 102 MET cc_start: 0.6988 (ttm) cc_final: 0.6481 (ttm) REVERT: D 115 TRP cc_start: 0.6818 (m100) cc_final: 0.6483 (m100) REVERT: D 130 MET cc_start: 0.7678 (tpp) cc_final: 0.7402 (tpp) REVERT: D 267 ASP cc_start: 0.7614 (m-30) cc_final: 0.7353 (m-30) REVERT: D 364 HIS cc_start: 0.7388 (p90) cc_final: 0.7058 (p90) REVERT: D 551 ARG cc_start: 0.8164 (ppt170) cc_final: 0.7833 (ptt180) REVERT: D 603 LYS cc_start: 0.8604 (pttt) cc_final: 0.8275 (tptp) REVERT: D 702 GLN cc_start: 0.6561 (OUTLIER) cc_final: 0.6239 (pm20) REVERT: D 743 MET cc_start: 0.7262 (mtm) cc_final: 0.6723 (mtm) REVERT: D 773 PHE cc_start: 0.8384 (t80) cc_final: 0.8069 (t80) REVERT: D 892 PHE cc_start: 0.8008 (m-80) cc_final: 0.7697 (m-80) REVERT: D 1361 THR cc_start: 0.9028 (p) cc_final: 0.8615 (t) REVERT: E 41 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7396 (mp0) REVERT: E 51 LEU cc_start: 0.6367 (mp) cc_final: 0.5879 (tt) outliers start: 83 outliers final: 44 residues processed: 443 average time/residue: 0.3552 time to fit residues: 257.9636 Evaluate side-chains 347 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 298 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 763 PHE Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 846 GLU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 162 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 243 optimal weight: 8.9990 chunk 199 optimal weight: 30.0000 chunk 80 optimal weight: 4.9990 chunk 292 optimal weight: 9.9990 chunk 316 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 290 optimal weight: 0.0020 chunk 99 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 75 GLN A 128 HIS C 554 HIS C 808 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN ** D 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 25777 Z= 0.320 Angle : 0.755 14.070 35441 Z= 0.390 Chirality : 0.047 0.239 4398 Planarity : 0.005 0.078 4505 Dihedral : 14.049 163.169 4341 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.43 % Favored : 91.05 % Rotamer: Outliers : 6.33 % Allowed : 15.47 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.13), residues: 3451 helix: -0.09 (0.14), residues: 1195 sheet: -0.74 (0.31), residues: 274 loop : -1.94 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 686 HIS 0.012 0.002 HIS D 469 PHE 0.027 0.002 PHE D 620 TYR 0.038 0.002 TYR C 810 ARG 0.006 0.001 ARG C1177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 304 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7724 (pt0) cc_final: 0.7322 (pp20) REVERT: A 60 GLU cc_start: 0.8724 (tt0) cc_final: 0.8244 (pm20) REVERT: A 83 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9229 (mp) REVERT: A 194 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8166 (pp30) REVERT: B 129 VAL cc_start: 0.7324 (t) cc_final: 0.7090 (m) REVERT: B 137 ASN cc_start: 0.8442 (m-40) cc_final: 0.8144 (p0) REVERT: B 212 ASP cc_start: 0.7156 (t0) cc_final: 0.6951 (t0) REVERT: C 183 TRP cc_start: 0.7506 (m-10) cc_final: 0.7301 (m-10) REVERT: C 357 ASN cc_start: 0.8470 (t0) cc_final: 0.8120 (p0) REVERT: C 428 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7823 (p) REVERT: C 514 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7237 (p90) REVERT: C 775 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7820 (pm20) REVERT: C 825 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8496 (tm-30) REVERT: C 850 ILE cc_start: 0.6439 (OUTLIER) cc_final: 0.6200 (pp) REVERT: C 952 GLN cc_start: 0.9518 (tp-100) cc_final: 0.9140 (mt0) REVERT: C 1149 TYR cc_start: 0.7917 (m-10) cc_final: 0.7438 (m-10) REVERT: C 1254 VAL cc_start: 0.7471 (t) cc_final: 0.7198 (m) REVERT: C 1269 ARG cc_start: 0.8144 (ptt-90) cc_final: 0.7271 (ptp-110) REVERT: C 1275 VAL cc_start: 0.9287 (t) cc_final: 0.8943 (p) REVERT: C 1319 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7121 (tpt) REVERT: D 53 ARG cc_start: 0.7789 (ttt180) cc_final: 0.7275 (tpp-160) REVERT: D 102 MET cc_start: 0.8032 (ttm) cc_final: 0.7761 (ttm) REVERT: D 115 TRP cc_start: 0.7375 (m100) cc_final: 0.6565 (m100) REVERT: D 130 MET cc_start: 0.7920 (tpp) cc_final: 0.7657 (tpp) REVERT: D 239 LEU cc_start: 0.4906 (OUTLIER) cc_final: 0.4678 (pp) REVERT: D 267 ASP cc_start: 0.7577 (m-30) cc_final: 0.7114 (m-30) REVERT: D 372 MET cc_start: 0.8836 (tpp) cc_final: 0.8500 (mpp) REVERT: D 465 GLN cc_start: 0.8924 (tt0) cc_final: 0.8597 (mt0) REVERT: D 478 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7906 (tt) REVERT: D 551 ARG cc_start: 0.8503 (ppt170) cc_final: 0.8145 (ptt180) REVERT: D 603 LYS cc_start: 0.8725 (pttt) cc_final: 0.8403 (tptp) REVERT: D 608 CYS cc_start: 0.8764 (t) cc_final: 0.8489 (t) REVERT: D 702 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.6821 (pm20) REVERT: D 716 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7261 (tt0) REVERT: D 757 THR cc_start: 0.7366 (p) cc_final: 0.7148 (p) REVERT: D 821 MET cc_start: 0.8846 (mmp) cc_final: 0.7958 (pmm) REVERT: D 822 MET cc_start: 0.7933 (tpp) cc_final: 0.7572 (tpp) REVERT: D 826 ILE cc_start: 0.8665 (pt) cc_final: 0.8254 (mt) REVERT: D 925 GLU cc_start: 0.9221 (tt0) cc_final: 0.8994 (tm-30) REVERT: E 41 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7486 (mp0) REVERT: E 52 ARG cc_start: 0.7076 (mtt180) cc_final: 0.6535 (mmp-170) outliers start: 131 outliers final: 72 residues processed: 402 average time/residue: 0.3218 time to fit residues: 216.8100 Evaluate side-chains 328 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 246 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 406 ASN Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 775 GLU Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 716 GLN Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 763 PHE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1319 PHE Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 160 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 289 optimal weight: 0.0670 chunk 220 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 196 optimal weight: 6.9990 chunk 293 optimal weight: 3.9990 chunk 311 optimal weight: 0.3980 chunk 153 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1350 ASN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25777 Z= 0.168 Angle : 0.625 11.623 35441 Z= 0.315 Chirality : 0.043 0.296 4398 Planarity : 0.004 0.080 4505 Dihedral : 13.730 166.974 4341 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.19 % Favored : 92.29 % Rotamer: Outliers : 4.69 % Allowed : 18.56 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3451 helix: 0.53 (0.15), residues: 1217 sheet: -0.43 (0.31), residues: 273 loop : -1.80 (0.13), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 580 HIS 0.006 0.001 HIS A 132 PHE 0.022 0.001 PHE C 812 TYR 0.020 0.001 TYR D 626 ARG 0.006 0.000 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 305 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7628 (pt0) cc_final: 0.7257 (pp20) REVERT: A 60 GLU cc_start: 0.8669 (tt0) cc_final: 0.8198 (pm20) REVERT: A 194 GLN cc_start: 0.8290 (tm-30) cc_final: 0.8078 (pp30) REVERT: B 78 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7757 (pp) REVERT: B 129 VAL cc_start: 0.7355 (t) cc_final: 0.7016 (m) REVERT: B 137 ASN cc_start: 0.8430 (m-40) cc_final: 0.8114 (p0) REVERT: B 212 ASP cc_start: 0.7051 (t0) cc_final: 0.6698 (t0) REVERT: C 357 ASN cc_start: 0.8498 (t0) cc_final: 0.8115 (p0) REVERT: C 530 ILE cc_start: 0.9181 (mm) cc_final: 0.8735 (mm) REVERT: C 637 ARG cc_start: 0.8258 (ptm160) cc_final: 0.8045 (ttp-110) REVERT: C 653 MET cc_start: 0.8281 (tpt) cc_final: 0.6987 (mtt) REVERT: C 850 ILE cc_start: 0.6393 (OUTLIER) cc_final: 0.6090 (pp) REVERT: C 1194 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7905 (tt0) REVERT: C 1269 ARG cc_start: 0.7928 (ptt-90) cc_final: 0.7071 (ptp-110) REVERT: C 1275 VAL cc_start: 0.9234 (t) cc_final: 0.8690 (p) REVERT: D 53 ARG cc_start: 0.7780 (ttt180) cc_final: 0.7280 (tpp-160) REVERT: D 102 MET cc_start: 0.7944 (ttm) cc_final: 0.7418 (ttm) REVERT: D 115 TRP cc_start: 0.7372 (m100) cc_final: 0.6539 (m100) REVERT: D 130 MET cc_start: 0.8143 (tpp) cc_final: 0.7862 (tpp) REVERT: D 267 ASP cc_start: 0.7546 (m-30) cc_final: 0.7049 (m-30) REVERT: D 372 MET cc_start: 0.8708 (tpp) cc_final: 0.8354 (tpp) REVERT: D 485 MET cc_start: 0.8647 (mmm) cc_final: 0.8211 (mmm) REVERT: D 551 ARG cc_start: 0.8410 (ppt170) cc_final: 0.8165 (ptt180) REVERT: D 603 LYS cc_start: 0.8739 (pttt) cc_final: 0.8448 (tppt) REVERT: D 702 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6857 (pm20) REVERT: D 716 GLN cc_start: 0.7696 (tp-100) cc_final: 0.7363 (tt0) REVERT: D 757 THR cc_start: 0.7418 (p) cc_final: 0.7198 (p) REVERT: D 818 GLU cc_start: 0.9151 (tp30) cc_final: 0.8921 (tt0) REVERT: D 821 MET cc_start: 0.8862 (mmp) cc_final: 0.7951 (pmm) REVERT: D 822 MET cc_start: 0.7932 (tpp) cc_final: 0.7541 (tpp) REVERT: D 826 ILE cc_start: 0.8623 (pt) cc_final: 0.8206 (mt) REVERT: D 1188 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6922 (tm-30) REVERT: E 41 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7469 (mp0) REVERT: E 51 LEU cc_start: 0.6720 (mp) cc_final: 0.5924 (tt) outliers start: 97 outliers final: 56 residues processed: 381 average time/residue: 0.3254 time to fit residues: 205.0340 Evaluate side-chains 329 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 270 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 763 PHE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 259 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 231 optimal weight: 0.0050 chunk 128 optimal weight: 0.9980 chunk 265 optimal weight: 0.0870 chunk 215 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 279 optimal weight: 40.0000 chunk 78 optimal weight: 2.9990 overall best weight: 1.8176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN C 808 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25777 Z= 0.211 Angle : 0.640 13.265 35441 Z= 0.322 Chirality : 0.043 0.262 4398 Planarity : 0.004 0.063 4505 Dihedral : 13.758 166.113 4341 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.35 % Favored : 91.05 % Rotamer: Outliers : 5.32 % Allowed : 18.51 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3451 helix: 0.77 (0.15), residues: 1218 sheet: -0.53 (0.31), residues: 284 loop : -1.80 (0.13), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 580 HIS 0.006 0.001 HIS D 469 PHE 0.013 0.001 PHE C 812 TYR 0.020 0.001 TYR C1229 ARG 0.005 0.000 ARG D 744 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 281 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8667 (tt0) cc_final: 0.8330 (pm20) REVERT: A 83 LEU cc_start: 0.9211 (mt) cc_final: 0.8984 (mp) REVERT: A 194 GLN cc_start: 0.8331 (tm-30) cc_final: 0.8120 (pp30) REVERT: B 78 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7846 (pp) REVERT: B 129 VAL cc_start: 0.7499 (t) cc_final: 0.7132 (m) REVERT: B 137 ASN cc_start: 0.8472 (m-40) cc_final: 0.8045 (p0) REVERT: B 212 ASP cc_start: 0.6815 (t0) cc_final: 0.6580 (t0) REVERT: C 289 VAL cc_start: 0.7891 (t) cc_final: 0.7631 (p) REVERT: C 357 ASN cc_start: 0.8345 (t0) cc_final: 0.7923 (p0) REVERT: C 428 VAL cc_start: 0.8173 (t) cc_final: 0.7844 (p) REVERT: C 514 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7339 (p90) REVERT: C 653 MET cc_start: 0.8310 (tpt) cc_final: 0.7058 (mtt) REVERT: C 850 ILE cc_start: 0.6337 (OUTLIER) cc_final: 0.5955 (pp) REVERT: C 954 LYS cc_start: 0.9480 (mmtp) cc_final: 0.9241 (mtmm) REVERT: D 53 ARG cc_start: 0.7830 (ttt180) cc_final: 0.7274 (tpp-160) REVERT: D 102 MET cc_start: 0.8134 (ttm) cc_final: 0.7538 (ttm) REVERT: D 115 TRP cc_start: 0.7369 (m100) cc_final: 0.6159 (m100) REVERT: D 130 MET cc_start: 0.8168 (tpp) cc_final: 0.7850 (tpp) REVERT: D 267 ASP cc_start: 0.7686 (m-30) cc_final: 0.7173 (m-30) REVERT: D 372 MET cc_start: 0.8784 (tpp) cc_final: 0.8482 (mpp) REVERT: D 746 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5753 (mt) REVERT: D 821 MET cc_start: 0.8912 (mmp) cc_final: 0.7930 (pmm) REVERT: D 822 MET cc_start: 0.7966 (tpp) cc_final: 0.7566 (tpp) REVERT: D 826 ILE cc_start: 0.8674 (pt) cc_final: 0.8266 (mt) REVERT: D 1188 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6927 (tm-30) REVERT: E 41 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7486 (mp0) REVERT: E 52 ARG cc_start: 0.7055 (mtt180) cc_final: 0.6414 (mmp-170) outliers start: 110 outliers final: 67 residues processed: 368 average time/residue: 0.3079 time to fit residues: 191.8312 Evaluate side-chains 325 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 254 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 250 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 6.9990 chunk 280 optimal weight: 0.0570 chunk 61 optimal weight: 0.0030 chunk 182 optimal weight: 9.9990 chunk 76 optimal weight: 0.0000 chunk 311 optimal weight: 7.9990 chunk 258 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.8116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN ** D 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 GLN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 25777 Z= 0.153 Angle : 0.612 12.206 35441 Z= 0.303 Chirality : 0.042 0.313 4398 Planarity : 0.004 0.068 4505 Dihedral : 13.567 168.343 4341 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.61 % Allowed : 7.30 % Favored : 92.09 % Rotamer: Outliers : 4.30 % Allowed : 19.48 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.82 (0.14), residues: 3451 helix: 1.01 (0.15), residues: 1241 sheet: -0.27 (0.32), residues: 268 loop : -1.71 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 580 HIS 0.004 0.001 HIS D 469 PHE 0.014 0.001 PHE D 620 TYR 0.014 0.001 TYR D 679 ARG 0.005 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 288 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8626 (tt0) cc_final: 0.8294 (pm20) REVERT: A 194 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7801 (pm20) REVERT: B 78 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7778 (pp) REVERT: B 129 VAL cc_start: 0.7449 (t) cc_final: 0.7108 (m) REVERT: B 137 ASN cc_start: 0.8371 (m-40) cc_final: 0.8069 (p0) REVERT: B 212 ASP cc_start: 0.7025 (t0) cc_final: 0.6665 (t0) REVERT: C 289 VAL cc_start: 0.7880 (t) cc_final: 0.7619 (p) REVERT: C 357 ASN cc_start: 0.8275 (t0) cc_final: 0.7881 (p0) REVERT: C 705 GLU cc_start: 0.8195 (pm20) cc_final: 0.7380 (mt-10) REVERT: C 817 LEU cc_start: 0.8697 (tp) cc_final: 0.8331 (tp) REVERT: C 850 ILE cc_start: 0.6529 (OUTLIER) cc_final: 0.6200 (pp) REVERT: C 954 LYS cc_start: 0.9476 (mmtp) cc_final: 0.9248 (mtmm) REVERT: C 1033 ARG cc_start: 0.9035 (ttt-90) cc_final: 0.8767 (tmt170) REVERT: D 53 ARG cc_start: 0.7688 (ttt180) cc_final: 0.7189 (tpp-160) REVERT: D 102 MET cc_start: 0.7948 (ttm) cc_final: 0.7331 (ttm) REVERT: D 130 MET cc_start: 0.8128 (tpp) cc_final: 0.7796 (tpp) REVERT: D 267 ASP cc_start: 0.7544 (m-30) cc_final: 0.7037 (m-30) REVERT: D 372 MET cc_start: 0.8619 (tpp) cc_final: 0.8307 (mpp) REVERT: D 625 MET cc_start: 0.8479 (tmm) cc_final: 0.7890 (tmm) REVERT: D 667 GLN cc_start: 0.7438 (mt0) cc_final: 0.7132 (mm110) REVERT: D 821 MET cc_start: 0.8919 (mmp) cc_final: 0.7892 (pmm) REVERT: D 822 MET cc_start: 0.7925 (tpp) cc_final: 0.7505 (tpp) REVERT: D 826 ILE cc_start: 0.8668 (pt) cc_final: 0.8311 (mt) REVERT: D 827 GLU cc_start: 0.8797 (tp30) cc_final: 0.8511 (pt0) REVERT: D 1188 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6999 (tm-30) REVERT: E 41 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7466 (mp0) REVERT: E 52 ARG cc_start: 0.7035 (mtt180) cc_final: 0.6500 (mmp-170) outliers start: 89 outliers final: 57 residues processed: 360 average time/residue: 0.3112 time to fit residues: 188.7569 Evaluate side-chains 326 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 267 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 686 GLN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 250 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 262 optimal weight: 0.6980 chunk 173 optimal weight: 10.0000 chunk 310 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 chunk 143 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25777 Z= 0.156 Angle : 0.617 11.512 35441 Z= 0.305 Chirality : 0.043 0.442 4398 Planarity : 0.004 0.060 4505 Dihedral : 13.504 168.574 4341 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.85 % Favored : 91.51 % Rotamer: Outliers : 4.16 % Allowed : 20.01 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.72 (0.14), residues: 3451 helix: 1.15 (0.15), residues: 1243 sheet: -0.50 (0.30), residues: 294 loop : -1.67 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 580 HIS 0.004 0.001 HIS A 132 PHE 0.011 0.001 PHE D 620 TYR 0.024 0.001 TYR D 626 ARG 0.004 0.000 ARG D 744 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 281 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8664 (tt0) cc_final: 0.8350 (pm20) REVERT: B 48 LEU cc_start: 0.9014 (tp) cc_final: 0.8788 (mt) REVERT: B 78 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7645 (pp) REVERT: B 104 LYS cc_start: 0.8430 (tptp) cc_final: 0.8160 (tptt) REVERT: B 129 VAL cc_start: 0.7456 (t) cc_final: 0.7114 (m) REVERT: B 137 ASN cc_start: 0.8237 (m-40) cc_final: 0.7929 (p0) REVERT: B 212 ASP cc_start: 0.6903 (t0) cc_final: 0.6535 (t0) REVERT: C 289 VAL cc_start: 0.7931 (t) cc_final: 0.7663 (p) REVERT: C 357 ASN cc_start: 0.8134 (t0) cc_final: 0.7708 (p0) REVERT: C 514 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7400 (p90) REVERT: C 705 GLU cc_start: 0.8163 (pm20) cc_final: 0.7439 (mt-10) REVERT: C 817 LEU cc_start: 0.8623 (tp) cc_final: 0.8339 (tp) REVERT: C 850 ILE cc_start: 0.6552 (OUTLIER) cc_final: 0.6175 (pp) REVERT: C 950 GLU cc_start: 0.8888 (pp20) cc_final: 0.8658 (pp20) REVERT: C 954 LYS cc_start: 0.9477 (mmtp) cc_final: 0.9257 (mtmm) REVERT: C 971 LEU cc_start: 0.8897 (tp) cc_final: 0.8472 (tt) REVERT: C 1033 ARG cc_start: 0.9007 (ttt-90) cc_final: 0.8743 (tmt170) REVERT: D 53 ARG cc_start: 0.7681 (ttt180) cc_final: 0.7182 (tpp-160) REVERT: D 102 MET cc_start: 0.7985 (ttm) cc_final: 0.7301 (ttm) REVERT: D 128 LEU cc_start: 0.7277 (mt) cc_final: 0.7065 (mp) REVERT: D 267 ASP cc_start: 0.7594 (m-30) cc_final: 0.7059 (m-30) REVERT: D 372 MET cc_start: 0.8631 (tpp) cc_final: 0.8389 (mpp) REVERT: D 667 GLN cc_start: 0.7371 (mt0) cc_final: 0.7063 (mm110) REVERT: D 702 GLN cc_start: 0.6624 (OUTLIER) cc_final: 0.6353 (pm20) REVERT: D 822 MET cc_start: 0.7943 (tpp) cc_final: 0.7600 (tpp) REVERT: D 826 ILE cc_start: 0.8668 (pt) cc_final: 0.8307 (mt) REVERT: D 827 GLU cc_start: 0.8840 (tp30) cc_final: 0.8571 (pt0) REVERT: D 1188 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7021 (tm-30) REVERT: E 41 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7424 (mp0) REVERT: E 52 ARG cc_start: 0.7017 (mtt180) cc_final: 0.6448 (mmp-170) outliers start: 86 outliers final: 69 residues processed: 347 average time/residue: 0.3065 time to fit residues: 180.8261 Evaluate side-chains 340 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 267 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 763 PHE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 250 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 185 optimal weight: 30.0000 chunk 93 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 chunk 197 optimal weight: 20.0000 chunk 211 optimal weight: 0.0870 chunk 153 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 243 optimal weight: 7.9990 chunk 282 optimal weight: 0.0060 overall best weight: 1.6356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 GLN C 808 ASN ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25777 Z= 0.189 Angle : 0.637 11.628 35441 Z= 0.317 Chirality : 0.043 0.401 4398 Planarity : 0.004 0.065 4505 Dihedral : 13.501 170.680 4341 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.37 % Favored : 91.02 % Rotamer: Outliers : 4.69 % Allowed : 20.20 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.69 (0.14), residues: 3451 helix: 1.19 (0.15), residues: 1246 sheet: -0.44 (0.31), residues: 286 loop : -1.67 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 580 HIS 0.004 0.001 HIS D 469 PHE 0.012 0.001 PHE D 620 TYR 0.023 0.001 TYR D 626 ARG 0.009 0.000 ARG D 417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 271 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8654 (tt0) cc_final: 0.8330 (pm20) REVERT: A 83 LEU cc_start: 0.9262 (mt) cc_final: 0.9016 (mp) REVERT: B 48 LEU cc_start: 0.9002 (tp) cc_final: 0.8733 (mt) REVERT: B 129 VAL cc_start: 0.7371 (t) cc_final: 0.7025 (m) REVERT: B 137 ASN cc_start: 0.8164 (m-40) cc_final: 0.7869 (p0) REVERT: B 212 ASP cc_start: 0.7003 (t0) cc_final: 0.6685 (t0) REVERT: C 289 VAL cc_start: 0.7843 (t) cc_final: 0.7543 (p) REVERT: C 357 ASN cc_start: 0.8137 (t0) cc_final: 0.7657 (p0) REVERT: C 428 VAL cc_start: 0.8187 (t) cc_final: 0.7843 (p) REVERT: C 514 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7414 (p90) REVERT: C 515 MET cc_start: 0.8863 (ptm) cc_final: 0.8552 (ptt) REVERT: C 717 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8539 (p) REVERT: C 817 LEU cc_start: 0.8670 (tp) cc_final: 0.8383 (tp) REVERT: C 850 ILE cc_start: 0.6416 (OUTLIER) cc_final: 0.6008 (pp) REVERT: C 971 LEU cc_start: 0.8905 (tp) cc_final: 0.8483 (tt) REVERT: C 1033 ARG cc_start: 0.9031 (ttt-90) cc_final: 0.8784 (tmt170) REVERT: D 53 ARG cc_start: 0.7631 (ttt180) cc_final: 0.7070 (tpp-160) REVERT: D 102 MET cc_start: 0.8059 (ttm) cc_final: 0.7380 (ttm) REVERT: D 128 LEU cc_start: 0.7511 (mt) cc_final: 0.7163 (mp) REVERT: D 267 ASP cc_start: 0.7642 (m-30) cc_final: 0.7103 (m-30) REVERT: D 372 MET cc_start: 0.8640 (tpp) cc_final: 0.8361 (mpp) REVERT: D 465 GLN cc_start: 0.8718 (tt0) cc_final: 0.8394 (mt0) REVERT: D 697 MET cc_start: 0.6572 (ttp) cc_final: 0.6359 (ttm) REVERT: D 702 GLN cc_start: 0.6815 (OUTLIER) cc_final: 0.6543 (pm20) REVERT: D 724 MET cc_start: 0.8905 (mmm) cc_final: 0.8353 (mmm) REVERT: D 821 MET cc_start: 0.8839 (mmp) cc_final: 0.7933 (pmm) REVERT: D 822 MET cc_start: 0.7887 (tpp) cc_final: 0.7459 (tpp) REVERT: D 826 ILE cc_start: 0.8707 (pt) cc_final: 0.8341 (mt) REVERT: D 827 GLU cc_start: 0.8813 (tp30) cc_final: 0.8540 (pt0) REVERT: D 1188 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7054 (tm-30) REVERT: E 41 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7370 (mp0) REVERT: E 52 ARG cc_start: 0.7101 (mtt180) cc_final: 0.6540 (mmp-170) outliers start: 97 outliers final: 76 residues processed: 346 average time/residue: 0.3042 time to fit residues: 179.0854 Evaluate side-chains 336 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 256 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 406 ASN Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 763 PHE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 250 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 297 optimal weight: 6.9990 chunk 271 optimal weight: 9.9990 chunk 289 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 273 optimal weight: 40.0000 chunk 288 optimal weight: 8.9990 chunk 189 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 75 GLN C 36 GLN C 808 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 667 GLN D 702 GLN D1252 HIS ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.6994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25777 Z= 0.359 Angle : 0.774 14.483 35441 Z= 0.397 Chirality : 0.047 0.418 4398 Planarity : 0.005 0.088 4505 Dihedral : 13.873 175.023 4341 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.67 % Allowed : 9.68 % Favored : 89.66 % Rotamer: Outliers : 5.03 % Allowed : 20.06 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.14), residues: 3451 helix: 0.60 (0.15), residues: 1248 sheet: -1.13 (0.30), residues: 297 loop : -1.98 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 115 HIS 0.010 0.002 HIS D 469 PHE 0.020 0.002 PHE C 812 TYR 0.027 0.002 TYR C1229 ARG 0.010 0.001 ARG D 417 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 253 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8408 (mp) REVERT: A 60 GLU cc_start: 0.8801 (tt0) cc_final: 0.8421 (pm20) REVERT: B 48 LEU cc_start: 0.9076 (tp) cc_final: 0.8781 (mt) REVERT: B 129 VAL cc_start: 0.7483 (t) cc_final: 0.7125 (m) REVERT: B 137 ASN cc_start: 0.7999 (m-40) cc_final: 0.7776 (p0) REVERT: C 289 VAL cc_start: 0.7869 (t) cc_final: 0.7595 (p) REVERT: C 428 VAL cc_start: 0.8273 (t) cc_final: 0.7946 (p) REVERT: C 514 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7480 (p90) REVERT: C 705 GLU cc_start: 0.8349 (pm20) cc_final: 0.8114 (mt-10) REVERT: C 717 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8635 (p) REVERT: C 850 ILE cc_start: 0.6467 (OUTLIER) cc_final: 0.6028 (pp) REVERT: C 954 LYS cc_start: 0.9484 (mmtp) cc_final: 0.9231 (mtmm) REVERT: C 1269 ARG cc_start: 0.8281 (ptt-90) cc_final: 0.7280 (ptp-110) REVERT: D 53 ARG cc_start: 0.7575 (ttt180) cc_final: 0.6917 (tpp-160) REVERT: D 102 MET cc_start: 0.7951 (ttm) cc_final: 0.7304 (ttm) REVERT: D 267 ASP cc_start: 0.7571 (m-30) cc_final: 0.6980 (m-30) REVERT: D 372 MET cc_start: 0.9018 (tpp) cc_final: 0.8634 (mpp) REVERT: D 724 MET cc_start: 0.9018 (mmm) cc_final: 0.8416 (mmm) REVERT: D 821 MET cc_start: 0.8902 (mmp) cc_final: 0.7928 (pmm) REVERT: D 826 ILE cc_start: 0.8761 (pt) cc_final: 0.8375 (mt) REVERT: D 827 GLU cc_start: 0.8719 (tp30) cc_final: 0.8399 (pt0) REVERT: D 1188 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6895 (tm-30) REVERT: D 1316 THR cc_start: 0.9000 (p) cc_final: 0.8690 (t) REVERT: E 4 VAL cc_start: 0.8429 (t) cc_final: 0.8197 (m) REVERT: E 15 ASN cc_start: 0.7773 (t0) cc_final: 0.7057 (t0) REVERT: E 41 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7380 (mp0) REVERT: E 52 ARG cc_start: 0.7423 (mtt180) cc_final: 0.6943 (mmp-170) outliers start: 104 outliers final: 81 residues processed: 337 average time/residue: 0.3212 time to fit residues: 182.7175 Evaluate side-chains 324 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 239 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 183 TRP Chi-restraints excluded: chain C residue 406 ASN Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 810 THR Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1319 PHE Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 6.9990 chunk 186 optimal weight: 20.0000 chunk 145 optimal weight: 8.9990 chunk 212 optimal weight: 0.7980 chunk 320 optimal weight: 20.0000 chunk 295 optimal weight: 8.9990 chunk 255 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 197 optimal weight: 20.0000 chunk 156 optimal weight: 0.7980 chunk 202 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 ASN C 952 GLN D 667 GLN ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25777 Z= 0.213 Angle : 0.675 12.456 35441 Z= 0.339 Chirality : 0.044 0.377 4398 Planarity : 0.004 0.073 4505 Dihedral : 13.663 174.734 4341 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.69 % Favored : 90.67 % Rotamer: Outliers : 3.77 % Allowed : 21.46 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 3451 helix: 0.96 (0.15), residues: 1233 sheet: -0.67 (0.31), residues: 265 loop : -1.91 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 115 HIS 0.007 0.001 HIS D 469 PHE 0.012 0.001 PHE D 620 TYR 0.029 0.001 TYR D 626 ARG 0.009 0.000 ARG D 417 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6902 Ramachandran restraints generated. 3451 Oldfield, 0 Emsley, 3451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 248 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8736 (tt0) cc_final: 0.8354 (pm20) REVERT: B 48 LEU cc_start: 0.9033 (tp) cc_final: 0.8722 (mt) REVERT: B 104 LYS cc_start: 0.7943 (tptp) cc_final: 0.7730 (tptm) REVERT: B 129 VAL cc_start: 0.7542 (t) cc_final: 0.7217 (m) REVERT: C 289 VAL cc_start: 0.7926 (t) cc_final: 0.7614 (p) REVERT: C 428 VAL cc_start: 0.8222 (t) cc_final: 0.7863 (p) REVERT: C 514 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7505 (p90) REVERT: C 705 GLU cc_start: 0.8376 (pm20) cc_final: 0.8133 (mt-10) REVERT: C 717 VAL cc_start: 0.9221 (OUTLIER) cc_final: 0.8637 (p) REVERT: C 824 GLN cc_start: 0.8469 (mp10) cc_final: 0.7550 (tm-30) REVERT: C 850 ILE cc_start: 0.6379 (OUTLIER) cc_final: 0.5966 (pp) REVERT: C 954 LYS cc_start: 0.9489 (mmtp) cc_final: 0.9267 (mtmm) REVERT: D 53 ARG cc_start: 0.7609 (ttt180) cc_final: 0.6950 (tpp-160) REVERT: D 102 MET cc_start: 0.7843 (ttm) cc_final: 0.7414 (ttm) REVERT: D 267 ASP cc_start: 0.7673 (m-30) cc_final: 0.7219 (m-30) REVERT: D 372 MET cc_start: 0.8913 (tpp) cc_final: 0.8550 (mpp) REVERT: D 667 GLN cc_start: 0.7185 (mt0) cc_final: 0.6873 (mm110) REVERT: D 724 MET cc_start: 0.8961 (mmm) cc_final: 0.8386 (mmm) REVERT: D 821 MET cc_start: 0.8957 (mmp) cc_final: 0.8199 (pmm) REVERT: D 826 ILE cc_start: 0.8731 (pt) cc_final: 0.8359 (mt) REVERT: D 827 GLU cc_start: 0.8721 (tp30) cc_final: 0.8412 (pt0) REVERT: D 1188 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6934 (tm-30) REVERT: D 1316 THR cc_start: 0.9023 (p) cc_final: 0.8758 (t) REVERT: E 15 ASN cc_start: 0.7820 (t0) cc_final: 0.7096 (t0) REVERT: E 41 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7378 (mp0) REVERT: E 52 ARG cc_start: 0.7391 (mtt180) cc_final: 0.6862 (mmp-170) outliers start: 78 outliers final: 66 residues processed: 310 average time/residue: 0.3175 time to fit residues: 168.5350 Evaluate side-chains 308 residues out of total 2978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 239 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 406 ASN Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 715 THR Chi-restraints excluded: chain C residue 717 VAL Chi-restraints excluded: chain C residue 731 ARG Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1335 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 599 LYS Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1244 GLN Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 50.0000 chunk 78 optimal weight: 6.9990 chunk 235 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 0.0770 chunk 255 optimal weight: 10.0000 chunk 107 optimal weight: 0.0980 chunk 262 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 47 optimal weight: 0.0060 chunk 224 optimal weight: 4.9990 overall best weight: 1.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 GLN C 808 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.131140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.106011 restraints weight = 69304.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.105239 restraints weight = 47642.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.105805 restraints weight = 40610.429| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.7023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25777 Z= 0.183 Angle : 0.652 11.954 35441 Z= 0.325 Chirality : 0.043 0.338 4398 Planarity : 0.004 0.071 4505 Dihedral : 13.541 174.738 4341 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.19 % Favored : 90.21 % Rotamer: Outliers : 3.29 % Allowed : 21.80 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.88 (0.14), residues: 3451 helix: 1.17 (0.15), residues: 1233 sheet: -0.58 (0.31), residues: 263 loop : -1.86 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 580 HIS 0.005 0.001 HIS D 469 PHE 0.011 0.001 PHE D 620 TYR 0.027 0.001 TYR D 626 ARG 0.009 0.000 ARG D 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5097.28 seconds wall clock time: 93 minutes 1.10 seconds (5581.10 seconds total)