Starting phenix.real_space_refine on Thu Mar 21 20:18:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebs_27996/03_2024/8ebs_27996_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebs_27996/03_2024/8ebs_27996.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebs_27996/03_2024/8ebs_27996_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebs_27996/03_2024/8ebs_27996_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebs_27996/03_2024/8ebs_27996_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebs_27996/03_2024/8ebs_27996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebs_27996/03_2024/8ebs_27996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebs_27996/03_2024/8ebs_27996_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebs_27996/03_2024/8ebs_27996_updated.pdb" } resolution = 4.0 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= 0.002 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 Zn 5 6.06 5 P 105 5.49 5 S 167 5.16 5 C 19436 2.51 5 N 5384 2.21 5 O 5932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 105": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 570": "OE1" <-> "OE2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A ARG 639": "NH1" <-> "NH2" Residue "A ARG 642": "NH1" <-> "NH2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A PHE 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 349": "OE1" <-> "OE2" Residue "D PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 191": "NH1" <-> "NH2" Residue "H ARG 192": "NH1" <-> "NH2" Residue "H ARG 196": "NH1" <-> "NH2" Residue "H ARG 220": "NH1" <-> "NH2" Residue "H PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 713": "NH1" <-> "NH2" Residue "H ARG 718": "NH1" <-> "NH2" Residue "H ARG 725": "NH1" <-> "NH2" Residue "H PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 826": "OE1" <-> "OE2" Residue "H ARG 834": "NH1" <-> "NH2" Residue "H ARG 908": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31035 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4931 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 24, 'TRANS': 586} Chain breaks: 1 Chain: "B" Number of atoms: 6120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6120 Classifications: {'peptide': 760} Link IDs: {'PTRANS': 32, 'TRANS': 727} Chain: "C" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2895 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 342} Chain breaks: 4 Chain: "D" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3557 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain: "E" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2792 Classifications: {'peptide': 355} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 336} Chain breaks: 1 Chain: "F" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2057 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 8, 'TRANS': 252} Chain breaks: 1 Chain: "G" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "H" Number of atoms: 4264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4264 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 24, 'TRANS': 494} Chain breaks: 3 Chain: "I" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 504 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 6, 'TRANS': 54} Chain: "J" Number of atoms: 1201 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1192 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3} Link IDs: {'PTRANS': 1, 'TRANS': 147} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 Conformer: "B" Number of residues, atoms: 149, 1192 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3} Link IDs: {'PTRANS': 1, 'TRANS': 147} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 bond proxies already assigned to first conformer: 1192 Chain: "L" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1091 Unusual residues: {'VM6': 1} Classifications: {'DNA': 51, 'undetermined': 1} Link IDs: {'rna3p': 49, None: 2} Not linked: pdbres=" DT L 29 " pdbres="VM6 L 30 " Not linked: pdbres="VM6 L 30 " pdbres=" DT L 31 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "M" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1078 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5874 SG CYS B 116 51.367 30.526 73.414 1.00227.83 S ATOM 6183 SG CYS B 155 51.017 25.318 69.344 1.00215.53 S ATOM 6014 SG CYS B 134 47.771 30.137 68.007 1.00233.83 S ATOM 6472 SG CYS B 190 46.020 27.118 73.123 1.00212.40 S ATOM 19973 SG CYS E 345 27.407 53.693 151.335 1.00190.60 S ATOM 19995 SG CYS E 348 28.578 56.975 152.607 1.00180.36 S ATOM 20152 SG CYS E 368 28.046 56.539 148.810 1.00194.11 S ATOM 20173 SG CYS E 371 30.916 54.787 150.514 1.00188.68 S ATOM 20093 SG CYS E 360 28.763 42.651 147.881 1.00195.38 S ATOM 20111 SG CYS E 363 28.156 42.346 151.541 1.00197.98 S ATOM 20260 SG CYS E 382 30.730 44.837 150.249 1.00182.89 S ATOM 20277 SG CYS E 385 31.482 41.111 149.958 1.00193.57 S ATOM 19537 SG CYS E 291 71.596 37.668 150.062 1.00199.70 S ATOM 19559 SG CYS E 294 75.129 37.868 148.611 1.00199.73 S ATOM 19648 SG CYS E 305 72.375 39.863 147.016 1.00188.68 S ATOM 19671 SG CYS E 308 72.238 36.151 146.696 1.00185.52 S ATOM 22173 SG CYS F 268 52.954 28.763 142.366 1.00173.17 S ATOM 22192 SG CYS F 271 49.579 29.163 144.206 1.00180.54 S ATOM 22277 SG CYS F 282 51.566 26.121 144.780 1.00185.54 S ATOM 22297 SG CYS F 285 49.971 26.563 141.432 1.00183.63 S ATOM 22065 SG CYS F 255 57.438 26.213 153.751 1.00192.21 S ATOM 22082 SG CYS F 257 55.753 22.891 153.757 1.00198.54 S ATOM 22231 SG CYS F 276 59.607 23.128 153.738 1.00203.04 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS J 127 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS J 127 " occ=0.50 Time building chain proxies: 16.32, per 1000 atoms: 0.53 Number of scatterers: 31035 At special positions: 0 Unit cell: (139.944, 180.761, 203.252, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 5 29.99 Fe 4 26.01 Ca 2 19.99 S 167 16.00 P 105 15.00 O 5932 8.00 N 5384 7.00 C 19436 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.69 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 345 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 371 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 348 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 368 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 360 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 382 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 363 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 385 " pdb=" ZN E 403 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 305 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 308 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 291 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 294 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 285 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 271 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " pdb=" ZN F 402 " pdb="ZN ZN F 402 " - pdb=" NE2 HIS F 258 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 255 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 257 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 276 " Number of angles added : 27 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6802 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 164 helices and 24 sheets defined 49.0% alpha, 8.9% beta 48 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 12.58 Creating SS restraints... Processing helix chain 'A' and resid 93 through 103 Processing helix chain 'A' and resid 120 through 129 Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 150 through 162 removed outlier: 4.101A pdb=" N SER A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 4.137A pdb=" N GLN A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.616A pdb=" N ILE A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'A' and resid 368 through 381 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 421 through 432 Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 449 through 457 removed outlier: 3.806A pdb=" N LEU A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 516 through 524 Processing helix chain 'A' and resid 528 through 536 removed outlier: 3.571A pdb=" N ILE A 531 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 532 " --> pdb=" O LYS A 529 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 534 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 586 through 598 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 633 through 643 removed outlier: 3.806A pdb=" N ALA A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 676 Processing helix chain 'A' and resid 678 through 683 removed outlier: 3.517A pdb=" N GLN A 683 " --> pdb=" O PHE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 719 removed outlier: 3.638A pdb=" N ALA A 719 " --> pdb=" O LYS A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 34 Processing helix chain 'B' and resid 48 through 62 Processing helix chain 'B' and resid 77 through 98 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 127 through 138 Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.713A pdb=" N ALA B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 163 removed outlier: 3.664A pdb=" N PHE B 161 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 191 through 200 removed outlier: 4.630A pdb=" N LEU B 200 " --> pdb=" O ARG B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 213 No H-bonds generated for 'chain 'B' and resid 210 through 213' Processing helix chain 'B' and resid 215 through 224 removed outlier: 4.439A pdb=" N ASP B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 223 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLU B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 253 through 276 Processing helix chain 'B' and resid 278 through 290 removed outlier: 3.647A pdb=" N GLU B 290 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 312 through 316 removed outlier: 3.787A pdb=" N GLN B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 312 through 316' Processing helix chain 'B' and resid 321 through 324 No H-bonds generated for 'chain 'B' and resid 321 through 324' Processing helix chain 'B' and resid 326 through 345 Processing helix chain 'B' and resid 354 through 365 Processing helix chain 'B' and resid 369 through 386 removed outlier: 3.747A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS B 375 " --> pdb=" O PRO B 371 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 409 Processing helix chain 'B' and resid 440 through 450 removed outlier: 3.663A pdb=" N LYS B 445 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Proline residue: B 446 - end of helix removed outlier: 3.556A pdb=" N ARG B 450 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 508 through 511 No H-bonds generated for 'chain 'B' and resid 508 through 511' Processing helix chain 'B' and resid 514 through 530 Processing helix chain 'B' and resid 542 through 555 Processing helix chain 'B' and resid 557 through 564 Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 604 through 607 No H-bonds generated for 'chain 'B' and resid 604 through 607' Processing helix chain 'B' and resid 631 through 644 Processing helix chain 'B' and resid 648 through 667 removed outlier: 4.079A pdb=" N ARG B 666 " --> pdb=" O GLN B 662 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ALA B 667 " --> pdb=" O CYS B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 685 No H-bonds generated for 'chain 'B' and resid 683 through 685' Processing helix chain 'B' and resid 687 through 692 removed outlier: 3.592A pdb=" N LYS B 692 " --> pdb=" O ASP B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 698 No H-bonds generated for 'chain 'B' and resid 695 through 698' Processing helix chain 'B' and resid 703 through 705 No H-bonds generated for 'chain 'B' and resid 703 through 705' Processing helix chain 'B' and resid 710 through 725 Processing helix chain 'B' and resid 730 through 733 No H-bonds generated for 'chain 'B' and resid 730 through 733' Processing helix chain 'B' and resid 741 through 744 No H-bonds generated for 'chain 'B' and resid 741 through 744' Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'C' and resid 112 through 120 Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 139 through 146 removed outlier: 4.285A pdb=" N ASN C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG C 146 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 199 Processing helix chain 'C' and resid 201 through 210 Processing helix chain 'C' and resid 217 through 226 Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 297 through 319 removed outlier: 3.711A pdb=" N LEU C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 358 Processing helix chain 'C' and resid 379 through 383 Processing helix chain 'C' and resid 399 through 412 Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 449 through 452 No H-bonds generated for 'chain 'C' and resid 449 through 452' Processing helix chain 'C' and resid 455 through 478 Processing helix chain 'C' and resid 484 through 515 removed outlier: 3.998A pdb=" N GLU C 488 " --> pdb=" O PRO C 484 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Proline residue: C 507 - end of helix removed outlier: 3.622A pdb=" N GLN C 515 " --> pdb=" O LYS C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 547 removed outlier: 3.820A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 25 Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.546A pdb=" N GLY D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 46 Processing helix chain 'D' and resid 50 through 61 removed outlier: 4.826A pdb=" N PHE D 61 " --> pdb=" O MET D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 74 removed outlier: 3.785A pdb=" N TRP D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 93 removed outlier: 4.191A pdb=" N LYS D 81 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 123 Processing helix chain 'D' and resid 133 through 135 No H-bonds generated for 'chain 'D' and resid 133 through 135' Processing helix chain 'D' and resid 145 through 164 Processing helix chain 'D' and resid 173 through 182 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.509A pdb=" N LEU D 205 " --> pdb=" O PHE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 223 through 226 removed outlier: 3.513A pdb=" N ARG D 226 " --> pdb=" O ALA D 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 223 through 226' Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 348 through 356 Processing helix chain 'D' and resid 361 through 370 Processing helix chain 'D' and resid 374 through 378 removed outlier: 3.561A pdb=" N LYS D 378 " --> pdb=" O PRO D 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 374 through 378' Processing helix chain 'D' and resid 385 through 399 removed outlier: 3.502A pdb=" N ASP D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 428 Processing helix chain 'D' and resid 445 through 461 removed outlier: 4.065A pdb=" N SER D 449 " --> pdb=" O PRO D 445 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP D 450 " --> pdb=" O ALA D 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 13 No H-bonds generated for 'chain 'E' and resid 11 through 13' Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 80 through 98 Processing helix chain 'E' and resid 124 through 136 removed outlier: 4.398A pdb=" N ASP E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 156 Processing helix chain 'E' and resid 183 through 191 Processing helix chain 'E' and resid 206 through 214 Processing helix chain 'E' and resid 225 through 236 Processing helix chain 'E' and resid 273 through 276 No H-bonds generated for 'chain 'E' and resid 273 through 276' Processing helix chain 'E' and resid 315 through 325 removed outlier: 4.046A pdb=" N SER E 321 " --> pdb=" O HIS E 317 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N HIS E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N HIS E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU E 325 " --> pdb=" O SER E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 377 removed outlier: 3.519A pdb=" N HIS E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 386 No H-bonds generated for 'chain 'E' and resid 383 through 386' Processing helix chain 'F' and resid 19 through 28 Processing helix chain 'F' and resid 34 through 51 Processing helix chain 'F' and resid 102 through 120 Processing helix chain 'F' and resid 133 through 150 Processing helix chain 'F' and resid 174 through 187 removed outlier: 3.580A pdb=" N ALA F 183 " --> pdb=" O ASN F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'F' and resid 220 through 229 removed outlier: 4.715A pdb=" N LEU F 224 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP F 229 " --> pdb=" O TYR F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 240 removed outlier: 3.674A pdb=" N GLN F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 26 Processing helix chain 'G' and resid 47 through 63 removed outlier: 4.654A pdb=" N ASN G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 224 Processing helix chain 'H' and resid 227 through 236 Processing helix chain 'H' and resid 239 through 242 No H-bonds generated for 'chain 'H' and resid 239 through 242' Processing helix chain 'H' and resid 246 through 248 No H-bonds generated for 'chain 'H' and resid 246 through 248' Processing helix chain 'H' and resid 251 through 264 Processing helix chain 'H' and resid 279 through 289 Processing helix chain 'H' and resid 295 through 309 removed outlier: 3.596A pdb=" N LEU H 309 " --> pdb=" O ILE H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 555 through 561 removed outlier: 3.664A pdb=" N LYS H 560 " --> pdb=" O LEU H 556 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 585 No H-bonds generated for 'chain 'H' and resid 582 through 585' Processing helix chain 'H' and resid 593 through 596 No H-bonds generated for 'chain 'H' and resid 593 through 596' Processing helix chain 'H' and resid 600 through 608 Processing helix chain 'H' and resid 615 through 629 Processing helix chain 'H' and resid 678 through 680 No H-bonds generated for 'chain 'H' and resid 678 through 680' Processing helix chain 'H' and resid 687 through 692 Processing helix chain 'H' and resid 712 through 720 Processing helix chain 'H' and resid 722 through 724 No H-bonds generated for 'chain 'H' and resid 722 through 724' Processing helix chain 'H' and resid 764 through 766 No H-bonds generated for 'chain 'H' and resid 764 through 766' Processing helix chain 'H' and resid 779 through 785 Processing helix chain 'H' and resid 815 through 864 removed outlier: 5.004A pdb=" N ASP H 819 " --> pdb=" O GLU H 816 " (cutoff:3.500A) Processing helix chain 'H' and resid 890 through 901 Processing helix chain 'H' and resid 904 through 912 removed outlier: 3.828A pdb=" N ARG H 908 " --> pdb=" O TRP H 904 " (cutoff:3.500A) Processing helix chain 'I' and resid 275 through 280 removed outlier: 3.909A pdb=" N PHE I 278 " --> pdb=" O PRO I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 294 Processing helix chain 'I' and resid 296 through 309 Proline residue: I 300 - end of helix removed outlier: 3.576A pdb=" N GLU I 309 " --> pdb=" O ILE I 306 " (cutoff:3.500A) Processing helix chain 'I' and resid 311 through 318 removed outlier: 4.034A pdb=" N SER I 318 " --> pdb=" O LEU I 314 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 328 Processing helix chain 'J' and resid 29 through 39 Processing helix chain 'J' and resid 51 through 59 removed outlier: 4.138A pdb=" N LYS J 54 " --> pdb=" O LYS J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 76 Processing helix chain 'J' and resid 86 through 113 Processing helix chain 'J' and resid 123 through 133 Processing helix chain 'J' and resid 139 through 148 Processing helix chain 'J' and resid 159 through 167 Processing sheet with id= A, first strand: chain 'A' and resid 76 through 78 removed outlier: 5.603A pdb=" N LYS A 117 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 167 through 171 Processing sheet with id= C, first strand: chain 'A' and resid 389 through 392 removed outlier: 6.642A pdb=" N VAL A 405 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE A 392 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE A 407 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS A 361 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N SER A 408 " --> pdb=" O CYS A 361 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL A 363 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 437 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N LEU A 364 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 439 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N CYS A 462 " --> pdb=" O MET A 438 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU A 440 " --> pdb=" O CYS A 462 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 464 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY A 336 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N THR A 467 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 338 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL A 339 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU A 490 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 688 through 690 removed outlier: 4.187A pdb=" N LYS A 688 " --> pdb=" O CYS A 507 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU A 509 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA A 657 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ALA A 508 " --> pdb=" O ALA A 657 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE A 659 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL A 510 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER A 661 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N CYS A 512 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 663 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER A 627 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N SER A 664 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 2 through 5 Processing sheet with id= F, first strand: chain 'B' and resid 757 through 759 removed outlier: 3.782A pdb=" N SER B 458 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 249 through 251 Processing sheet with id= H, first strand: chain 'B' and resid 490 through 494 removed outlier: 8.020A pdb=" N GLY B 675 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N MET B 493 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N MET B 677 " --> pdb=" O MET B 493 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 9.410A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 177 through 179 Processing sheet with id= J, first strand: chain 'D' and resid 96 through 100 Processing sheet with id= K, first strand: chain 'D' and resid 248 through 250 Processing sheet with id= L, first strand: chain 'D' and resid 307 through 310 removed outlier: 3.741A pdb=" N ARG D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLN D 345 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N MET D 334 " --> pdb=" O GLN D 345 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 407 through 409 Processing sheet with id= N, first strand: chain 'E' and resid 113 through 115 removed outlier: 7.023A pdb=" N SER E 164 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N TYR E 62 " --> pdb=" O SER E 164 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLU E 166 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N VAL E 64 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU E 168 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ASP E 66 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE E 170 " --> pdb=" O ASP E 66 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 332 through 335 Processing sheet with id= P, first strand: chain 'F' and resid 67 through 71 removed outlier: 6.445A pdb=" N VAL F 59 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA F 58 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU F 156 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU F 10 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LYS F 158 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL F 12 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG F 160 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL F 14 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU F 162 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ASP F 16 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE F 164 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU F 190 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL F 163 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP F 192 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LYS F 165 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS F 194 " --> pdb=" O LYS F 165 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 253 through 255 removed outlier: 4.162A pdb=" N ALA F 253 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN F 260 " --> pdb=" O CYS F 255 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 8 through 11 Processing sheet with id= S, first strand: chain 'H' and resid 578 through 580 Processing sheet with id= T, first strand: chain 'H' and resid 695 through 697 Processing sheet with id= U, first strand: chain 'H' and resid 705 through 707 removed outlier: 3.832A pdb=" N LYS H 705 " --> pdb=" O LEU H 732 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 771 through 774 Processing sheet with id= W, first strand: chain 'H' and resid 794 through 798 removed outlier: 6.320A pdb=" N VAL H 807 " --> pdb=" O THR H 795 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE H 797 " --> pdb=" O HIS H 805 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS H 805 " --> pdb=" O PHE H 797 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 47 through 49 1237 hydrogen bonds defined for protein. 3352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 11.37 Time building geometry restraints manager: 13.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 13553 1.43 - 1.64: 18075 1.64 - 1.85: 253 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 31893 Sorted by residual: bond pdb=" C5 VM6 L 30 " pdb=" C6 VM6 L 30 " ideal model delta sigma weight residual 1.556 1.353 0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C8 VM6 L 30 " pdb=" C9 VM6 L 30 " ideal model delta sigma weight residual 1.550 1.368 0.182 2.00e-02 2.50e+03 8.31e+01 bond pdb=" C7 VM6 L 30 " pdb=" C8 VM6 L 30 " ideal model delta sigma weight residual 1.563 1.391 0.172 2.00e-02 2.50e+03 7.42e+01 bond pdb=" C4 VM6 L 30 " pdb=" N2 VM6 L 30 " ideal model delta sigma weight residual 1.502 1.352 0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" OP1 VM6 L 30 " pdb=" P VM6 L 30 " ideal model delta sigma weight residual 1.512 1.658 -0.146 2.00e-02 2.50e+03 5.35e+01 ... (remaining 31888 not shown) Histogram of bond angle deviations from ideal: 73.65 - 85.72: 12 85.72 - 97.80: 0 97.80 - 109.87: 4640 109.87 - 121.95: 32519 121.95 - 134.02: 6406 Bond angle restraints: 43577 Sorted by residual: angle pdb=" C5 VM6 L 30 " pdb=" C4 VM6 L 30 " pdb=" N2 VM6 L 30 " ideal model delta sigma weight residual 68.46 121.47 -53.01 3.00e+00 1.11e-01 3.12e+02 angle pdb=" C2 VM6 L 30 " pdb=" C4 VM6 L 30 " pdb=" C5 VM6 L 30 " ideal model delta sigma weight residual 156.44 129.42 27.02 3.00e+00 1.11e-01 8.11e+01 angle pdb=" C6 VM6 L 30 " pdb=" C7 VM6 L 30 " pdb=" C8 VM6 L 30 " ideal model delta sigma weight residual 152.65 129.26 23.39 3.00e+00 1.11e-01 6.08e+01 angle pdb=" C7 VM6 L 30 " pdb=" C8 VM6 L 30 " pdb=" C9 VM6 L 30 " ideal model delta sigma weight residual 109.47 126.90 -17.43 3.00e+00 1.11e-01 3.38e+01 angle pdb=" C5 VM6 L 30 " pdb=" C6 VM6 L 30 " pdb=" C7 VM6 L 30 " ideal model delta sigma weight residual 112.22 129.10 -16.88 3.00e+00 1.11e-01 3.17e+01 ... (remaining 43572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.90: 18192 28.90 - 57.81: 766 57.81 - 86.71: 71 86.71 - 115.61: 5 115.61 - 144.52: 3 Dihedral angle restraints: 19037 sinusoidal: 8534 harmonic: 10503 Sorted by residual: dihedral pdb=" C23 VM6 L 30 " pdb=" C24 VM6 L 30 " pdb=" C25 VM6 L 30 " pdb=" O2 VM6 L 30 " ideal model delta sinusoidal sigma weight residual 163.49 -65.06 -131.45 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" CA THR D 380 " pdb=" C THR D 380 " pdb=" N PRO D 381 " pdb=" CA PRO D 381 " ideal model delta harmonic sigma weight residual 180.00 160.95 19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" C4' DG M 37 " pdb=" C3' DG M 37 " pdb=" O3' DG M 37 " pdb=" P DC M 38 " ideal model delta sinusoidal sigma weight residual 220.00 75.48 144.52 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 19034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3201 0.026 - 0.053: 1010 0.053 - 0.079: 336 0.079 - 0.106: 222 0.106 - 0.132: 82 Chirality restraints: 4851 Sorted by residual: chirality pdb=" CA ILE H 237 " pdb=" N ILE H 237 " pdb=" C ILE H 237 " pdb=" CB ILE H 237 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA PRO A 447 " pdb=" N PRO A 447 " pdb=" C PRO A 447 " pdb=" CB PRO A 447 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ILE A 580 " pdb=" N ILE A 580 " pdb=" C ILE A 580 " pdb=" CB ILE A 580 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 4848 not shown) Planarity restraints: 5228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 VM6 L 30 " 0.006 2.00e-02 2.50e+03 1.67e-02 3.49e+00 pdb=" C20 VM6 L 30 " 0.003 2.00e-02 2.50e+03 pdb=" C8 VM6 L 30 " -0.020 2.00e-02 2.50e+03 pdb=" C9 VM6 L 30 " 0.027 2.00e-02 2.50e+03 pdb=" N1 VM6 L 30 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 582 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO A 583 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 74 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 75 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.021 5.00e-02 4.00e+02 ... (remaining 5225 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 505 2.65 - 3.21: 29173 3.21 - 3.77: 51189 3.77 - 4.34: 68219 4.34 - 4.90: 106031 Nonbonded interactions: 255117 Sorted by model distance: nonbonded pdb=" ND1 HIS F 258 " pdb="ZN ZN F 402 " model vdw 2.084 1.848 nonbonded pdb=" O LEU E 211 " pdb=" OG1 THR E 215 " model vdw 2.122 2.440 nonbonded pdb=" OH TYR D 35 " pdb=" O LEU D 93 " model vdw 2.153 2.440 nonbonded pdb=" O CYS F 255 " pdb=" N ARG F 259 " model vdw 2.169 2.520 nonbonded pdb=" O SER H 711 " pdb=" N ARG H 715 " model vdw 2.218 2.520 ... (remaining 255112 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.390 Check model and map are aligned: 0.510 Set scattering table: 0.230 Process input model: 96.450 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 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 : 0.004 0.203 31893 Z= 0.207 Angle : 0.574 53.005 43577 Z= 0.297 Chirality : 0.036 0.132 4851 Planarity : 0.003 0.041 5228 Dihedral : 14.394 144.518 12235 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.12 % Rotamer: Outliers : 3.89 % Allowed : 4.81 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.15), residues: 3550 helix: 2.54 (0.13), residues: 1759 sheet: 0.26 (0.28), residues: 387 loop : 0.28 (0.18), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 904 HIS 0.003 0.001 HIS G 42 PHE 0.011 0.001 PHE D 403 TYR 0.016 0.001 TYR H 189 ARG 0.003 0.000 ARG H 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 479 time to evaluate : 3.727 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8986 (p) REVERT: A 105 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7521 (mt-10) REVERT: A 276 MET cc_start: 0.7463 (mmt) cc_final: 0.6741 (mmt) REVERT: A 287 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9031 (mm) REVERT: A 326 LYS cc_start: 0.8423 (mmtt) cc_final: 0.7892 (mptt) REVERT: A 380 MET cc_start: 0.8816 (ttm) cc_final: 0.7472 (ttm) REVERT: A 412 MET cc_start: 0.8171 (mmm) cc_final: 0.7850 (mmt) REVERT: A 463 LYS cc_start: 0.8575 (pttt) cc_final: 0.8299 (pttp) REVERT: A 470 LEU cc_start: 0.8993 (mt) cc_final: 0.8780 (tt) REVERT: A 490 GLU cc_start: 0.8422 (tt0) cc_final: 0.7869 (tm-30) REVERT: A 518 PHE cc_start: 0.8792 (m-80) cc_final: 0.8468 (m-80) REVERT: A 519 TYR cc_start: 0.8554 (t80) cc_final: 0.6686 (t80) REVERT: A 525 ILE cc_start: 0.8856 (mt) cc_final: 0.8574 (pt) REVERT: A 569 LYS cc_start: 0.9266 (mttt) cc_final: 0.8815 (mmtp) REVERT: A 609 LYS cc_start: 0.9143 (tttt) cc_final: 0.8911 (ttpp) REVERT: A 635 GLN cc_start: 0.8128 (tp-100) cc_final: 0.7918 (tp40) REVERT: A 660 TYR cc_start: 0.8118 (m-80) cc_final: 0.7757 (m-10) REVERT: A 682 ASP cc_start: 0.8632 (m-30) cc_final: 0.8392 (m-30) REVERT: A 685 TYR cc_start: 0.8574 (m-80) cc_final: 0.8336 (m-80) REVERT: B 42 MET cc_start: 0.7791 (tpt) cc_final: 0.7500 (tpp) REVERT: B 211 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7874 (t80) REVERT: B 384 HIS cc_start: 0.9422 (OUTLIER) cc_final: 0.9067 (p-80) REVERT: B 493 MET cc_start: 0.8738 (ptp) cc_final: 0.8492 (ptp) REVERT: B 677 MET cc_start: 0.9105 (mtt) cc_final: 0.8746 (mtm) REVERT: C 117 MET cc_start: 0.7153 (mtt) cc_final: 0.6675 (ptp) REVERT: C 307 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.9108 (m-80) REVERT: C 310 HIS cc_start: 0.9123 (OUTLIER) cc_final: 0.8910 (p-80) REVERT: C 452 MET cc_start: 0.5913 (mtp) cc_final: 0.3826 (mtp) REVERT: D 34 LEU cc_start: 0.9235 (mt) cc_final: 0.8876 (mt) REVERT: D 57 MET cc_start: 0.9063 (mmm) cc_final: 0.8537 (mmp) REVERT: D 185 MET cc_start: 0.8362 (mtp) cc_final: 0.7479 (mtm) REVERT: D 201 PHE cc_start: 0.8756 (m-80) cc_final: 0.8386 (m-10) REVERT: D 205 LEU cc_start: 0.8842 (mt) cc_final: 0.8578 (tt) REVERT: D 318 TYR cc_start: 0.8163 (m-10) cc_final: 0.7895 (m-80) REVERT: D 335 LEU cc_start: 0.9319 (mt) cc_final: 0.8915 (mt) REVERT: D 345 GLN cc_start: 0.8510 (tt0) cc_final: 0.8162 (tt0) REVERT: D 390 GLN cc_start: 0.8814 (tp40) cc_final: 0.8603 (tp40) REVERT: D 392 ARG cc_start: 0.8945 (mtt180) cc_final: 0.8503 (ttm110) REVERT: E 52 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8549 (mm110) REVERT: F 42 MET cc_start: 0.9218 (mtm) cc_final: 0.8480 (mtt) REVERT: F 147 MET cc_start: 0.9007 (mmp) cc_final: 0.8718 (mmp) REVERT: F 175 MET cc_start: 0.8987 (ttt) cc_final: 0.8663 (tmm) REVERT: G 13 ASP cc_start: 0.8409 (p0) cc_final: 0.7584 (p0) REVERT: G 16 MET cc_start: 0.9014 (mmp) cc_final: 0.8331 (mmm) REVERT: G 33 PHE cc_start: 0.7102 (m-80) cc_final: 0.6850 (m-80) REVERT: G 59 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8311 (mm-30) REVERT: G 60 LEU cc_start: 0.9247 (tp) cc_final: 0.9016 (tp) REVERT: H 568 TYR cc_start: 0.2362 (OUTLIER) cc_final: 0.1548 (m-80) REVERT: H 688 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8027 (t0) REVERT: H 726 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8160 (pm20) REVERT: H 845 LEU cc_start: 0.9381 (mt) cc_final: 0.9114 (mt) REVERT: H 859 GLU cc_start: 0.8923 (tt0) cc_final: 0.8493 (tp30) REVERT: H 862 LYS cc_start: 0.8960 (mttt) cc_final: 0.8694 (mptt) REVERT: H 895 GLU cc_start: 0.8401 (tp30) cc_final: 0.8002 (tp30) REVERT: H 909 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8186 (mm-30) REVERT: I 276 LEU cc_start: 0.7075 (mp) cc_final: 0.6671 (tt) REVERT: I 313 LEU cc_start: 0.7571 (tp) cc_final: 0.7200 (tp) REVERT: J 72 MET cc_start: 0.4528 (ptm) cc_final: 0.4298 (ptt) REVERT: J 104 GLU cc_start: 0.9076 (tt0) cc_final: 0.8829 (tm-30) REVERT: J 108 LYS cc_start: 0.9528 (mtpt) cc_final: 0.9272 (mmmt) outliers start: 123 outliers final: 48 residues processed: 585 average time/residue: 0.4719 time to fit residues: 420.6923 Evaluate side-chains 363 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 305 time to evaluate : 3.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 15 TYR Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 688 ASP Chi-restraints excluded: chain H residue 708 LYS Chi-restraints excluded: chain H residue 787 ASP Chi-restraints excluded: chain H residue 790 CYS Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 834 ARG Chi-restraints excluded: chain J residue 116 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 0.8980 chunk 275 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 186 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 285 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 173 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 330 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 ASN A 506 GLN A 625 GLN A 665 GLN A 709 GLN ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS D 20 GLN ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 GLN ** E 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31893 Z= 0.261 Angle : 0.622 19.269 43577 Z= 0.318 Chirality : 0.040 0.196 4851 Planarity : 0.004 0.049 5228 Dihedral : 16.533 145.402 5188 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.70 % Allowed : 10.82 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.15), residues: 3550 helix: 1.95 (0.12), residues: 1767 sheet: 0.33 (0.28), residues: 370 loop : 0.13 (0.18), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 55 HIS 0.012 0.001 HIS I 320 PHE 0.030 0.002 PHE H 302 TYR 0.022 0.001 TYR A 163 ARG 0.012 0.001 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 314 time to evaluate : 3.515 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 92 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.9043 (p) REVERT: A 276 MET cc_start: 0.7075 (mmt) cc_final: 0.6844 (mmt) REVERT: A 322 LYS cc_start: 0.8824 (tptp) cc_final: 0.8566 (tptp) REVERT: A 326 LYS cc_start: 0.8420 (mmtt) cc_final: 0.7972 (mptt) REVERT: A 373 GLN cc_start: 0.8638 (mp10) cc_final: 0.8350 (mm-40) REVERT: A 375 LYS cc_start: 0.9238 (tttt) cc_final: 0.8989 (ttmt) REVERT: A 380 MET cc_start: 0.8780 (ttm) cc_final: 0.8324 (ttm) REVERT: A 412 MET cc_start: 0.8160 (mmm) cc_final: 0.7946 (mmt) REVERT: A 424 GLU cc_start: 0.8659 (tp30) cc_final: 0.8272 (tp30) REVERT: A 463 LYS cc_start: 0.8800 (pttt) cc_final: 0.8404 (pttp) REVERT: A 470 LEU cc_start: 0.9074 (mt) cc_final: 0.8806 (tt) REVERT: A 482 PHE cc_start: 0.7940 (t80) cc_final: 0.7715 (t80) REVERT: A 490 GLU cc_start: 0.8450 (tt0) cc_final: 0.7898 (tm-30) REVERT: A 518 PHE cc_start: 0.8875 (m-80) cc_final: 0.8527 (m-80) REVERT: A 519 TYR cc_start: 0.8245 (t80) cc_final: 0.7371 (t80) REVERT: A 569 LYS cc_start: 0.9235 (mttt) cc_final: 0.8839 (mmtp) REVERT: A 589 ARG cc_start: 0.9177 (ttp-170) cc_final: 0.8919 (ttp-170) REVERT: A 609 LYS cc_start: 0.9161 (tttt) cc_final: 0.8950 (ttpp) REVERT: A 639 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7953 (ptm160) REVERT: A 666 ASP cc_start: 0.7533 (t0) cc_final: 0.7048 (t0) REVERT: A 678 ARG cc_start: 0.8450 (ptp90) cc_final: 0.8213 (ptp90) REVERT: A 682 ASP cc_start: 0.8640 (m-30) cc_final: 0.8397 (m-30) REVERT: A 696 MET cc_start: 0.8359 (mtp) cc_final: 0.7998 (mmm) REVERT: B 211 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7777 (t80) REVERT: C 140 GLU cc_start: 0.9347 (OUTLIER) cc_final: 0.9130 (pp20) REVERT: C 307 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.9157 (m-80) REVERT: C 310 HIS cc_start: 0.9193 (OUTLIER) cc_final: 0.8936 (p-80) REVERT: C 313 MET cc_start: 0.8883 (mmt) cc_final: 0.8653 (mmm) REVERT: C 545 MET cc_start: 0.4461 (mtt) cc_final: 0.4124 (ptt) REVERT: D 34 LEU cc_start: 0.9285 (mt) cc_final: 0.8935 (mt) REVERT: D 57 MET cc_start: 0.9082 (mmm) cc_final: 0.8587 (mmm) REVERT: D 205 LEU cc_start: 0.8972 (mt) cc_final: 0.8665 (tt) REVERT: D 392 ARG cc_start: 0.8949 (mtt180) cc_final: 0.8479 (ttm110) REVERT: F 147 MET cc_start: 0.9130 (mmp) cc_final: 0.8753 (mmp) REVERT: F 175 MET cc_start: 0.9085 (ttt) cc_final: 0.8774 (tmm) REVERT: G 13 ASP cc_start: 0.8637 (p0) cc_final: 0.8019 (p0) REVERT: G 16 MET cc_start: 0.9137 (mmp) cc_final: 0.8832 (mmm) REVERT: H 566 MET cc_start: 0.5267 (OUTLIER) cc_final: 0.4804 (mtt) REVERT: H 568 TYR cc_start: 0.2118 (OUTLIER) cc_final: 0.1474 (m-80) REVERT: H 688 ASP cc_start: 0.9050 (OUTLIER) cc_final: 0.8129 (t0) REVERT: H 726 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8133 (pm20) REVERT: H 859 GLU cc_start: 0.8980 (tt0) cc_final: 0.8629 (tp30) REVERT: H 862 LYS cc_start: 0.9115 (mttt) cc_final: 0.8789 (mptt) REVERT: H 909 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8268 (tm-30) REVERT: J 104 GLU cc_start: 0.9040 (tt0) cc_final: 0.8824 (tm-30) REVERT: J 108 LYS cc_start: 0.9524 (mtpt) cc_final: 0.9227 (mmmt) outliers start: 117 outliers final: 70 residues processed: 412 average time/residue: 0.4663 time to fit residues: 294.7589 Evaluate side-chains 346 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 267 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 15 TYR Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 209 HIS Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain H residue 566 MET Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 688 ASP Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 708 LYS Chi-restraints excluded: chain H residue 787 ASP Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 136 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 275 optimal weight: 9.9990 chunk 225 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 331 optimal weight: 2.9990 chunk 357 optimal weight: 8.9990 chunk 294 optimal weight: 9.9990 chunk 328 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 265 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 537 ASN ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 31893 Z= 0.296 Angle : 0.636 18.057 43577 Z= 0.329 Chirality : 0.041 0.185 4851 Planarity : 0.004 0.052 5228 Dihedral : 16.696 143.768 5165 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.11 % Allowed : 11.26 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.14), residues: 3550 helix: 1.56 (0.12), residues: 1768 sheet: 0.11 (0.28), residues: 370 loop : 0.01 (0.18), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 55 HIS 0.011 0.001 HIS I 320 PHE 0.030 0.002 PHE G 19 TYR 0.042 0.002 TYR D 318 ARG 0.009 0.001 ARG A 425 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 276 time to evaluate : 3.550 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.8428 (mmtt) cc_final: 0.8014 (mmtm) REVERT: A 346 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8409 (ptpp) REVERT: A 375 LYS cc_start: 0.9268 (tttt) cc_final: 0.8979 (ttpt) REVERT: A 380 MET cc_start: 0.8813 (ttm) cc_final: 0.8587 (ttm) REVERT: A 424 GLU cc_start: 0.8704 (tp30) cc_final: 0.8247 (tp30) REVERT: A 425 ARG cc_start: 0.9018 (mmm160) cc_final: 0.8357 (mmm160) REVERT: A 463 LYS cc_start: 0.8850 (pttt) cc_final: 0.8473 (pttp) REVERT: A 470 LEU cc_start: 0.9082 (mt) cc_final: 0.8789 (tt) REVERT: A 482 PHE cc_start: 0.8020 (t80) cc_final: 0.7711 (t80) REVERT: A 490 GLU cc_start: 0.8447 (tt0) cc_final: 0.7900 (tm-30) REVERT: A 518 PHE cc_start: 0.8888 (m-80) cc_final: 0.8455 (m-80) REVERT: A 519 TYR cc_start: 0.8281 (t80) cc_final: 0.7170 (t80) REVERT: A 540 LYS cc_start: 0.9427 (ttmt) cc_final: 0.9099 (ttpp) REVERT: A 569 LYS cc_start: 0.9271 (mttt) cc_final: 0.8923 (mmtp) REVERT: A 609 LYS cc_start: 0.9153 (tttt) cc_final: 0.8883 (ttpp) REVERT: A 639 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7793 (ptm160) REVERT: A 666 ASP cc_start: 0.7488 (t0) cc_final: 0.7146 (t0) REVERT: A 669 GLU cc_start: 0.8719 (tt0) cc_final: 0.8349 (tt0) REVERT: B 42 MET cc_start: 0.8222 (ttt) cc_final: 0.7757 (ppp) REVERT: B 211 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7752 (t80) REVERT: B 220 LEU cc_start: 0.9365 (tt) cc_final: 0.9030 (tt) REVERT: B 493 MET cc_start: 0.9010 (ptp) cc_final: 0.8685 (ptp) REVERT: B 545 MET cc_start: 0.9595 (OUTLIER) cc_final: 0.9213 (ttm) REVERT: B 620 MET cc_start: 0.9051 (mmm) cc_final: 0.8758 (mmm) REVERT: C 307 PHE cc_start: 0.9451 (OUTLIER) cc_final: 0.9099 (m-10) REVERT: C 310 HIS cc_start: 0.9167 (OUTLIER) cc_final: 0.8920 (p-80) REVERT: C 313 MET cc_start: 0.8857 (mmt) cc_final: 0.8595 (mmm) REVERT: D 34 LEU cc_start: 0.9288 (mt) cc_final: 0.8920 (mt) REVERT: D 57 MET cc_start: 0.9074 (mmm) cc_final: 0.8584 (mmm) REVERT: D 205 LEU cc_start: 0.9006 (mt) cc_final: 0.8739 (tt) REVERT: D 392 ARG cc_start: 0.8970 (mtt180) cc_final: 0.8565 (ttm110) REVERT: D 401 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8801 (mp) REVERT: E 21 ILE cc_start: 0.6932 (OUTLIER) cc_final: 0.6726 (mp) REVERT: E 52 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8520 (mm110) REVERT: F 42 MET cc_start: 0.9155 (mtp) cc_final: 0.8445 (mpp) REVERT: F 147 MET cc_start: 0.9097 (mmp) cc_final: 0.8753 (mmp) REVERT: F 175 MET cc_start: 0.9080 (ttt) cc_final: 0.8752 (tmm) REVERT: G 13 ASP cc_start: 0.8974 (p0) cc_final: 0.8077 (p0) REVERT: G 16 MET cc_start: 0.9177 (mmp) cc_final: 0.8908 (mmm) REVERT: G 56 ARG cc_start: 0.8997 (mpt180) cc_final: 0.8703 (mpt180) REVERT: H 566 MET cc_start: 0.5271 (OUTLIER) cc_final: 0.4892 (mtt) REVERT: H 568 TYR cc_start: 0.1955 (OUTLIER) cc_final: 0.1317 (m-80) REVERT: H 688 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8128 (t0) REVERT: H 718 ARG cc_start: 0.3477 (OUTLIER) cc_final: 0.2911 (ptp-170) REVERT: H 726 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8052 (pm20) REVERT: H 859 GLU cc_start: 0.9048 (tt0) cc_final: 0.8661 (tp30) REVERT: H 862 LYS cc_start: 0.9166 (mttt) cc_final: 0.8827 (mptt) REVERT: H 863 ARG cc_start: 0.8804 (ptt-90) cc_final: 0.8543 (ptt90) REVERT: H 909 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8247 (tm-30) REVERT: J 104 GLU cc_start: 0.9046 (tt0) cc_final: 0.8787 (tm-30) REVERT: J 108 LYS cc_start: 0.9535 (mtpt) cc_final: 0.9179 (mmmt) outliers start: 130 outliers final: 84 residues processed: 382 average time/residue: 0.4533 time to fit residues: 270.3806 Evaluate side-chains 353 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 256 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 15 TYR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 209 HIS Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain H residue 566 MET Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 643 ASN Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 688 ASP Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 708 LYS Chi-restraints excluded: chain H residue 718 ARG Chi-restraints excluded: chain H residue 787 ASP Chi-restraints excluded: chain H residue 792 GLN Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain I residue 310 ASN Chi-restraints excluded: chain J residue 136 ASN Chi-restraints excluded: chain J residue 145 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 0.5980 chunk 248 optimal weight: 9.9990 chunk 171 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 222 optimal weight: 0.6980 chunk 332 optimal weight: 7.9990 chunk 351 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 314 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 overall best weight: 1.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31893 Z= 0.179 Angle : 0.570 17.847 43577 Z= 0.288 Chirality : 0.039 0.267 4851 Planarity : 0.004 0.051 5228 Dihedral : 16.673 141.376 5160 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.48 % Allowed : 12.65 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.15), residues: 3550 helix: 1.74 (0.12), residues: 1764 sheet: 0.10 (0.28), residues: 386 loop : 0.03 (0.18), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 55 HIS 0.007 0.001 HIS I 320 PHE 0.026 0.001 PHE G 19 TYR 0.025 0.001 TYR C 414 ARG 0.009 0.000 ARG A 678 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 282 time to evaluate : 3.803 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.7041 (mmt) cc_final: 0.6192 (mmt) REVERT: A 279 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7401 (mt-10) REVERT: A 322 LYS cc_start: 0.8800 (tptp) cc_final: 0.8415 (tptp) REVERT: A 326 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7843 (mptt) REVERT: A 346 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8395 (ptpp) REVERT: A 375 LYS cc_start: 0.9270 (tttt) cc_final: 0.9051 (ttmt) REVERT: A 380 MET cc_start: 0.8801 (ttm) cc_final: 0.8567 (ttm) REVERT: A 391 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.7644 (mtm-85) REVERT: A 412 MET cc_start: 0.8528 (mmt) cc_final: 0.7920 (mmm) REVERT: A 418 LYS cc_start: 0.7802 (tptt) cc_final: 0.7545 (tptt) REVERT: A 425 ARG cc_start: 0.8963 (mmm160) cc_final: 0.8661 (mmm160) REVERT: A 463 LYS cc_start: 0.8764 (pttt) cc_final: 0.8402 (pttp) REVERT: A 490 GLU cc_start: 0.8430 (tt0) cc_final: 0.7816 (tm-30) REVERT: A 518 PHE cc_start: 0.8847 (m-80) cc_final: 0.8430 (m-80) REVERT: A 519 TYR cc_start: 0.8122 (t80) cc_final: 0.6943 (t80) REVERT: A 589 ARG cc_start: 0.9186 (ttp-170) cc_final: 0.8806 (ttp-170) REVERT: A 609 LYS cc_start: 0.9150 (tttt) cc_final: 0.8902 (ttpp) REVERT: A 660 TYR cc_start: 0.8151 (m-80) cc_final: 0.7873 (m-10) REVERT: A 666 ASP cc_start: 0.7455 (t0) cc_final: 0.7086 (t0) REVERT: A 682 ASP cc_start: 0.8741 (m-30) cc_final: 0.8389 (m-30) REVERT: B 42 MET cc_start: 0.8466 (ttt) cc_final: 0.7948 (ppp) REVERT: B 199 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9220 (mm) REVERT: B 211 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.7806 (t80) REVERT: B 220 LEU cc_start: 0.9369 (tt) cc_final: 0.9090 (tt) REVERT: B 384 HIS cc_start: 0.9439 (OUTLIER) cc_final: 0.9084 (p-80) REVERT: B 493 MET cc_start: 0.8998 (ptp) cc_final: 0.8705 (ptp) REVERT: B 545 MET cc_start: 0.9571 (OUTLIER) cc_final: 0.8926 (ttm) REVERT: B 677 MET cc_start: 0.9182 (mtm) cc_final: 0.8948 (mtm) REVERT: C 140 GLU cc_start: 0.9364 (OUTLIER) cc_final: 0.9151 (pp20) REVERT: C 307 PHE cc_start: 0.9427 (OUTLIER) cc_final: 0.9073 (m-10) REVERT: C 310 HIS cc_start: 0.9123 (OUTLIER) cc_final: 0.8870 (p-80) REVERT: C 313 MET cc_start: 0.8873 (mmt) cc_final: 0.8655 (mmm) REVERT: D 34 LEU cc_start: 0.9282 (mt) cc_final: 0.8908 (mt) REVERT: D 57 MET cc_start: 0.8989 (mmm) cc_final: 0.8505 (mmm) REVERT: D 161 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.8405 (t-90) REVERT: D 201 PHE cc_start: 0.8796 (m-80) cc_final: 0.8375 (m-10) REVERT: D 205 LEU cc_start: 0.8920 (mt) cc_final: 0.8627 (tt) REVERT: D 345 GLN cc_start: 0.8405 (tt0) cc_final: 0.8112 (tt0) REVERT: D 392 ARG cc_start: 0.8921 (mtt180) cc_final: 0.8565 (ttm110) REVERT: D 422 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8530 (mm) REVERT: E 52 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8368 (mm110) REVERT: E 58 MET cc_start: 0.8425 (tpp) cc_final: 0.8080 (tpt) REVERT: F 42 MET cc_start: 0.9162 (mtp) cc_final: 0.8839 (mmm) REVERT: F 51 MET cc_start: 0.9103 (mmm) cc_final: 0.8143 (mmm) REVERT: F 147 MET cc_start: 0.9105 (mmp) cc_final: 0.8727 (mmp) REVERT: F 175 MET cc_start: 0.9032 (ttt) cc_final: 0.8814 (ttp) REVERT: F 177 PHE cc_start: 0.9393 (t80) cc_final: 0.8923 (t80) REVERT: F 178 MET cc_start: 0.9042 (mmm) cc_final: 0.8834 (mmm) REVERT: G 13 ASP cc_start: 0.8947 (p0) cc_final: 0.8016 (p0) REVERT: G 16 MET cc_start: 0.9144 (mmp) cc_final: 0.8879 (mmm) REVERT: G 60 LEU cc_start: 0.9422 (tp) cc_final: 0.9195 (tt) REVERT: H 568 TYR cc_start: 0.2052 (OUTLIER) cc_final: 0.1465 (m-80) REVERT: H 688 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8104 (t0) REVERT: H 726 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8092 (pm20) REVERT: H 859 GLU cc_start: 0.9095 (tt0) cc_final: 0.8699 (tp30) REVERT: H 862 LYS cc_start: 0.9105 (mttt) cc_final: 0.8767 (mptt) REVERT: H 863 ARG cc_start: 0.8816 (ptt-90) cc_final: 0.8455 (ptt90) REVERT: H 909 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8171 (tm-30) REVERT: J 104 GLU cc_start: 0.8953 (tt0) cc_final: 0.8664 (tm-30) REVERT: J 108 LYS cc_start: 0.9527 (mtpt) cc_final: 0.9175 (mmmt) outliers start: 110 outliers final: 73 residues processed: 377 average time/residue: 0.4523 time to fit residues: 266.6094 Evaluate side-chains 342 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 256 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 90 TYR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 209 HIS Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 688 ASP Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 787 ASP Chi-restraints excluded: chain H residue 792 GLN Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain I residue 314 LEU Chi-restraints excluded: chain J residue 136 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 50.0000 chunk 199 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 300 optimal weight: 2.9990 chunk 243 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 315 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 316 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31893 Z= 0.193 Angle : 0.578 17.723 43577 Z= 0.293 Chirality : 0.039 0.260 4851 Planarity : 0.004 0.049 5228 Dihedral : 16.598 141.890 5149 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.76 % Allowed : 13.00 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.15), residues: 3550 helix: 1.70 (0.12), residues: 1767 sheet: 0.06 (0.28), residues: 386 loop : -0.01 (0.18), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 552 HIS 0.008 0.001 HIS D 373 PHE 0.035 0.001 PHE J 162 TYR 0.019 0.001 TYR D 318 ARG 0.008 0.000 ARG A 678 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 267 time to evaluate : 3.837 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6993 (mmt) cc_final: 0.6190 (mmt) REVERT: A 279 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7403 (mt-10) REVERT: A 326 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8048 (mmtt) REVERT: A 346 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8374 (ptpp) REVERT: A 375 LYS cc_start: 0.9276 (tttt) cc_final: 0.8860 (ttpt) REVERT: A 380 MET cc_start: 0.8845 (ttm) cc_final: 0.8609 (ttm) REVERT: A 412 MET cc_start: 0.8591 (mmt) cc_final: 0.7958 (mmm) REVERT: A 425 ARG cc_start: 0.9019 (mmm160) cc_final: 0.8683 (mmm160) REVERT: A 463 LYS cc_start: 0.8780 (pttt) cc_final: 0.8415 (pttp) REVERT: A 490 GLU cc_start: 0.8463 (tt0) cc_final: 0.7818 (tm-30) REVERT: A 518 PHE cc_start: 0.8810 (m-80) cc_final: 0.8440 (m-80) REVERT: A 519 TYR cc_start: 0.8115 (t80) cc_final: 0.6755 (t80) REVERT: A 530 ARG cc_start: 0.8698 (mtm180) cc_final: 0.8452 (mtm-85) REVERT: A 589 ARG cc_start: 0.9175 (ttp-170) cc_final: 0.8905 (ttp-170) REVERT: A 609 LYS cc_start: 0.9171 (tttt) cc_final: 0.8912 (ttpp) REVERT: A 613 THR cc_start: 0.6311 (OUTLIER) cc_final: 0.5537 (t) REVERT: A 635 GLN cc_start: 0.8323 (tp40) cc_final: 0.8041 (tp40) REVERT: A 666 ASP cc_start: 0.7526 (t0) cc_final: 0.7051 (t0) REVERT: A 668 GLN cc_start: 0.8904 (tt0) cc_final: 0.8470 (tp-100) REVERT: A 682 ASP cc_start: 0.8730 (m-30) cc_final: 0.8396 (m-30) REVERT: B 42 MET cc_start: 0.8467 (ttt) cc_final: 0.7910 (ppp) REVERT: B 199 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9178 (mm) REVERT: B 211 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7804 (t80) REVERT: B 220 LEU cc_start: 0.9387 (tt) cc_final: 0.9104 (tt) REVERT: B 384 HIS cc_start: 0.9443 (OUTLIER) cc_final: 0.9087 (p-80) REVERT: B 493 MET cc_start: 0.9006 (ptp) cc_final: 0.8713 (ptp) REVERT: B 545 MET cc_start: 0.9580 (OUTLIER) cc_final: 0.8958 (ttm) REVERT: B 599 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8391 (m) REVERT: B 677 MET cc_start: 0.9168 (mtm) cc_final: 0.8914 (mtm) REVERT: C 140 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.9162 (pp20) REVERT: C 233 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.6325 (t70) REVERT: C 307 PHE cc_start: 0.9428 (OUTLIER) cc_final: 0.9075 (m-10) REVERT: C 310 HIS cc_start: 0.9146 (OUTLIER) cc_final: 0.8886 (p-80) REVERT: D 34 LEU cc_start: 0.9255 (mt) cc_final: 0.8856 (mt) REVERT: D 57 MET cc_start: 0.8983 (mmm) cc_final: 0.8493 (mmm) REVERT: D 161 HIS cc_start: 0.8625 (OUTLIER) cc_final: 0.8406 (t-90) REVERT: D 201 PHE cc_start: 0.8816 (m-80) cc_final: 0.8408 (m-10) REVERT: D 205 LEU cc_start: 0.8912 (mt) cc_final: 0.8616 (tt) REVERT: D 345 GLN cc_start: 0.8412 (tt0) cc_final: 0.8050 (tt0) REVERT: D 392 ARG cc_start: 0.8946 (mtt180) cc_final: 0.8581 (ttm110) REVERT: D 422 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8504 (mm) REVERT: E 52 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8510 (mm110) REVERT: E 252 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7759 (mmm) REVERT: F 42 MET cc_start: 0.9152 (mtp) cc_final: 0.8842 (mmm) REVERT: F 51 MET cc_start: 0.9132 (mmm) cc_final: 0.8175 (mmm) REVERT: F 147 MET cc_start: 0.9124 (mmp) cc_final: 0.8751 (mmp) REVERT: F 175 MET cc_start: 0.9037 (ttt) cc_final: 0.8823 (ttp) REVERT: F 177 PHE cc_start: 0.9398 (t80) cc_final: 0.9182 (t80) REVERT: G 13 ASP cc_start: 0.8982 (p0) cc_final: 0.8101 (p0) REVERT: G 16 MET cc_start: 0.9162 (mmp) cc_final: 0.8930 (mmm) REVERT: H 568 TYR cc_start: 0.1883 (OUTLIER) cc_final: 0.1370 (m-80) REVERT: H 688 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8101 (t0) REVERT: H 726 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8018 (pm20) REVERT: H 858 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8378 (tpp-160) REVERT: H 859 GLU cc_start: 0.9091 (tt0) cc_final: 0.8497 (tp30) REVERT: H 862 LYS cc_start: 0.9099 (mttt) cc_final: 0.8707 (mptt) REVERT: H 863 ARG cc_start: 0.8819 (ptt-90) cc_final: 0.8164 (ptt90) REVERT: H 909 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8149 (tm-30) REVERT: I 316 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7827 (pp30) REVERT: J 104 GLU cc_start: 0.8947 (tt0) cc_final: 0.8645 (tm-30) REVERT: J 108 LYS cc_start: 0.9530 (mtpt) cc_final: 0.9172 (mmmt) outliers start: 119 outliers final: 78 residues processed: 366 average time/residue: 0.4543 time to fit residues: 262.8046 Evaluate side-chains 347 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 250 time to evaluate : 3.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 90 TYR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 209 HIS Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 643 ASN Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 671 ARG Chi-restraints excluded: chain H residue 688 ASP Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 787 ASP Chi-restraints excluded: chain H residue 792 GLN Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 858 ARG Chi-restraints excluded: chain I residue 316 GLN Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 136 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 0.0770 chunk 316 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 352 optimal weight: 0.0370 chunk 292 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 29 optimal weight: 0.0010 chunk 116 optimal weight: 10.0000 chunk 184 optimal weight: 0.0000 overall best weight: 0.6228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 HIS ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 643 ASN ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31893 Z= 0.149 Angle : 0.576 17.837 43577 Z= 0.288 Chirality : 0.039 0.244 4851 Planarity : 0.004 0.049 5228 Dihedral : 16.517 141.213 5145 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.19 % Allowed : 13.69 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.15), residues: 3550 helix: 1.77 (0.12), residues: 1768 sheet: 0.06 (0.27), residues: 401 loop : 0.02 (0.18), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 552 HIS 0.012 0.001 HIS I 320 PHE 0.038 0.001 PHE J 162 TYR 0.021 0.001 TYR A 163 ARG 0.008 0.000 ARG A 678 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 278 time to evaluate : 3.336 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: 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 276 MET cc_start: 0.7035 (mmt) cc_final: 0.6077 (mmt) REVERT: A 279 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7388 (mt-10) REVERT: A 322 LYS cc_start: 0.8754 (tptp) cc_final: 0.8367 (tptp) REVERT: A 326 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7787 (mptt) REVERT: A 375 LYS cc_start: 0.9273 (tttt) cc_final: 0.8844 (ttpt) REVERT: A 380 MET cc_start: 0.8859 (ttm) cc_final: 0.8229 (ttm) REVERT: A 412 MET cc_start: 0.8528 (mmt) cc_final: 0.7979 (mmm) REVERT: A 425 ARG cc_start: 0.9004 (mmm160) cc_final: 0.8754 (mmm160) REVERT: A 463 LYS cc_start: 0.8712 (pttt) cc_final: 0.8335 (pttp) REVERT: A 490 GLU cc_start: 0.8496 (tt0) cc_final: 0.7815 (tm-30) REVERT: A 518 PHE cc_start: 0.8791 (m-80) cc_final: 0.8469 (m-80) REVERT: A 519 TYR cc_start: 0.8034 (t80) cc_final: 0.6667 (t80) REVERT: A 569 LYS cc_start: 0.9000 (mmtp) cc_final: 0.8773 (mmtp) REVERT: A 609 LYS cc_start: 0.9159 (tttt) cc_final: 0.8891 (ttpp) REVERT: A 634 ARG cc_start: 0.8052 (ptm-80) cc_final: 0.7792 (ppt170) REVERT: A 666 ASP cc_start: 0.7398 (t0) cc_final: 0.7191 (t0) REVERT: A 668 GLN cc_start: 0.8798 (tt0) cc_final: 0.8271 (tp-100) REVERT: A 669 GLU cc_start: 0.8291 (tp30) cc_final: 0.8072 (tp30) REVERT: A 682 ASP cc_start: 0.8698 (m-30) cc_final: 0.8396 (m-30) REVERT: B 42 MET cc_start: 0.8515 (ttt) cc_final: 0.7990 (ppp) REVERT: B 211 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7743 (t80) REVERT: B 220 LEU cc_start: 0.9374 (tt) cc_final: 0.9065 (tt) REVERT: B 384 HIS cc_start: 0.9448 (OUTLIER) cc_final: 0.9091 (p-80) REVERT: B 493 MET cc_start: 0.8971 (ptp) cc_final: 0.8714 (ptp) REVERT: B 527 MET cc_start: 0.9532 (mmm) cc_final: 0.9171 (mmm) REVERT: B 545 MET cc_start: 0.9598 (OUTLIER) cc_final: 0.9305 (ttm) REVERT: B 599 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8409 (m) REVERT: B 677 MET cc_start: 0.9161 (mtm) cc_final: 0.8902 (mtm) REVERT: C 117 MET cc_start: 0.7169 (mmm) cc_final: 0.6760 (ptp) REVERT: C 140 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.9141 (pp20) REVERT: C 307 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.9052 (m-10) REVERT: C 310 HIS cc_start: 0.9104 (OUTLIER) cc_final: 0.8839 (p-80) REVERT: C 313 MET cc_start: 0.8904 (mmp) cc_final: 0.8520 (mmm) REVERT: C 411 MET cc_start: 0.8883 (ppp) cc_final: 0.8550 (ppp) REVERT: D 34 LEU cc_start: 0.9235 (mt) cc_final: 0.8825 (mt) REVERT: D 57 MET cc_start: 0.8942 (mmm) cc_final: 0.8433 (mmm) REVERT: D 161 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.8343 (t-90) REVERT: D 201 PHE cc_start: 0.8700 (m-80) cc_final: 0.8279 (m-10) REVERT: D 205 LEU cc_start: 0.8800 (mt) cc_final: 0.8502 (tt) REVERT: D 345 GLN cc_start: 0.8455 (tt0) cc_final: 0.8025 (tt0) REVERT: D 392 ARG cc_start: 0.8911 (mtt180) cc_final: 0.8509 (ttm110) REVERT: D 400 ARG cc_start: 0.7771 (ttm170) cc_final: 0.7028 (ttm170) REVERT: D 422 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8492 (mm) REVERT: E 20 GLU cc_start: 0.5985 (tt0) cc_final: 0.5743 (tt0) REVERT: E 52 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8536 (mm110) REVERT: F 42 MET cc_start: 0.9122 (mtp) cc_final: 0.8822 (mmm) REVERT: F 51 MET cc_start: 0.9124 (mmm) cc_final: 0.8222 (mmm) REVERT: F 147 MET cc_start: 0.9150 (mmp) cc_final: 0.8746 (mmp) REVERT: F 157 MET cc_start: 0.8623 (ptt) cc_final: 0.8413 (ptp) REVERT: F 175 MET cc_start: 0.8998 (ttt) cc_final: 0.8750 (tmm) REVERT: F 177 PHE cc_start: 0.9381 (t80) cc_final: 0.8891 (t80) REVERT: G 13 ASP cc_start: 0.8893 (p0) cc_final: 0.7977 (p0) REVERT: G 16 MET cc_start: 0.9171 (mmp) cc_final: 0.8900 (mmm) REVERT: H 568 TYR cc_start: 0.2015 (OUTLIER) cc_final: 0.1592 (m-80) REVERT: H 688 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8054 (t0) REVERT: H 710 PHE cc_start: 0.5970 (OUTLIER) cc_final: 0.4278 (t80) REVERT: H 726 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7999 (pm20) REVERT: H 859 GLU cc_start: 0.9070 (tt0) cc_final: 0.8473 (tp30) REVERT: H 862 LYS cc_start: 0.8997 (mttt) cc_final: 0.8595 (mptt) REVERT: H 863 ARG cc_start: 0.8753 (ptt-90) cc_final: 0.8092 (ptt90) REVERT: H 909 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8122 (tm-30) REVERT: J 104 GLU cc_start: 0.8930 (tt0) cc_final: 0.8612 (tm-30) REVERT: J 108 LYS cc_start: 0.9516 (mtpt) cc_final: 0.9148 (mmmt) outliers start: 101 outliers final: 69 residues processed: 362 average time/residue: 0.4441 time to fit residues: 253.3302 Evaluate side-chains 335 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 253 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 209 HIS Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 593 THR Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 688 ASP Chi-restraints excluded: chain H residue 689 THR Chi-restraints excluded: chain H residue 710 PHE Chi-restraints excluded: chain H residue 787 ASP Chi-restraints excluded: chain H residue 792 GLN Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain J residue 116 ASP Chi-restraints excluded: chain J residue 136 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 chunk 350 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 213 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 HIS ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 31893 Z= 0.343 Angle : 0.690 17.446 43577 Z= 0.359 Chirality : 0.041 0.208 4851 Planarity : 0.005 0.046 5228 Dihedral : 16.734 142.167 5143 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.14 % Allowed : 13.73 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3550 helix: 1.37 (0.12), residues: 1761 sheet: -0.29 (0.27), residues: 403 loop : -0.08 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 55 HIS 0.012 0.002 HIS H 780 PHE 0.037 0.002 PHE J 162 TYR 0.036 0.002 TYR A 163 ARG 0.007 0.001 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 242 time to evaluate : 3.684 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: 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 326 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8169 (mmtt) REVERT: A 346 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8549 (ptpp) REVERT: A 374 TRP cc_start: 0.8958 (m100) cc_final: 0.8662 (m100) REVERT: A 380 MET cc_start: 0.8821 (ttm) cc_final: 0.8587 (ttm) REVERT: A 412 MET cc_start: 0.8811 (mmt) cc_final: 0.8335 (mmm) REVERT: A 425 ARG cc_start: 0.9140 (mmm160) cc_final: 0.8692 (mmm160) REVERT: A 428 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 463 LYS cc_start: 0.8894 (pttt) cc_final: 0.8495 (pttp) REVERT: A 490 GLU cc_start: 0.8479 (tt0) cc_final: 0.7949 (tm-30) REVERT: A 518 PHE cc_start: 0.8892 (m-80) cc_final: 0.8464 (m-80) REVERT: A 519 TYR cc_start: 0.8403 (t80) cc_final: 0.7003 (t80) REVERT: A 530 ARG cc_start: 0.8749 (mtm180) cc_final: 0.8509 (mtm-85) REVERT: A 569 LYS cc_start: 0.9037 (mmtp) cc_final: 0.8810 (mmtp) REVERT: A 609 LYS cc_start: 0.9169 (tttt) cc_final: 0.8922 (ttpp) REVERT: A 613 THR cc_start: 0.6566 (OUTLIER) cc_final: 0.5907 (t) REVERT: A 635 GLN cc_start: 0.8241 (tp40) cc_final: 0.8011 (tp40) REVERT: A 668 GLN cc_start: 0.9072 (tt0) cc_final: 0.8650 (tp-100) REVERT: A 669 GLU cc_start: 0.8588 (tp30) cc_final: 0.8342 (tp30) REVERT: A 678 ARG cc_start: 0.8279 (ptt90) cc_final: 0.7904 (ptt90) REVERT: A 682 ASP cc_start: 0.8773 (m-30) cc_final: 0.8433 (m-30) REVERT: B 42 MET cc_start: 0.8320 (ttt) cc_final: 0.8104 (ttm) REVERT: B 211 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7903 (t80) REVERT: B 527 MET cc_start: 0.9561 (mmm) cc_final: 0.9269 (mmm) REVERT: B 545 MET cc_start: 0.9609 (OUTLIER) cc_final: 0.8953 (ttm) REVERT: B 599 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8422 (m) REVERT: C 233 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.6207 (t70) REVERT: C 307 PHE cc_start: 0.9447 (OUTLIER) cc_final: 0.9122 (m-10) REVERT: C 310 HIS cc_start: 0.9174 (OUTLIER) cc_final: 0.8936 (p-80) REVERT: C 313 MET cc_start: 0.8933 (mmp) cc_final: 0.8546 (mmm) REVERT: D 57 MET cc_start: 0.9065 (mmm) cc_final: 0.8582 (mmm) REVERT: D 59 MET cc_start: 0.8553 (mpp) cc_final: 0.8024 (mmt) REVERT: D 205 LEU cc_start: 0.9001 (mt) cc_final: 0.8775 (tt) REVERT: D 345 GLN cc_start: 0.8416 (tt0) cc_final: 0.8068 (tt0) REVERT: D 392 ARG cc_start: 0.8942 (mtt180) cc_final: 0.8608 (ttm110) REVERT: D 422 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8550 (mm) REVERT: E 52 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8404 (mm110) REVERT: F 42 MET cc_start: 0.9187 (mtp) cc_final: 0.8920 (mmm) REVERT: F 51 MET cc_start: 0.9193 (mmm) cc_final: 0.8373 (mmm) REVERT: F 143 TYR cc_start: 0.9258 (t80) cc_final: 0.9009 (t80) REVERT: F 147 MET cc_start: 0.9112 (mmp) cc_final: 0.8725 (mmp) REVERT: F 175 MET cc_start: 0.9076 (ttt) cc_final: 0.8765 (tpp) REVERT: F 178 MET cc_start: 0.9142 (mmm) cc_final: 0.8834 (mmp) REVERT: G 13 ASP cc_start: 0.9019 (p0) cc_final: 0.8177 (p0) REVERT: G 16 MET cc_start: 0.9209 (mmp) cc_final: 0.9004 (mmm) REVERT: H 568 TYR cc_start: 0.2194 (OUTLIER) cc_final: 0.1740 (m-80) REVERT: H 644 HIS cc_start: 0.7724 (OUTLIER) cc_final: 0.7501 (t70) REVERT: H 688 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8041 (t0) REVERT: H 718 ARG cc_start: 0.3419 (OUTLIER) cc_final: 0.2416 (ptp-110) REVERT: H 726 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7967 (pm20) REVERT: H 859 GLU cc_start: 0.9115 (tt0) cc_final: 0.8496 (tp30) REVERT: H 862 LYS cc_start: 0.9155 (mttt) cc_final: 0.8780 (mptt) REVERT: H 863 ARG cc_start: 0.8901 (ptt-90) cc_final: 0.8265 (ptt90) REVERT: H 909 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8156 (tm-30) REVERT: I 287 GLN cc_start: 0.9628 (tp-100) cc_final: 0.9384 (mt0) REVERT: J 104 GLU cc_start: 0.8965 (tt0) cc_final: 0.8655 (tm-30) REVERT: J 108 LYS cc_start: 0.9564 (mtpt) cc_final: 0.9213 (mmmt) outliers start: 131 outliers final: 90 residues processed: 352 average time/residue: 0.4227 time to fit residues: 236.5529 Evaluate side-chains 343 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 239 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 448 HIS Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 90 TYR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 209 HIS Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 593 THR Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 643 ASN Chi-restraints excluded: chain H residue 644 HIS Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 688 ASP Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 718 ARG Chi-restraints excluded: chain H residue 787 ASP Chi-restraints excluded: chain H residue 792 GLN Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain J residue 136 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 0.2980 chunk 140 optimal weight: 5.9990 chunk 209 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 239 optimal weight: 0.0470 chunk 173 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 275 optimal weight: 0.3980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 GLN G 36 GLN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 HIS ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31893 Z= 0.160 Angle : 0.609 17.924 43577 Z= 0.305 Chirality : 0.040 0.196 4851 Planarity : 0.004 0.049 5228 Dihedral : 16.670 138.463 5141 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.16 % Allowed : 15.02 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.15), residues: 3550 helix: 1.65 (0.12), residues: 1764 sheet: -0.03 (0.28), residues: 400 loop : -0.00 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP D 55 HIS 0.010 0.001 HIS I 320 PHE 0.037 0.001 PHE J 162 TYR 0.020 0.001 TYR A 660 ARG 0.011 0.000 ARG H 608 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 258 time to evaluate : 3.724 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.7125 (mmt) cc_final: 0.6413 (mmt) REVERT: A 279 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7582 (mt-10) REVERT: A 326 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8166 (mmtm) REVERT: A 380 MET cc_start: 0.8843 (ttm) cc_final: 0.8205 (ttm) REVERT: A 412 MET cc_start: 0.8552 (mmt) cc_final: 0.8063 (mmm) REVERT: A 422 GLU cc_start: 0.8773 (pm20) cc_final: 0.8495 (pm20) REVERT: A 425 ARG cc_start: 0.9061 (mmm160) cc_final: 0.8613 (mmm160) REVERT: A 463 LYS cc_start: 0.8750 (pttt) cc_final: 0.8370 (pttp) REVERT: A 490 GLU cc_start: 0.8505 (tt0) cc_final: 0.7842 (tm-30) REVERT: A 518 PHE cc_start: 0.8726 (m-80) cc_final: 0.8404 (m-10) REVERT: A 530 ARG cc_start: 0.8632 (mtm180) cc_final: 0.8286 (mtm-85) REVERT: A 609 LYS cc_start: 0.9168 (tttt) cc_final: 0.8879 (ttpp) REVERT: A 668 GLN cc_start: 0.8828 (tt0) cc_final: 0.8529 (tp40) REVERT: A 669 GLU cc_start: 0.8294 (tp30) cc_final: 0.8010 (tp30) REVERT: A 678 ARG cc_start: 0.8046 (ptt90) cc_final: 0.7608 (ptt90) REVERT: A 682 ASP cc_start: 0.8712 (m-30) cc_final: 0.8386 (m-30) REVERT: A 696 MET cc_start: 0.8699 (mmm) cc_final: 0.8492 (mmm) REVERT: B 211 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.7714 (t80) REVERT: B 384 HIS cc_start: 0.9445 (OUTLIER) cc_final: 0.9079 (p-80) REVERT: B 527 MET cc_start: 0.9560 (mmm) cc_final: 0.9270 (mmm) REVERT: B 545 MET cc_start: 0.9587 (OUTLIER) cc_final: 0.9342 (ttp) REVERT: B 599 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8286 (m) REVERT: C 307 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.9069 (m-10) REVERT: C 310 HIS cc_start: 0.9076 (OUTLIER) cc_final: 0.8830 (p-80) REVERT: C 313 MET cc_start: 0.8952 (mmp) cc_final: 0.8601 (mmm) REVERT: D 57 MET cc_start: 0.8901 (mmm) cc_final: 0.8455 (mmm) REVERT: D 161 HIS cc_start: 0.8590 (OUTLIER) cc_final: 0.8376 (t-90) REVERT: D 201 PHE cc_start: 0.8707 (m-80) cc_final: 0.8262 (m-10) REVERT: D 205 LEU cc_start: 0.8797 (mt) cc_final: 0.8521 (tt) REVERT: D 392 ARG cc_start: 0.8877 (mtt180) cc_final: 0.8511 (ttm110) REVERT: D 422 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8414 (mm) REVERT: D 441 MET cc_start: 0.8003 (mmm) cc_final: 0.7732 (mmm) REVERT: E 52 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8487 (mm110) REVERT: F 42 MET cc_start: 0.9140 (mtp) cc_final: 0.8856 (mmm) REVERT: F 51 MET cc_start: 0.9197 (mmm) cc_final: 0.8361 (mmm) REVERT: F 143 TYR cc_start: 0.9222 (t80) cc_final: 0.8991 (t80) REVERT: F 147 MET cc_start: 0.9142 (mmp) cc_final: 0.8677 (mmp) REVERT: F 175 MET cc_start: 0.8968 (ttt) cc_final: 0.8701 (tpp) REVERT: F 177 PHE cc_start: 0.9390 (t80) cc_final: 0.9116 (t80) REVERT: G 13 ASP cc_start: 0.8939 (p0) cc_final: 0.8088 (p0) REVERT: G 16 MET cc_start: 0.9153 (mmp) cc_final: 0.8893 (mmm) REVERT: G 66 PHE cc_start: 0.8847 (t80) cc_final: 0.8006 (t80) REVERT: H 568 TYR cc_start: 0.2337 (OUTLIER) cc_final: 0.1931 (m-80) REVERT: H 688 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8058 (t0) REVERT: H 710 PHE cc_start: 0.6123 (OUTLIER) cc_final: 0.4545 (t80) REVERT: H 726 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7952 (mp0) REVERT: H 859 GLU cc_start: 0.9081 (tt0) cc_final: 0.8797 (tp30) REVERT: H 862 LYS cc_start: 0.8990 (mttt) cc_final: 0.8602 (mptt) REVERT: H 909 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8060 (tm-30) REVERT: I 287 GLN cc_start: 0.9641 (tp-100) cc_final: 0.9430 (mt0) REVERT: J 104 GLU cc_start: 0.8913 (tt0) cc_final: 0.8586 (tm-30) REVERT: J 108 LYS cc_start: 0.9554 (mtpt) cc_final: 0.9172 (mmmt) outliers start: 100 outliers final: 69 residues processed: 338 average time/residue: 0.4315 time to fit residues: 234.3887 Evaluate side-chains 326 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 245 time to evaluate : 3.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 397 LYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 209 HIS Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 593 THR Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 688 ASP Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 710 PHE Chi-restraints excluded: chain H residue 787 ASP Chi-restraints excluded: chain H residue 792 GLN Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain J residue 136 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 5.9990 chunk 336 optimal weight: 20.0000 chunk 306 optimal weight: 10.0000 chunk 326 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 295 optimal weight: 20.0000 chunk 309 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 HIS ** H 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 31893 Z= 0.459 Angle : 0.775 17.205 43577 Z= 0.406 Chirality : 0.043 0.290 4851 Planarity : 0.005 0.060 5228 Dihedral : 16.926 141.179 5141 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 26.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.16 % Allowed : 15.34 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3550 helix: 1.05 (0.12), residues: 1768 sheet: -0.30 (0.27), residues: 386 loop : -0.23 (0.18), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 55 HIS 0.011 0.002 HIS H 780 PHE 0.037 0.002 PHE J 162 TYR 0.038 0.002 TYR A 163 ARG 0.010 0.001 ARG D 400 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 234 time to evaluate : 3.544 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: 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 276 MET cc_start: 0.7225 (mmt) cc_final: 0.6342 (mmp) REVERT: A 279 GLU cc_start: 0.7930 (mt-10) cc_final: 0.5990 (mt-10) REVERT: A 326 LYS cc_start: 0.8525 (mmtt) cc_final: 0.8320 (mmtm) REVERT: A 346 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8588 (ptpp) REVERT: A 374 TRP cc_start: 0.8971 (m100) cc_final: 0.8712 (m100) REVERT: A 380 MET cc_start: 0.8834 (ttm) cc_final: 0.8589 (ttm) REVERT: A 412 MET cc_start: 0.8882 (mmt) cc_final: 0.8446 (mmm) REVERT: A 425 ARG cc_start: 0.9241 (mmm160) cc_final: 0.8823 (mmm160) REVERT: A 428 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7820 (tm-30) REVERT: A 490 GLU cc_start: 0.8495 (tt0) cc_final: 0.8011 (tm-30) REVERT: A 518 PHE cc_start: 0.8925 (m-80) cc_final: 0.8493 (m-80) REVERT: A 519 TYR cc_start: 0.8324 (t80) cc_final: 0.8075 (t80) REVERT: A 530 ARG cc_start: 0.8786 (mtm180) cc_final: 0.8579 (mtm-85) REVERT: A 589 ARG cc_start: 0.9142 (ttm170) cc_final: 0.8757 (ttm110) REVERT: A 609 LYS cc_start: 0.9148 (tttt) cc_final: 0.8881 (ttpp) REVERT: A 613 THR cc_start: 0.6855 (OUTLIER) cc_final: 0.6263 (t) REVERT: A 668 GLN cc_start: 0.9029 (tt0) cc_final: 0.8678 (tp40) REVERT: A 669 GLU cc_start: 0.8681 (tp30) cc_final: 0.8433 (tp30) REVERT: A 678 ARG cc_start: 0.8302 (ptt90) cc_final: 0.8047 (ptt90) REVERT: A 682 ASP cc_start: 0.8807 (m-30) cc_final: 0.8440 (m-30) REVERT: B 42 MET cc_start: 0.7602 (ttm) cc_final: 0.7346 (ppp) REVERT: B 211 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.8111 (t80) REVERT: B 478 MET cc_start: 0.7995 (mpp) cc_final: 0.7578 (mpp) REVERT: B 527 MET cc_start: 0.9567 (mmm) cc_final: 0.9298 (mmm) REVERT: B 545 MET cc_start: 0.9611 (OUTLIER) cc_final: 0.8974 (ttm) REVERT: B 599 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8416 (m) REVERT: C 233 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.6152 (t70) REVERT: C 307 PHE cc_start: 0.9467 (OUTLIER) cc_final: 0.9178 (m-10) REVERT: C 310 HIS cc_start: 0.9166 (OUTLIER) cc_final: 0.8937 (p-80) REVERT: C 313 MET cc_start: 0.8937 (mmp) cc_final: 0.8562 (mmm) REVERT: D 57 MET cc_start: 0.9039 (mmm) cc_final: 0.8634 (mmm) REVERT: D 205 LEU cc_start: 0.9050 (mt) cc_final: 0.8847 (tt) REVERT: D 392 ARG cc_start: 0.8963 (mtt180) cc_final: 0.8594 (ttm110) REVERT: D 422 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8550 (mm) REVERT: D 441 MET cc_start: 0.8198 (mmm) cc_final: 0.7878 (mmm) REVERT: E 17 ARG cc_start: 0.7641 (tpp80) cc_final: 0.7377 (tpp80) REVERT: E 52 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8386 (mm110) REVERT: F 42 MET cc_start: 0.9259 (mtp) cc_final: 0.9050 (mmm) REVERT: F 51 MET cc_start: 0.9279 (mmm) cc_final: 0.8466 (mmm) REVERT: F 143 TYR cc_start: 0.9276 (t80) cc_final: 0.9003 (t80) REVERT: F 147 MET cc_start: 0.8992 (mmp) cc_final: 0.8550 (mmp) REVERT: F 157 MET cc_start: 0.8555 (ptp) cc_final: 0.8207 (pmm) REVERT: F 175 MET cc_start: 0.9076 (ttt) cc_final: 0.8856 (tpp) REVERT: G 13 ASP cc_start: 0.8971 (p0) cc_final: 0.8114 (p0) REVERT: G 16 MET cc_start: 0.9218 (mmp) cc_final: 0.8980 (mmm) REVERT: H 568 TYR cc_start: 0.2406 (OUTLIER) cc_final: 0.2086 (m-80) REVERT: H 644 HIS cc_start: 0.7717 (OUTLIER) cc_final: 0.7467 (t-170) REVERT: H 688 ASP cc_start: 0.9003 (OUTLIER) cc_final: 0.8012 (t0) REVERT: H 726 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7975 (mp0) REVERT: H 859 GLU cc_start: 0.9135 (tt0) cc_final: 0.8851 (tp30) REVERT: H 862 LYS cc_start: 0.9190 (mttt) cc_final: 0.8814 (mptt) REVERT: H 909 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8128 (tm-30) REVERT: I 287 GLN cc_start: 0.9619 (tp-100) cc_final: 0.9389 (mt0) REVERT: J 104 GLU cc_start: 0.8980 (tt0) cc_final: 0.8648 (tm-30) REVERT: J 108 LYS cc_start: 0.9588 (mtpt) cc_final: 0.9225 (mmmt) outliers start: 100 outliers final: 74 residues processed: 318 average time/residue: 0.4509 time to fit residues: 230.8232 Evaluate side-chains 315 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 228 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 397 LYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 448 HIS Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 209 HIS Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 643 ASN Chi-restraints excluded: chain H residue 644 HIS Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 688 ASP Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 787 ASP Chi-restraints excluded: chain H residue 792 GLN Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 136 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 7.9990 chunk 345 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 240 optimal weight: 20.0000 chunk 362 optimal weight: 0.5980 chunk 333 optimal weight: 0.1980 chunk 288 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 GLN ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 HIS ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31893 Z= 0.173 Angle : 0.646 17.862 43577 Z= 0.321 Chirality : 0.041 0.212 4851 Planarity : 0.004 0.054 5228 Dihedral : 16.855 139.378 5139 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.34 % Allowed : 16.54 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.15), residues: 3550 helix: 1.48 (0.12), residues: 1764 sheet: -0.14 (0.28), residues: 380 loop : -0.09 (0.18), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 55 HIS 0.009 0.001 HIS I 320 PHE 0.044 0.001 PHE J 162 TYR 0.018 0.001 TYR G 22 ARG 0.016 0.001 ARG A 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 244 time to evaluate : 3.473 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.7149 (mmt) cc_final: 0.6409 (mmt) REVERT: A 279 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7532 (mt-10) REVERT: A 326 LYS cc_start: 0.8365 (mmtt) cc_final: 0.8079 (mmtt) REVERT: A 373 GLN cc_start: 0.8892 (mm110) cc_final: 0.8504 (mp10) REVERT: A 374 TRP cc_start: 0.8885 (m100) cc_final: 0.8558 (m100) REVERT: A 375 LYS cc_start: 0.9216 (ttmt) cc_final: 0.8918 (ttpt) REVERT: A 380 MET cc_start: 0.8845 (ttm) cc_final: 0.8207 (ttm) REVERT: A 412 MET cc_start: 0.8602 (mmt) cc_final: 0.8109 (mmm) REVERT: A 425 ARG cc_start: 0.9115 (mmm160) cc_final: 0.8796 (mmm160) REVERT: A 463 LYS cc_start: 0.8764 (pttt) cc_final: 0.8388 (pttp) REVERT: A 464 LEU cc_start: 0.8954 (tt) cc_final: 0.8709 (tp) REVERT: A 490 GLU cc_start: 0.8515 (tt0) cc_final: 0.7915 (tm-30) REVERT: A 518 PHE cc_start: 0.8745 (m-80) cc_final: 0.8458 (m-80) REVERT: A 519 TYR cc_start: 0.7929 (t80) cc_final: 0.7663 (t80) REVERT: A 530 ARG cc_start: 0.8656 (mtm180) cc_final: 0.8304 (mtm-85) REVERT: A 609 LYS cc_start: 0.9175 (tttt) cc_final: 0.8953 (ttpp) REVERT: A 666 ASP cc_start: 0.7509 (t0) cc_final: 0.7222 (t0) REVERT: A 669 GLU cc_start: 0.8305 (tp30) cc_final: 0.7688 (tp30) REVERT: A 678 ARG cc_start: 0.7864 (ptt90) cc_final: 0.7630 (ptt90) REVERT: A 682 ASP cc_start: 0.8677 (m-30) cc_final: 0.8367 (m-30) REVERT: B 42 MET cc_start: 0.7659 (ttm) cc_final: 0.7433 (ppp) REVERT: B 211 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7925 (t80) REVERT: B 384 HIS cc_start: 0.9443 (OUTLIER) cc_final: 0.9069 (p-80) REVERT: B 493 MET cc_start: 0.9070 (ptp) cc_final: 0.8566 (ptp) REVERT: B 527 MET cc_start: 0.9564 (mmm) cc_final: 0.9295 (mmm) REVERT: B 599 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8299 (m) REVERT: B 677 MET cc_start: 0.9194 (mtm) cc_final: 0.8678 (pmm) REVERT: C 307 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.9142 (m-10) REVERT: C 310 HIS cc_start: 0.9085 (OUTLIER) cc_final: 0.8852 (p-80) REVERT: C 313 MET cc_start: 0.8932 (mmp) cc_final: 0.8571 (mmm) REVERT: D 57 MET cc_start: 0.8913 (mmm) cc_final: 0.8425 (mmm) REVERT: D 201 PHE cc_start: 0.8735 (m-80) cc_final: 0.8295 (m-10) REVERT: D 205 LEU cc_start: 0.8852 (mt) cc_final: 0.8597 (tt) REVERT: D 392 ARG cc_start: 0.8871 (mtt180) cc_final: 0.8478 (ttm110) REVERT: D 422 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8452 (mm) REVERT: D 441 MET cc_start: 0.8141 (mmm) cc_final: 0.7790 (tpp) REVERT: E 52 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8504 (mm110) REVERT: F 42 MET cc_start: 0.9185 (mtp) cc_final: 0.8931 (mmm) REVERT: F 51 MET cc_start: 0.9143 (mmm) cc_final: 0.8341 (mmm) REVERT: F 143 TYR cc_start: 0.9218 (t80) cc_final: 0.9003 (t80) REVERT: F 147 MET cc_start: 0.9058 (mmp) cc_final: 0.8643 (mmp) REVERT: F 175 MET cc_start: 0.8972 (ttt) cc_final: 0.8704 (tpp) REVERT: F 177 PHE cc_start: 0.9368 (t80) cc_final: 0.9045 (t80) REVERT: G 13 ASP cc_start: 0.8920 (p0) cc_final: 0.8072 (p0) REVERT: G 16 MET cc_start: 0.9164 (mmp) cc_final: 0.8875 (mmm) REVERT: H 568 TYR cc_start: 0.2410 (OUTLIER) cc_final: 0.2078 (m-80) REVERT: H 688 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.7919 (t0) REVERT: H 726 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7975 (mp0) REVERT: H 859 GLU cc_start: 0.9098 (tt0) cc_final: 0.8703 (tp30) REVERT: H 862 LYS cc_start: 0.9033 (mttt) cc_final: 0.8654 (mptt) REVERT: H 863 ARG cc_start: 0.8841 (ptt-90) cc_final: 0.8555 (ptt90) REVERT: H 909 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8079 (tm-30) REVERT: J 104 GLU cc_start: 0.8919 (tt0) cc_final: 0.8635 (tm-30) REVERT: J 106 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8705 (pt) REVERT: J 108 LYS cc_start: 0.9562 (mtpt) cc_final: 0.9167 (mmmt) outliers start: 74 outliers final: 59 residues processed: 306 average time/residue: 0.4119 time to fit residues: 204.8699 Evaluate side-chains 305 residues out of total 3163 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 236 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 397 LYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 209 HIS Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 688 ASP Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 787 ASP Chi-restraints excluded: chain H residue 792 GLN Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 136 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 8.9990 chunk 307 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 289 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 296 optimal weight: 40.0000 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 HIS ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.070003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.050254 restraints weight = 222699.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.051624 restraints weight = 120098.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.052460 restraints weight = 78280.425| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31893 Z= 0.194 Angle : 0.634 17.693 43577 Z= 0.317 Chirality : 0.040 0.243 4851 Planarity : 0.004 0.070 5228 Dihedral : 16.748 140.455 5138 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.31 % Allowed : 16.41 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.15), residues: 3550 helix: 1.51 (0.12), residues: 1771 sheet: -0.20 (0.28), residues: 391 loop : -0.10 (0.18), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 55 HIS 0.008 0.001 HIS I 320 PHE 0.041 0.001 PHE J 162 TYR 0.020 0.001 TYR A 95 ARG 0.014 0.000 ARG A 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6556.40 seconds wall clock time: 119 minutes 54.63 seconds (7194.63 seconds total)