Starting phenix.real_space_refine on Sat Feb 17 21:26:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4f_22667/02_2024/7k4f_22667_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4f_22667/02_2024/7k4f_22667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4f_22667/02_2024/7k4f_22667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4f_22667/02_2024/7k4f_22667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4f_22667/02_2024/7k4f_22667_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4f_22667/02_2024/7k4f_22667_neut_updated.pdb" } resolution = 3.75 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= 0.011 sd= 0.091 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 160 5.16 5 C 12855 2.51 5 N 3359 2.21 5 O 3485 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 224": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "B ARG 26": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "C ARG 26": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 350": "NH1" <-> "NH2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 636": "NH1" <-> "NH2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 224": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D ARG 350": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 615": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 636": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19875 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4931 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "B" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4931 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "C" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4931 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "D" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4931 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 26, 'TRANS': 587} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' CA': 1, '5GK': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'5GK': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'5GK': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'5GK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.54, per 1000 atoms: 0.53 Number of scatterers: 19875 At special positions: 0 Unit cell: (146.012, 146.012, 124.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 160 16.00 F 15 9.00 O 3485 8.00 N 3359 7.00 C 12855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.08 Conformation dependent library (CDL) restraints added in 3.5 seconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 4 sheets defined 54.1% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'A' and resid 28 through 43 removed outlier: 4.283A pdb=" N GLU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 58 through 65 removed outlier: 3.540A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.533A pdb=" N ALA A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.671A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 removed outlier: 4.169A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.862A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 166 through 172 Processing helix chain 'A' and resid 176 through 185 removed outlier: 3.694A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.511A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 223 removed outlier: 3.599A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.703A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.688A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.879A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 323 removed outlier: 3.534A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 4.102A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.990A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.528A pdb=" N PHE A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 409' Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 419 through 422 No H-bonds generated for 'chain 'A' and resid 419 through 422' Processing helix chain 'A' and resid 425 through 444 removed outlier: 4.436A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 464 removed outlier: 3.563A pdb=" N ASN A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 477 through 486 removed outlier: 3.636A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 509 removed outlier: 4.046A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 537 removed outlier: 5.090A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 566 removed outlier: 3.561A pdb=" N THR A 558 " --> pdb=" O MET A 554 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 583 removed outlier: 3.813A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 removed outlier: 3.845A pdb=" N ASP A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 4.283A pdb=" N GLU B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 58 through 65 removed outlier: 3.540A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 removed outlier: 3.534A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 101 removed outlier: 3.671A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 removed outlier: 4.170A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.862A pdb=" N ALA B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 176 through 185 removed outlier: 3.694A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.511A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 removed outlier: 3.598A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASP B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.703A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.688A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.880A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 323 removed outlier: 3.535A pdb=" N ARG B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 342 removed outlier: 4.102A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 348 Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.990A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.527A pdb=" N PHE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 409' Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 419 through 422 No H-bonds generated for 'chain 'B' and resid 419 through 422' Processing helix chain 'B' and resid 425 through 444 removed outlier: 4.435A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 464 removed outlier: 3.562A pdb=" N ASN B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 468 No H-bonds generated for 'chain 'B' and resid 466 through 468' Processing helix chain 'B' and resid 477 through 486 removed outlier: 3.636A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET B 485 " --> pdb=" O MET B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 509 removed outlier: 4.046A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 removed outlier: 5.089A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 566 removed outlier: 3.561A pdb=" N THR B 558 " --> pdb=" O MET B 554 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 583 removed outlier: 3.814A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 removed outlier: 3.844A pdb=" N ASP B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 43 removed outlier: 4.282A pdb=" N GLU C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 58 through 65 removed outlier: 3.540A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 removed outlier: 3.533A pdb=" N ALA C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 101 removed outlier: 3.671A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 removed outlier: 4.169A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.862A pdb=" N ALA C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 138 Processing helix chain 'C' and resid 166 through 172 Processing helix chain 'C' and resid 176 through 185 removed outlier: 3.694A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.511A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 223 removed outlier: 3.598A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.703A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.689A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.880A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 323 removed outlier: 3.535A pdb=" N ARG C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 4.101A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.990A pdb=" N ILE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.527A pdb=" N PHE C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 409' Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 419 through 422 No H-bonds generated for 'chain 'C' and resid 419 through 422' Processing helix chain 'C' and resid 425 through 444 removed outlier: 4.436A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 464 removed outlier: 3.562A pdb=" N ASN C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 468 No H-bonds generated for 'chain 'C' and resid 466 through 468' Processing helix chain 'C' and resid 477 through 486 removed outlier: 3.635A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 509 removed outlier: 4.046A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 505 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 537 removed outlier: 5.091A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 536 " --> pdb=" O SER C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 566 removed outlier: 3.561A pdb=" N THR C 558 " --> pdb=" O MET C 554 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 583 removed outlier: 3.813A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 3.845A pdb=" N ASP C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 591 " --> pdb=" O HIS C 587 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 43 removed outlier: 4.283A pdb=" N GLU D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.540A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 removed outlier: 3.533A pdb=" N ALA D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 removed outlier: 3.672A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 106 removed outlier: 4.169A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 120 through 126 removed outlier: 3.861A pdb=" N ALA D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 138 Processing helix chain 'D' and resid 166 through 172 Processing helix chain 'D' and resid 176 through 185 removed outlier: 3.695A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.511A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 223 removed outlier: 3.598A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 253 through 263 removed outlier: 3.702A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 removed outlier: 3.688A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.879A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 323 removed outlier: 3.535A pdb=" N ARG D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 342 removed outlier: 4.101A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 348 Processing helix chain 'D' and resid 382 through 401 removed outlier: 3.991A pdb=" N ILE D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 3.527A pdb=" N PHE D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 404 through 409' Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 419 through 422 No H-bonds generated for 'chain 'D' and resid 419 through 422' Processing helix chain 'D' and resid 425 through 444 removed outlier: 4.436A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET D 440 " --> pdb=" O VAL D 436 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 464 removed outlier: 3.563A pdb=" N ASN D 464 " --> pdb=" O LEU D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 468 No H-bonds generated for 'chain 'D' and resid 466 through 468' Processing helix chain 'D' and resid 477 through 486 removed outlier: 3.635A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET D 485 " --> pdb=" O MET D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 509 removed outlier: 4.046A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 502 " --> pdb=" O ALA D 498 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D 505 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 537 removed outlier: 5.091A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 536 " --> pdb=" O SER D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 566 removed outlier: 3.561A pdb=" N THR D 558 " --> pdb=" O MET D 554 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 583 removed outlier: 3.813A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 3.844A pdb=" N ASP D 590 " --> pdb=" O ALA D 586 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU D 591 " --> pdb=" O HIS D 587 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 273 through 278 removed outlier: 3.658A pdb=" N LEU A 631 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.658A pdb=" N LEU B 631 " --> pdb=" O TYR B 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.658A pdb=" N LEU C 631 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.658A pdb=" N LEU D 631 " --> pdb=" O TYR D 278 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.95 Time building geometry restraints manager: 7.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6162 1.34 - 1.45: 3606 1.45 - 1.57: 10291 1.57 - 1.69: 10 1.69 - 1.81: 272 Bond restraints: 20341 Sorted by residual: bond pdb=" C01 5GK A 702 " pdb=" O01 5GK A 702 " ideal model delta sigma weight residual 1.230 1.403 -0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" C01 5GK D 701 " pdb=" O01 5GK D 701 " ideal model delta sigma weight residual 1.230 1.393 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" C01 5GK C 701 " pdb=" O01 5GK C 701 " ideal model delta sigma weight residual 1.230 1.393 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" C01 5GK A 701 " pdb=" O01 5GK A 701 " ideal model delta sigma weight residual 1.230 1.392 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" C01 5GK B 701 " pdb=" O01 5GK B 701 " ideal model delta sigma weight residual 1.230 1.392 -0.162 2.00e-02 2.50e+03 6.55e+01 ... (remaining 20336 not shown) Histogram of bond angle deviations from ideal: 95.87 - 103.66: 323 103.66 - 111.45: 8289 111.45 - 119.24: 8450 119.24 - 127.03: 10258 127.03 - 134.82: 287 Bond angle restraints: 27607 Sorted by residual: angle pdb=" C ARG C 224 " pdb=" N HIS C 225 " pdb=" CA HIS C 225 " ideal model delta sigma weight residual 121.54 132.34 -10.80 1.91e+00 2.74e-01 3.20e+01 angle pdb=" C ARG B 224 " pdb=" N HIS B 225 " pdb=" CA HIS B 225 " ideal model delta sigma weight residual 121.54 132.29 -10.75 1.91e+00 2.74e-01 3.17e+01 angle pdb=" C ARG A 224 " pdb=" N HIS A 225 " pdb=" CA HIS A 225 " ideal model delta sigma weight residual 121.54 132.28 -10.74 1.91e+00 2.74e-01 3.16e+01 angle pdb=" C ARG D 224 " pdb=" N HIS D 225 " pdb=" CA HIS D 225 " ideal model delta sigma weight residual 121.54 132.28 -10.74 1.91e+00 2.74e-01 3.16e+01 angle pdb=" C TYR B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 ... (remaining 27602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 11248 16.73 - 33.47: 775 33.47 - 50.20: 208 50.20 - 66.94: 19 66.94 - 83.67: 9 Dihedral angle restraints: 12259 sinusoidal: 5075 harmonic: 7184 Sorted by residual: dihedral pdb=" CA SER D 361 " pdb=" C SER D 361 " pdb=" N PRO D 362 " pdb=" CA PRO D 362 " ideal model delta harmonic sigma weight residual -180.00 -121.57 -58.43 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA SER A 361 " pdb=" C SER A 361 " pdb=" N PRO A 362 " pdb=" CA PRO A 362 " ideal model delta harmonic sigma weight residual -180.00 -121.61 -58.39 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA SER C 361 " pdb=" C SER C 361 " pdb=" N PRO C 362 " pdb=" CA PRO C 362 " ideal model delta harmonic sigma weight residual -180.00 -121.65 -58.35 0 5.00e+00 4.00e-02 1.36e+02 ... (remaining 12256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2587 0.081 - 0.162: 460 0.162 - 0.243: 57 0.243 - 0.324: 13 0.324 - 0.405: 1 Chirality restraints: 3118 Sorted by residual: chirality pdb=" C14 5GK A 702 " pdb=" C13 5GK A 702 " pdb=" C15 5GK A 702 " pdb=" C22 5GK A 702 " both_signs ideal model delta sigma weight residual False -2.50 -2.90 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" C14 5GK A 701 " pdb=" C13 5GK A 701 " pdb=" C15 5GK A 701 " pdb=" C22 5GK A 701 " both_signs ideal model delta sigma weight residual False -2.50 -2.77 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CG LEU C 574 " pdb=" CB LEU C 574 " pdb=" CD1 LEU C 574 " pdb=" CD2 LEU C 574 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 3115 not shown) Planarity restraints: 3474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 526 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.98e+00 pdb=" N PRO B 527 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 526 " 0.053 5.00e-02 4.00e+02 7.90e-02 9.98e+00 pdb=" N PRO D 527 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO D 527 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 527 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 526 " 0.052 5.00e-02 4.00e+02 7.89e-02 9.97e+00 pdb=" N PRO A 527 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.045 5.00e-02 4.00e+02 ... (remaining 3471 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4266 2.76 - 3.30: 18642 3.30 - 3.83: 31330 3.83 - 4.37: 35817 4.37 - 4.90: 58331 Nonbonded interactions: 148386 Sorted by model distance: nonbonded pdb=" OG SER D 506 " pdb=" OH TYR D 526 " model vdw 2.231 2.440 nonbonded pdb=" OG SER A 506 " pdb=" OH TYR A 526 " model vdw 2.231 2.440 nonbonded pdb=" OG SER B 506 " pdb=" OH TYR B 526 " model vdw 2.232 2.440 nonbonded pdb=" OG SER C 506 " pdb=" OH TYR C 526 " model vdw 2.232 2.440 nonbonded pdb=" O ASP B 590 " pdb=" NH1 ARG B 594 " model vdw 2.305 2.520 ... (remaining 148381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 639 or resid 701)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.530 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 50.460 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.012 0.173 20341 Z= 0.773 Angle : 1.381 17.439 27607 Z= 0.683 Chirality : 0.065 0.405 3118 Planarity : 0.008 0.079 3474 Dihedral : 12.592 83.670 7619 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 1.50 % Allowed : 9.76 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -5.98 (0.12), residues: 2448 helix: -4.20 (0.07), residues: 1324 sheet: -3.72 (0.52), residues: 40 loop : -3.55 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 629 HIS 0.013 0.003 HIS B 201 PHE 0.027 0.003 PHE C 523 TYR 0.021 0.003 TYR B 328 ARG 0.008 0.001 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 788 time to evaluate : 2.393 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 68 GLU cc_start: 0.8083 (tt0) cc_final: 0.7865 (mm-30) REVERT: A 92 LEU cc_start: 0.9243 (tt) cc_final: 0.8863 (tt) REVERT: A 96 MET cc_start: 0.8731 (mtp) cc_final: 0.8169 (mtm) REVERT: A 113 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8301 (tm-30) REVERT: A 150 THR cc_start: 0.9275 (p) cc_final: 0.8701 (p) REVERT: A 167 LEU cc_start: 0.8857 (pt) cc_final: 0.8583 (tp) REVERT: A 177 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8492 (tm-30) REVERT: A 208 ASN cc_start: 0.8223 (t0) cc_final: 0.7871 (t0) REVERT: A 255 MET cc_start: 0.9371 (mmm) cc_final: 0.9146 (mmt) REVERT: A 306 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8848 (tm-30) REVERT: A 322 LYS cc_start: 0.9120 (tttt) cc_final: 0.8887 (ttmm) REVERT: A 331 MET cc_start: 0.7571 (mmp) cc_final: 0.7344 (tmm) REVERT: A 489 ASP cc_start: 0.8184 (m-30) cc_final: 0.7932 (m-30) REVERT: A 495 TRP cc_start: 0.8798 (m100) cc_final: 0.8540 (m100) REVERT: A 525 ASP cc_start: 0.8478 (t0) cc_final: 0.8262 (t70) REVERT: A 527 PRO cc_start: 0.9418 (Cg_exo) cc_final: 0.9173 (Cg_endo) REVERT: A 547 TYR cc_start: 0.9231 (m-10) cc_final: 0.8937 (m-10) REVERT: A 577 MET cc_start: 0.8873 (ptm) cc_final: 0.8459 (ptm) REVERT: A 622 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8051 (tp30) REVERT: B 92 LEU cc_start: 0.9159 (tt) cc_final: 0.8867 (tt) REVERT: B 96 MET cc_start: 0.8798 (mtp) cc_final: 0.8336 (mtm) REVERT: B 113 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8566 (tm-30) REVERT: B 128 GLN cc_start: 0.8091 (pt0) cc_final: 0.7783 (tm-30) REVERT: B 150 THR cc_start: 0.9188 (p) cc_final: 0.8809 (t) REVERT: B 177 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8543 (tm-30) REVERT: B 178 ILE cc_start: 0.9386 (mm) cc_final: 0.9171 (mm) REVERT: B 188 ASP cc_start: 0.8234 (t0) cc_final: 0.7842 (t0) REVERT: B 208 ASN cc_start: 0.8245 (t0) cc_final: 0.7859 (t0) REVERT: B 214 GLN cc_start: 0.9160 (tt0) cc_final: 0.8936 (tm-30) REVERT: B 294 GLU cc_start: 0.8365 (tt0) cc_final: 0.8154 (tt0) REVERT: B 300 LYS cc_start: 0.8319 (mttt) cc_final: 0.8066 (mttt) REVERT: B 322 LYS cc_start: 0.9126 (tttt) cc_final: 0.8852 (ttmm) REVERT: B 491 MET cc_start: 0.8249 (tpt) cc_final: 0.7994 (tpp) REVERT: B 527 PRO cc_start: 0.9344 (Cg_exo) cc_final: 0.9082 (Cg_endo) REVERT: B 622 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8139 (tp30) REVERT: C 113 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8416 (tm-30) REVERT: C 128 GLN cc_start: 0.8099 (pt0) cc_final: 0.7801 (tm-30) REVERT: C 150 THR cc_start: 0.9216 (p) cc_final: 0.8637 (p) REVERT: C 177 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8606 (tm-30) REVERT: C 178 ILE cc_start: 0.9415 (mm) cc_final: 0.9196 (mm) REVERT: C 188 ASP cc_start: 0.8181 (t0) cc_final: 0.7729 (t0) REVERT: C 208 ASN cc_start: 0.8332 (t0) cc_final: 0.7926 (t0) REVERT: C 214 GLN cc_start: 0.9174 (tt0) cc_final: 0.8954 (tm-30) REVERT: C 294 GLU cc_start: 0.8408 (tt0) cc_final: 0.8198 (tt0) REVERT: C 300 LYS cc_start: 0.8301 (mttt) cc_final: 0.8083 (mttt) REVERT: C 306 GLN cc_start: 0.9225 (tm-30) cc_final: 0.9010 (tm-30) REVERT: C 315 GLU cc_start: 0.9375 (mm-30) cc_final: 0.9130 (mm-30) REVERT: C 321 TRP cc_start: 0.8769 (t60) cc_final: 0.8386 (t-100) REVERT: C 322 LYS cc_start: 0.9156 (tttt) cc_final: 0.8861 (ttmm) REVERT: C 367 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8758 (tt) REVERT: C 489 ASP cc_start: 0.8097 (m-30) cc_final: 0.7715 (m-30) REVERT: C 527 PRO cc_start: 0.9394 (Cg_exo) cc_final: 0.9158 (Cg_endo) REVERT: C 528 MET cc_start: 0.9074 (tpt) cc_final: 0.8832 (tpp) REVERT: C 577 MET cc_start: 0.8897 (ptm) cc_final: 0.8180 (ptm) REVERT: C 622 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8015 (tp30) REVERT: D 96 MET cc_start: 0.8919 (mtp) cc_final: 0.8322 (mtp) REVERT: D 113 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8397 (tp30) REVERT: D 177 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8591 (tm-30) REVERT: D 208 ASN cc_start: 0.8618 (t0) cc_final: 0.8332 (t0) REVERT: D 259 LEU cc_start: 0.9248 (mt) cc_final: 0.8999 (mt) REVERT: D 264 LYS cc_start: 0.8320 (pttt) cc_final: 0.8098 (pttm) REVERT: D 294 GLU cc_start: 0.8639 (tt0) cc_final: 0.8383 (tt0) REVERT: D 306 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8531 (tm-30) REVERT: D 322 LYS cc_start: 0.9190 (tttt) cc_final: 0.8789 (ttmm) REVERT: D 345 MET cc_start: 0.8098 (tpp) cc_final: 0.7705 (mmt) REVERT: D 367 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8156 (tt) REVERT: D 377 TYR cc_start: 0.7055 (m-10) cc_final: 0.6817 (m-10) REVERT: D 382 ASP cc_start: 0.8366 (m-30) cc_final: 0.7923 (m-30) REVERT: D 473 GLN cc_start: 0.8696 (tp40) cc_final: 0.7790 (pm20) REVERT: D 525 ASP cc_start: 0.8344 (t0) cc_final: 0.8133 (t0) REVERT: D 528 MET cc_start: 0.9061 (tpt) cc_final: 0.8774 (tpp) REVERT: D 622 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7760 (tp30) REVERT: D 627 ASP cc_start: 0.8915 (m-30) cc_final: 0.8675 (m-30) outliers start: 32 outliers final: 6 residues processed: 805 average time/residue: 0.3155 time to fit residues: 380.3219 Evaluate side-chains 461 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 453 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 116 optimal weight: 0.3980 chunk 142 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 252 ASN ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN A 464 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 252 ASN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN B 464 ASN B 546 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 252 ASN ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 365 ASN C 546 ASN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN D 252 ASN ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN D 365 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20341 Z= 0.225 Angle : 0.823 10.874 27607 Z= 0.400 Chirality : 0.044 0.211 3118 Planarity : 0.006 0.063 3474 Dihedral : 7.529 49.610 2887 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.58 % Favored : 91.05 % Rotamer: Outliers : 5.68 % Allowed : 14.68 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -4.13 (0.14), residues: 2448 helix: -2.25 (0.11), residues: 1316 sheet: -1.36 (0.60), residues: 56 loop : -3.44 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 613 HIS 0.006 0.001 HIS C 582 PHE 0.014 0.001 PHE A 162 TYR 0.013 0.001 TYR D 67 ARG 0.004 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 543 time to evaluate : 2.386 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: A 68 GLU cc_start: 0.8175 (tt0) cc_final: 0.7868 (mm-30) REVERT: A 113 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8194 (tm-30) REVERT: A 150 THR cc_start: 0.9235 (p) cc_final: 0.8632 (p) REVERT: A 176 GLU cc_start: 0.8910 (pm20) cc_final: 0.7967 (pm20) REVERT: A 177 GLU cc_start: 0.9226 (mt-10) cc_final: 0.9000 (mp0) REVERT: A 195 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8778 (tm) REVERT: A 302 ARG cc_start: 0.7537 (tpm170) cc_final: 0.6513 (tpm170) REVERT: A 305 ARG cc_start: 0.8792 (ttm110) cc_final: 0.8096 (ttp80) REVERT: A 306 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8753 (tm-30) REVERT: A 322 LYS cc_start: 0.9145 (tttt) cc_final: 0.8885 (ttmm) REVERT: A 347 CYS cc_start: 0.8931 (t) cc_final: 0.8552 (t) REVERT: A 442 MET cc_start: 0.8935 (ttm) cc_final: 0.8533 (ttm) REVERT: A 489 ASP cc_start: 0.8285 (m-30) cc_final: 0.8039 (m-30) REVERT: A 536 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8899 (tt) REVERT: A 547 TYR cc_start: 0.9094 (m-10) cc_final: 0.8559 (m-10) REVERT: A 577 MET cc_start: 0.8599 (ptm) cc_final: 0.8198 (ptm) REVERT: A 583 TRP cc_start: 0.8789 (p-90) cc_final: 0.8560 (p-90) REVERT: A 605 GLU cc_start: 0.8743 (tt0) cc_final: 0.8016 (tt0) REVERT: A 622 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8072 (tp30) REVERT: B 113 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8303 (tm-30) REVERT: B 150 THR cc_start: 0.9184 (p) cc_final: 0.8674 (p) REVERT: B 177 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8487 (tm-30) REVERT: B 195 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8959 (tm) REVERT: B 214 GLN cc_start: 0.9157 (tt0) cc_final: 0.8748 (tm-30) REVERT: B 279 ASP cc_start: 0.7805 (t70) cc_final: 0.7253 (t70) REVERT: B 300 LYS cc_start: 0.8307 (mttt) cc_final: 0.8085 (mttt) REVERT: B 305 ARG cc_start: 0.8730 (ttm110) cc_final: 0.8233 (ttp80) REVERT: B 306 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8728 (tm-30) REVERT: B 321 TRP cc_start: 0.8748 (t60) cc_final: 0.8087 (t-100) REVERT: B 322 LYS cc_start: 0.9136 (tttt) cc_final: 0.8868 (ttmm) REVERT: B 345 MET cc_start: 0.8448 (tpp) cc_final: 0.8239 (mmt) REVERT: B 347 CYS cc_start: 0.9001 (t) cc_final: 0.8651 (t) REVERT: B 363 ARG cc_start: 0.7945 (mmt180) cc_final: 0.7239 (mmp80) REVERT: B 442 MET cc_start: 0.8884 (ttm) cc_final: 0.8494 (ttm) REVERT: B 536 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8891 (tt) REVERT: B 605 GLU cc_start: 0.8775 (tt0) cc_final: 0.8078 (tt0) REVERT: B 622 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8122 (tp30) REVERT: C 113 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8258 (tm-30) REVERT: C 128 GLN cc_start: 0.7879 (pt0) cc_final: 0.7627 (tm-30) REVERT: C 150 THR cc_start: 0.9210 (p) cc_final: 0.8688 (p) REVERT: C 177 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8537 (tm-30) REVERT: C 195 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8975 (tm) REVERT: C 270 TYR cc_start: 0.8789 (t80) cc_final: 0.8438 (t80) REVERT: C 279 ASP cc_start: 0.7867 (t70) cc_final: 0.7336 (t70) REVERT: C 294 GLU cc_start: 0.8355 (tt0) cc_final: 0.8119 (tt0) REVERT: C 300 LYS cc_start: 0.8258 (mttt) cc_final: 0.8021 (mttt) REVERT: C 305 ARG cc_start: 0.8655 (ttp80) cc_final: 0.8341 (ttp80) REVERT: C 306 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8843 (tm-30) REVERT: C 321 TRP cc_start: 0.8762 (t60) cc_final: 0.7936 (t-100) REVERT: C 322 LYS cc_start: 0.9134 (tttt) cc_final: 0.8854 (ttmm) REVERT: C 347 CYS cc_start: 0.9009 (t) cc_final: 0.8655 (t) REVERT: C 367 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8342 (tt) REVERT: C 442 MET cc_start: 0.8828 (ttm) cc_final: 0.8431 (ttm) REVERT: C 489 ASP cc_start: 0.8236 (m-30) cc_final: 0.8008 (m-30) REVERT: C 536 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9060 (tt) REVERT: C 618 ILE cc_start: 0.8605 (mp) cc_final: 0.8370 (pt) REVERT: C 622 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8002 (tp30) REVERT: D 107 PHE cc_start: 0.7967 (m-80) cc_final: 0.7732 (m-80) REVERT: D 208 ASN cc_start: 0.8340 (t0) cc_final: 0.7885 (t0) REVERT: D 279 ASP cc_start: 0.8405 (t0) cc_final: 0.8111 (t70) REVERT: D 294 GLU cc_start: 0.8556 (tt0) cc_final: 0.8261 (tt0) REVERT: D 306 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8451 (tm-30) REVERT: D 322 LYS cc_start: 0.9064 (tttt) cc_final: 0.8723 (ttmm) REVERT: D 345 MET cc_start: 0.8080 (tpp) cc_final: 0.7812 (mmt) REVERT: D 367 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7921 (tt) REVERT: D 442 MET cc_start: 0.8774 (mmm) cc_final: 0.8465 (ttm) REVERT: D 473 GLN cc_start: 0.8696 (tp40) cc_final: 0.7858 (pm20) REVERT: D 495 TRP cc_start: 0.8730 (m100) cc_final: 0.8486 (m100) REVERT: D 522 HIS cc_start: 0.9075 (OUTLIER) cc_final: 0.7513 (t-90) REVERT: D 528 MET cc_start: 0.9056 (tpt) cc_final: 0.8851 (tpp) REVERT: D 536 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8811 (tt) REVERT: D 578 MET cc_start: 0.9006 (ttm) cc_final: 0.8699 (mtm) REVERT: D 622 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7683 (tp30) outliers start: 121 outliers final: 45 residues processed: 621 average time/residue: 0.3289 time to fit residues: 321.6913 Evaluate side-chains 511 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 456 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 0.1980 chunk 184 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 221 optimal weight: 20.0000 chunk 239 optimal weight: 0.8980 chunk 197 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN B 118 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN D 74 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS D 546 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20341 Z= 0.180 Angle : 0.795 11.912 27607 Z= 0.370 Chirality : 0.043 0.205 3118 Planarity : 0.005 0.049 3474 Dihedral : 6.707 49.027 2879 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.86 % Favored : 90.85 % Rotamer: Outliers : 5.53 % Allowed : 19.42 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -3.18 (0.15), residues: 2448 helix: -1.27 (0.13), residues: 1352 sheet: -1.28 (0.61), residues: 56 loop : -3.33 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 321 HIS 0.006 0.001 HIS D 201 PHE 0.014 0.001 PHE A 107 TYR 0.016 0.001 TYR D 324 ARG 0.003 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 496 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8211 (tt0) cc_final: 0.7869 (mm-30) REVERT: A 113 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8274 (tm-30) REVERT: A 150 THR cc_start: 0.9257 (p) cc_final: 0.8755 (p) REVERT: A 176 GLU cc_start: 0.8950 (pm20) cc_final: 0.8126 (pm20) REVERT: A 195 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8797 (tm) REVERT: A 306 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8659 (tm-30) REVERT: A 322 LYS cc_start: 0.9158 (tttt) cc_final: 0.8893 (ttmm) REVERT: A 442 MET cc_start: 0.8820 (ttm) cc_final: 0.8442 (ttm) REVERT: A 489 ASP cc_start: 0.8337 (m-30) cc_final: 0.8123 (m-30) REVERT: A 536 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8840 (tt) REVERT: A 547 TYR cc_start: 0.8987 (m-10) cc_final: 0.8439 (m-10) REVERT: A 577 MET cc_start: 0.8549 (ptm) cc_final: 0.8264 (ptm) REVERT: A 622 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8049 (tp30) REVERT: B 99 MET cc_start: 0.8106 (mtp) cc_final: 0.7821 (mtm) REVERT: B 113 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8339 (tm-30) REVERT: B 150 THR cc_start: 0.9229 (p) cc_final: 0.8767 (p) REVERT: B 176 GLU cc_start: 0.8990 (pm20) cc_final: 0.8401 (pm20) REVERT: B 195 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8894 (tm) REVERT: B 227 ASP cc_start: 0.6484 (m-30) cc_final: 0.5781 (t70) REVERT: B 284 ASP cc_start: 0.8329 (t70) cc_final: 0.8083 (t0) REVERT: B 300 LYS cc_start: 0.8231 (mttt) cc_final: 0.7983 (mttt) REVERT: B 306 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8695 (tm-30) REVERT: B 321 TRP cc_start: 0.8707 (t60) cc_final: 0.8162 (t-100) REVERT: B 322 LYS cc_start: 0.9162 (tttt) cc_final: 0.8856 (ttmm) REVERT: B 363 ARG cc_start: 0.7901 (mmt180) cc_final: 0.7219 (mmp80) REVERT: B 442 MET cc_start: 0.8848 (ttm) cc_final: 0.8484 (ttm) REVERT: B 536 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8994 (tt) REVERT: B 605 GLU cc_start: 0.8775 (tt0) cc_final: 0.8132 (tt0) REVERT: B 622 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8013 (tp30) REVERT: C 71 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7224 (pmmt) REVERT: C 99 MET cc_start: 0.8106 (mtp) cc_final: 0.7845 (mtm) REVERT: C 113 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8494 (tp30) REVERT: C 177 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8559 (tm-30) REVERT: C 195 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8922 (tm) REVERT: C 270 TYR cc_start: 0.8690 (t80) cc_final: 0.8286 (t80) REVERT: C 279 ASP cc_start: 0.7860 (t70) cc_final: 0.7261 (t0) REVERT: C 284 ASP cc_start: 0.8338 (t70) cc_final: 0.7995 (t0) REVERT: C 305 ARG cc_start: 0.8531 (ttp80) cc_final: 0.8294 (ttp80) REVERT: C 306 GLN cc_start: 0.9239 (tm-30) cc_final: 0.8513 (tm-30) REVERT: C 321 TRP cc_start: 0.8737 (t60) cc_final: 0.8095 (t-100) REVERT: C 322 LYS cc_start: 0.9117 (tttt) cc_final: 0.8814 (ttmm) REVERT: C 326 ARG cc_start: 0.7759 (mtp180) cc_final: 0.7261 (ttm110) REVERT: C 367 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8171 (tt) REVERT: C 442 MET cc_start: 0.8838 (ttm) cc_final: 0.8473 (ttm) REVERT: C 536 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9022 (tt) REVERT: C 622 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7984 (tp30) REVERT: D 54 LYS cc_start: 0.8270 (tptp) cc_final: 0.7795 (tptp) REVERT: D 80 GLU cc_start: 0.8445 (pm20) cc_final: 0.8183 (pm20) REVERT: D 164 GLU cc_start: 0.8304 (mp0) cc_final: 0.7548 (mp0) REVERT: D 177 GLU cc_start: 0.9249 (mp0) cc_final: 0.8950 (mp0) REVERT: D 279 ASP cc_start: 0.8369 (t0) cc_final: 0.7996 (t0) REVERT: D 294 GLU cc_start: 0.8547 (tt0) cc_final: 0.8268 (tt0) REVERT: D 302 ARG cc_start: 0.7652 (tpm170) cc_final: 0.7306 (tpp-160) REVERT: D 306 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8362 (tm-30) REVERT: D 322 LYS cc_start: 0.9117 (tttt) cc_final: 0.8736 (ttmm) REVERT: D 345 MET cc_start: 0.8100 (tpp) cc_final: 0.7811 (mmt) REVERT: D 367 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.7977 (tt) REVERT: D 442 MET cc_start: 0.8899 (mmm) cc_final: 0.8625 (ttm) REVERT: D 473 GLN cc_start: 0.8728 (tp40) cc_final: 0.7883 (pm20) REVERT: D 522 HIS cc_start: 0.9014 (OUTLIER) cc_final: 0.7544 (t-90) REVERT: D 536 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8937 (tt) REVERT: D 622 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7633 (tp30) outliers start: 118 outliers final: 65 residues processed: 569 average time/residue: 0.2865 time to fit residues: 253.3057 Evaluate side-chains 525 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 449 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 342 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 149 optimal weight: 0.6980 chunk 222 optimal weight: 20.0000 chunk 235 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20341 Z= 0.206 Angle : 0.773 13.134 27607 Z= 0.359 Chirality : 0.042 0.202 3118 Planarity : 0.004 0.043 3474 Dihedral : 6.215 50.891 2877 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.50 % Favored : 91.26 % Rotamer: Outliers : 5.58 % Allowed : 21.34 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.57 (0.16), residues: 2448 helix: -0.62 (0.14), residues: 1352 sheet: -2.28 (0.52), residues: 76 loop : -3.21 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 613 HIS 0.005 0.001 HIS D 201 PHE 0.015 0.001 PHE D 107 TYR 0.018 0.001 TYR D 324 ARG 0.003 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 472 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8167 (tt0) cc_final: 0.7860 (mm-30) REVERT: A 113 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8424 (tm-30) REVERT: A 150 THR cc_start: 0.9275 (p) cc_final: 0.8869 (p) REVERT: A 176 GLU cc_start: 0.8807 (pm20) cc_final: 0.8607 (pm20) REVERT: A 195 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8841 (tm) REVERT: A 227 ASP cc_start: 0.6342 (m-30) cc_final: 0.5738 (t70) REVERT: A 239 GLN cc_start: 0.9465 (OUTLIER) cc_final: 0.9001 (tm-30) REVERT: A 279 ASP cc_start: 0.7915 (t0) cc_final: 0.7690 (t70) REVERT: A 306 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8626 (tm-30) REVERT: A 322 LYS cc_start: 0.9158 (tttt) cc_final: 0.8865 (ttmm) REVERT: A 440 MET cc_start: 0.8694 (ptm) cc_final: 0.8412 (tmm) REVERT: A 442 MET cc_start: 0.8843 (ttm) cc_final: 0.8519 (ttm) REVERT: A 450 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8531 (tm-30) REVERT: A 489 ASP cc_start: 0.8392 (m-30) cc_final: 0.8123 (m-30) REVERT: A 523 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8319 (p90) REVERT: A 536 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8855 (tt) REVERT: A 547 TYR cc_start: 0.9004 (m-10) cc_final: 0.8735 (m-10) REVERT: A 577 MET cc_start: 0.8613 (ptm) cc_final: 0.8231 (ptm) REVERT: A 605 GLU cc_start: 0.8739 (tt0) cc_final: 0.8371 (tt0) REVERT: A 622 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8054 (tp30) REVERT: B 67 TYR cc_start: 0.6456 (m-80) cc_final: 0.6256 (m-80) REVERT: B 71 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7103 (pmmt) REVERT: B 96 MET cc_start: 0.8394 (mtm) cc_final: 0.7885 (mmm) REVERT: B 113 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8413 (tm-30) REVERT: B 150 THR cc_start: 0.9242 (p) cc_final: 0.8817 (p) REVERT: B 195 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8922 (tm) REVERT: B 227 ASP cc_start: 0.6451 (m-30) cc_final: 0.5897 (t70) REVERT: B 239 GLN cc_start: 0.9515 (OUTLIER) cc_final: 0.8954 (tm-30) REVERT: B 279 ASP cc_start: 0.7783 (t70) cc_final: 0.7150 (t0) REVERT: B 306 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8638 (tm-30) REVERT: B 321 TRP cc_start: 0.8746 (t60) cc_final: 0.8064 (t-100) REVERT: B 322 LYS cc_start: 0.9147 (tttt) cc_final: 0.8847 (ttmm) REVERT: B 363 ARG cc_start: 0.7837 (mmt180) cc_final: 0.7186 (mmp80) REVERT: B 440 MET cc_start: 0.8706 (ptm) cc_final: 0.8401 (tmm) REVERT: B 442 MET cc_start: 0.8861 (ttm) cc_final: 0.8518 (ttm) REVERT: B 536 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8977 (tt) REVERT: B 622 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8006 (tp30) REVERT: C 113 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8531 (tm-30) REVERT: C 176 GLU cc_start: 0.9004 (pm20) cc_final: 0.8144 (pm20) REVERT: C 195 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8931 (tm) REVERT: C 239 GLN cc_start: 0.9507 (OUTLIER) cc_final: 0.9037 (tm-30) REVERT: C 261 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8414 (mm-40) REVERT: C 279 ASP cc_start: 0.7859 (t70) cc_final: 0.7249 (t0) REVERT: C 306 GLN cc_start: 0.9276 (tm-30) cc_final: 0.8491 (tm-30) REVERT: C 321 TRP cc_start: 0.8799 (t60) cc_final: 0.8062 (t-100) REVERT: C 322 LYS cc_start: 0.9117 (tttt) cc_final: 0.8820 (ttmm) REVERT: C 326 ARG cc_start: 0.7725 (mtp180) cc_final: 0.7170 (ttm110) REVERT: C 367 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8158 (tt) REVERT: C 434 PHE cc_start: 0.7929 (t80) cc_final: 0.7550 (m-80) REVERT: C 442 MET cc_start: 0.8842 (ttm) cc_final: 0.8512 (ttm) REVERT: C 518 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8827 (tt0) REVERT: C 547 TYR cc_start: 0.8810 (m-10) cc_final: 0.8523 (m-80) REVERT: C 622 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8011 (tp30) REVERT: D 71 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6886 (pmmt) REVERT: D 78 MET cc_start: 0.8073 (ptp) cc_final: 0.7723 (ptp) REVERT: D 164 GLU cc_start: 0.8287 (mp0) cc_final: 0.7545 (mp0) REVERT: D 177 GLU cc_start: 0.9265 (mp0) cc_final: 0.8900 (mp0) REVERT: D 239 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.8811 (tp40) REVERT: D 279 ASP cc_start: 0.8345 (t0) cc_final: 0.7748 (t0) REVERT: D 294 GLU cc_start: 0.8583 (tt0) cc_final: 0.8338 (tt0) REVERT: D 306 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8349 (tm-30) REVERT: D 322 LYS cc_start: 0.9151 (tttt) cc_final: 0.8757 (ttmm) REVERT: D 345 MET cc_start: 0.8167 (tpp) cc_final: 0.7882 (mmt) REVERT: D 367 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7959 (tt) REVERT: D 442 MET cc_start: 0.8875 (mmm) cc_final: 0.8673 (ttm) REVERT: D 522 HIS cc_start: 0.9031 (OUTLIER) cc_final: 0.7827 (t-90) REVERT: D 536 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8973 (tt) REVERT: D 546 ASN cc_start: 0.9301 (t0) cc_final: 0.9089 (t0) REVERT: D 622 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7679 (tp30) outliers start: 119 outliers final: 69 residues processed: 546 average time/residue: 0.2911 time to fit residues: 247.3599 Evaluate side-chains 527 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 440 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 201 optimal weight: 0.2980 chunk 163 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN ** D 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20341 Z= 0.174 Angle : 0.755 14.341 27607 Z= 0.347 Chirality : 0.042 0.213 3118 Planarity : 0.004 0.042 3474 Dihedral : 5.926 48.777 2877 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.78 % Favored : 91.14 % Rotamer: Outliers : 5.86 % Allowed : 22.33 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -2.14 (0.17), residues: 2448 helix: -0.21 (0.14), residues: 1352 sheet: -2.32 (0.53), residues: 76 loop : -3.10 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 613 HIS 0.006 0.001 HIS C 522 PHE 0.023 0.001 PHE A 553 TYR 0.036 0.001 TYR A 324 ARG 0.006 0.000 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 472 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8194 (tt0) cc_final: 0.7827 (mm-30) REVERT: A 113 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8514 (tm-30) REVERT: A 150 THR cc_start: 0.9308 (p) cc_final: 0.8958 (p) REVERT: A 176 GLU cc_start: 0.8816 (pm20) cc_final: 0.8493 (pm20) REVERT: A 195 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8791 (tm) REVERT: A 227 ASP cc_start: 0.6280 (m-30) cc_final: 0.5719 (t70) REVERT: A 239 GLN cc_start: 0.9451 (OUTLIER) cc_final: 0.9013 (tm-30) REVERT: A 279 ASP cc_start: 0.7984 (t0) cc_final: 0.7735 (t70) REVERT: A 306 GLN cc_start: 0.9144 (tm-30) cc_final: 0.8318 (tm-30) REVERT: A 321 TRP cc_start: 0.8719 (t60) cc_final: 0.8090 (t-100) REVERT: A 322 LYS cc_start: 0.9166 (tttt) cc_final: 0.8861 (ttmm) REVERT: A 440 MET cc_start: 0.8737 (ptm) cc_final: 0.8486 (tmm) REVERT: A 442 MET cc_start: 0.8816 (ttm) cc_final: 0.8500 (ttm) REVERT: A 450 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8501 (tm-30) REVERT: A 489 ASP cc_start: 0.8423 (m-30) cc_final: 0.8117 (m-30) REVERT: A 523 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8327 (p90) REVERT: A 536 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8800 (tt) REVERT: A 547 TYR cc_start: 0.9026 (m-10) cc_final: 0.8785 (m-10) REVERT: A 577 MET cc_start: 0.8639 (ptm) cc_final: 0.8223 (ptm) REVERT: A 605 GLU cc_start: 0.8720 (tt0) cc_final: 0.8306 (tt0) REVERT: A 622 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8041 (tp30) REVERT: B 40 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: B 67 TYR cc_start: 0.6430 (m-80) cc_final: 0.6150 (m-80) REVERT: B 71 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7128 (pmmt) REVERT: B 113 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8430 (tm-30) REVERT: B 150 THR cc_start: 0.9253 (p) cc_final: 0.8869 (p) REVERT: B 195 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8882 (tm) REVERT: B 227 ASP cc_start: 0.6402 (m-30) cc_final: 0.5897 (t70) REVERT: B 239 GLN cc_start: 0.9506 (OUTLIER) cc_final: 0.8994 (tm-30) REVERT: B 260 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8838 (tpp) REVERT: B 279 ASP cc_start: 0.7763 (t70) cc_final: 0.7112 (t0) REVERT: B 306 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8628 (tm-30) REVERT: B 321 TRP cc_start: 0.8760 (t60) cc_final: 0.8167 (t-100) REVERT: B 322 LYS cc_start: 0.9111 (tttt) cc_final: 0.8815 (ttmm) REVERT: B 326 ARG cc_start: 0.7673 (mtp180) cc_final: 0.7153 (ttm110) REVERT: B 363 ARG cc_start: 0.7790 (mmt180) cc_final: 0.7138 (mmp80) REVERT: B 440 MET cc_start: 0.8748 (ptm) cc_final: 0.8483 (tmm) REVERT: B 442 MET cc_start: 0.8833 (ttm) cc_final: 0.8503 (ttm) REVERT: B 536 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8830 (tt) REVERT: B 622 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8002 (tp30) REVERT: C 113 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8528 (tm-30) REVERT: C 195 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8939 (tm) REVERT: C 227 ASP cc_start: 0.6465 (m-30) cc_final: 0.5969 (t70) REVERT: C 239 GLN cc_start: 0.9488 (OUTLIER) cc_final: 0.9030 (tm-30) REVERT: C 261 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8373 (mm-40) REVERT: C 279 ASP cc_start: 0.7884 (t70) cc_final: 0.7257 (t0) REVERT: C 306 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8439 (tm-30) REVERT: C 321 TRP cc_start: 0.8780 (t60) cc_final: 0.8109 (t-100) REVERT: C 322 LYS cc_start: 0.9098 (tttt) cc_final: 0.8818 (ttmm) REVERT: C 326 ARG cc_start: 0.7686 (mtp180) cc_final: 0.7148 (ttm110) REVERT: C 367 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8158 (tt) REVERT: C 434 PHE cc_start: 0.7899 (t80) cc_final: 0.7548 (m-80) REVERT: C 442 MET cc_start: 0.8833 (ttm) cc_final: 0.8508 (ttm) REVERT: C 454 MET cc_start: 0.9079 (tpt) cc_final: 0.8877 (tpt) REVERT: C 518 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8826 (tt0) REVERT: C 536 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8964 (tt) REVERT: C 574 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8269 (tt) REVERT: C 577 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8904 (ttm) REVERT: C 622 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8002 (tp30) REVERT: D 40 GLN cc_start: 0.8792 (tt0) cc_final: 0.8588 (tt0) REVERT: D 54 LYS cc_start: 0.8411 (tptp) cc_final: 0.8081 (tptp) REVERT: D 72 VAL cc_start: 0.8546 (m) cc_final: 0.8332 (p) REVERT: D 164 GLU cc_start: 0.8247 (mp0) cc_final: 0.7606 (mp0) REVERT: D 177 GLU cc_start: 0.9268 (mp0) cc_final: 0.8902 (mp0) REVERT: D 239 GLN cc_start: 0.9337 (OUTLIER) cc_final: 0.8789 (tp40) REVERT: D 279 ASP cc_start: 0.8259 (t0) cc_final: 0.7676 (t0) REVERT: D 294 GLU cc_start: 0.8595 (tt0) cc_final: 0.8350 (tt0) REVERT: D 306 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8486 (tm-30) REVERT: D 322 LYS cc_start: 0.9113 (tttt) cc_final: 0.8688 (ttmm) REVERT: D 345 MET cc_start: 0.8078 (tpp) cc_final: 0.7835 (mmt) REVERT: D 367 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.7928 (tt) REVERT: D 454 MET cc_start: 0.8733 (tpt) cc_final: 0.8295 (tpt) REVERT: D 474 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7425 (ttp) REVERT: D 522 HIS cc_start: 0.9004 (OUTLIER) cc_final: 0.7757 (t-90) REVERT: D 536 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8951 (tt) REVERT: D 546 ASN cc_start: 0.9270 (t0) cc_final: 0.8935 (t0) REVERT: D 578 MET cc_start: 0.9049 (ttm) cc_final: 0.8786 (mtm) REVERT: D 622 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7689 (tp30) outliers start: 125 outliers final: 65 residues processed: 552 average time/residue: 0.2866 time to fit residues: 249.2686 Evaluate side-chains 527 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 439 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 577 MET Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 0.3980 chunk 212 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 236 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 118 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20341 Z= 0.292 Angle : 0.791 14.392 27607 Z= 0.371 Chirality : 0.044 0.212 3118 Planarity : 0.004 0.042 3474 Dihedral : 5.877 46.854 2877 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.33 % Favored : 89.58 % Rotamer: Outliers : 6.61 % Allowed : 22.19 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -1.91 (0.17), residues: 2448 helix: 0.00 (0.14), residues: 1352 sheet: -2.38 (0.53), residues: 76 loop : -3.01 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 268 HIS 0.006 0.001 HIS C 522 PHE 0.022 0.002 PHE A 553 TYR 0.019 0.002 TYR A 324 ARG 0.004 0.000 ARG B 305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 440 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8188 (tt0) cc_final: 0.7882 (mm-30) REVERT: A 113 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8542 (tm-30) REVERT: A 150 THR cc_start: 0.9278 (p) cc_final: 0.8943 (p) REVERT: A 164 GLU cc_start: 0.6537 (mt-10) cc_final: 0.6332 (mt-10) REVERT: A 176 GLU cc_start: 0.8994 (pm20) cc_final: 0.8785 (pm20) REVERT: A 227 ASP cc_start: 0.6383 (m-30) cc_final: 0.5705 (t70) REVERT: A 239 GLN cc_start: 0.9453 (OUTLIER) cc_final: 0.9035 (tm-30) REVERT: A 279 ASP cc_start: 0.8197 (t0) cc_final: 0.7931 (t0) REVERT: A 306 GLN cc_start: 0.9231 (tm-30) cc_final: 0.8413 (tm-30) REVERT: A 322 LYS cc_start: 0.9154 (tttt) cc_final: 0.8859 (ttmm) REVERT: A 440 MET cc_start: 0.8774 (ptm) cc_final: 0.8521 (tmm) REVERT: A 442 MET cc_start: 0.8835 (ttm) cc_final: 0.8504 (ttm) REVERT: A 489 ASP cc_start: 0.8466 (m-30) cc_final: 0.8026 (m-30) REVERT: A 536 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8829 (tt) REVERT: A 547 TYR cc_start: 0.9100 (m-10) cc_final: 0.8888 (m-10) REVERT: A 577 MET cc_start: 0.8791 (ptm) cc_final: 0.8228 (ptm) REVERT: A 622 GLU cc_start: 0.8588 (mm-30) cc_final: 0.7980 (tp30) REVERT: B 67 TYR cc_start: 0.6613 (m-80) cc_final: 0.6327 (m-80) REVERT: B 99 MET cc_start: 0.8248 (mtp) cc_final: 0.7996 (mtm) REVERT: B 113 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8466 (tm-30) REVERT: B 150 THR cc_start: 0.9233 (p) cc_final: 0.8805 (p) REVERT: B 176 GLU cc_start: 0.8749 (pm20) cc_final: 0.8467 (pm20) REVERT: B 195 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8977 (tm) REVERT: B 227 ASP cc_start: 0.6470 (m-30) cc_final: 0.5872 (t70) REVERT: B 239 GLN cc_start: 0.9498 (OUTLIER) cc_final: 0.8999 (tm-30) REVERT: B 279 ASP cc_start: 0.8032 (t70) cc_final: 0.7362 (t0) REVERT: B 303 GLU cc_start: 0.8665 (mp0) cc_final: 0.8453 (mp0) REVERT: B 306 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8672 (tm-30) REVERT: B 322 LYS cc_start: 0.9124 (tttt) cc_final: 0.8828 (ttmm) REVERT: B 363 ARG cc_start: 0.7792 (mmt180) cc_final: 0.7091 (mmp80) REVERT: B 440 MET cc_start: 0.8807 (ptm) cc_final: 0.8544 (tmm) REVERT: B 442 MET cc_start: 0.8850 (ttm) cc_final: 0.8529 (ttm) REVERT: B 536 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8851 (tt) REVERT: B 578 MET cc_start: 0.9063 (ttm) cc_final: 0.8755 (mtm) REVERT: B 622 GLU cc_start: 0.8648 (mm-30) cc_final: 0.7988 (tp30) REVERT: C 113 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8448 (tm-30) REVERT: C 195 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8988 (tm) REVERT: C 239 GLN cc_start: 0.9479 (OUTLIER) cc_final: 0.9058 (tm-30) REVERT: C 261 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8371 (mm-40) REVERT: C 279 ASP cc_start: 0.8041 (t70) cc_final: 0.7420 (t0) REVERT: C 306 GLN cc_start: 0.9341 (tm-30) cc_final: 0.8502 (tm-30) REVERT: C 322 LYS cc_start: 0.9099 (tttt) cc_final: 0.8826 (ttmm) REVERT: C 367 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8141 (tt) REVERT: C 434 PHE cc_start: 0.7970 (t80) cc_final: 0.7623 (m-80) REVERT: C 442 MET cc_start: 0.8860 (ttm) cc_final: 0.8546 (ttm) REVERT: C 519 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8122 (tt0) REVERT: C 522 HIS cc_start: 0.9185 (OUTLIER) cc_final: 0.7754 (t-90) REVERT: C 523 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8416 (p90) REVERT: C 536 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8867 (tt) REVERT: C 604 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8933 (tm) REVERT: C 622 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8024 (tp30) REVERT: D 40 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8385 (tt0) REVERT: D 54 LYS cc_start: 0.8538 (tptp) cc_final: 0.8043 (tptp) REVERT: D 71 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6888 (pmmt) REVERT: D 113 GLU cc_start: 0.8841 (tt0) cc_final: 0.7939 (tm-30) REVERT: D 177 GLU cc_start: 0.9262 (mp0) cc_final: 0.8939 (mp0) REVERT: D 208 ASN cc_start: 0.8049 (t0) cc_final: 0.7676 (t0) REVERT: D 215 MET cc_start: 0.8927 (ttp) cc_final: 0.8447 (tmm) REVERT: D 239 GLN cc_start: 0.9373 (OUTLIER) cc_final: 0.8467 (tm-30) REVERT: D 279 ASP cc_start: 0.8294 (t0) cc_final: 0.7711 (t0) REVERT: D 294 GLU cc_start: 0.8649 (tt0) cc_final: 0.8410 (tt0) REVERT: D 306 GLN cc_start: 0.9236 (tm-30) cc_final: 0.8389 (tm-30) REVERT: D 322 LYS cc_start: 0.9130 (tttt) cc_final: 0.8733 (ttmm) REVERT: D 326 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7495 (mtm-85) REVERT: D 345 MET cc_start: 0.8272 (tpp) cc_final: 0.7976 (mmt) REVERT: D 367 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7959 (tt) REVERT: D 474 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7553 (ttp) REVERT: D 495 TRP cc_start: 0.8832 (m100) cc_final: 0.8397 (m100) REVERT: D 522 HIS cc_start: 0.9206 (OUTLIER) cc_final: 0.7990 (t-90) REVERT: D 523 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8029 (p90) REVERT: D 536 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9003 (tt) REVERT: D 546 ASN cc_start: 0.9405 (t0) cc_final: 0.9067 (t0) REVERT: D 622 GLU cc_start: 0.8633 (mm-30) cc_final: 0.7727 (tp30) outliers start: 141 outliers final: 87 residues processed: 534 average time/residue: 0.3040 time to fit residues: 254.8257 Evaluate side-chains 529 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 420 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 522 HIS Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 198 optimal weight: 0.0170 chunk 131 optimal weight: 6.9990 chunk 235 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 overall best weight: 1.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20341 Z= 0.194 Angle : 0.761 15.648 27607 Z= 0.351 Chirality : 0.042 0.199 3118 Planarity : 0.004 0.040 3474 Dihedral : 5.705 47.028 2877 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.99 % Favored : 90.89 % Rotamer: Outliers : 5.91 % Allowed : 23.45 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -1.68 (0.17), residues: 2448 helix: 0.16 (0.14), residues: 1368 sheet: -1.47 (0.63), residues: 56 loop : -2.97 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 583 HIS 0.008 0.001 HIS C 522 PHE 0.021 0.001 PHE A 553 TYR 0.018 0.001 TYR A 216 ARG 0.006 0.000 ARG C 323 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 457 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8155 (tt0) cc_final: 0.7806 (mm-30) REVERT: A 113 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8564 (tm-30) REVERT: A 150 THR cc_start: 0.9314 (p) cc_final: 0.8980 (p) REVERT: A 176 GLU cc_start: 0.8964 (pm20) cc_final: 0.8752 (pm20) REVERT: A 211 PHE cc_start: 0.8716 (m-80) cc_final: 0.8429 (m-80) REVERT: A 227 ASP cc_start: 0.6362 (m-30) cc_final: 0.5722 (t70) REVERT: A 239 GLN cc_start: 0.9439 (OUTLIER) cc_final: 0.9084 (tm-30) REVERT: A 279 ASP cc_start: 0.8171 (t0) cc_final: 0.7942 (t0) REVERT: A 306 GLN cc_start: 0.9234 (tm-30) cc_final: 0.8390 (tm-30) REVERT: A 322 LYS cc_start: 0.9165 (tttt) cc_final: 0.8852 (ttmm) REVERT: A 440 MET cc_start: 0.8789 (ptm) cc_final: 0.8555 (tmm) REVERT: A 442 MET cc_start: 0.8801 (ttm) cc_final: 0.8486 (ttm) REVERT: A 450 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8441 (tm-30) REVERT: A 489 ASP cc_start: 0.8413 (m-30) cc_final: 0.8084 (m-30) REVERT: A 536 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8833 (tt) REVERT: A 547 TYR cc_start: 0.9054 (m-10) cc_final: 0.8804 (m-10) REVERT: A 574 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8063 (tt) REVERT: A 577 MET cc_start: 0.8802 (ptm) cc_final: 0.8321 (ptm) REVERT: A 622 GLU cc_start: 0.8564 (mm-30) cc_final: 0.7971 (tp30) REVERT: B 67 TYR cc_start: 0.6674 (m-80) cc_final: 0.6357 (m-80) REVERT: B 99 MET cc_start: 0.8282 (mtp) cc_final: 0.8038 (mtm) REVERT: B 113 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8491 (tm-30) REVERT: B 150 THR cc_start: 0.9236 (p) cc_final: 0.8850 (p) REVERT: B 195 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8958 (tm) REVERT: B 227 ASP cc_start: 0.6339 (m-30) cc_final: 0.5836 (t70) REVERT: B 239 GLN cc_start: 0.9468 (OUTLIER) cc_final: 0.9076 (tm-30) REVERT: B 279 ASP cc_start: 0.7977 (t70) cc_final: 0.7315 (t0) REVERT: B 294 GLU cc_start: 0.8284 (tt0) cc_final: 0.7632 (pt0) REVERT: B 303 GLU cc_start: 0.8636 (mp0) cc_final: 0.8428 (mp0) REVERT: B 306 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8635 (tm-30) REVERT: B 322 LYS cc_start: 0.9075 (tttt) cc_final: 0.8800 (ttmm) REVERT: B 363 ARG cc_start: 0.7719 (mmt180) cc_final: 0.7011 (mmp80) REVERT: B 440 MET cc_start: 0.8798 (ptm) cc_final: 0.8564 (tmm) REVERT: B 442 MET cc_start: 0.8814 (ttm) cc_final: 0.8491 (ttm) REVERT: B 536 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8873 (tt) REVERT: B 578 MET cc_start: 0.9118 (ttm) cc_final: 0.8716 (mtm) REVERT: B 605 GLU cc_start: 0.8774 (tt0) cc_final: 0.8198 (tt0) REVERT: B 622 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7973 (tp30) REVERT: C 113 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8445 (tm-30) REVERT: C 195 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8959 (tm) REVERT: C 239 GLN cc_start: 0.9442 (OUTLIER) cc_final: 0.9062 (tm-30) REVERT: C 268 TRP cc_start: 0.8969 (p-90) cc_final: 0.8759 (p-90) REVERT: C 279 ASP cc_start: 0.8025 (t70) cc_final: 0.7403 (t0) REVERT: C 306 GLN cc_start: 0.9281 (tm-30) cc_final: 0.8409 (tm-30) REVERT: C 321 TRP cc_start: 0.8820 (t60) cc_final: 0.8310 (t-100) REVERT: C 322 LYS cc_start: 0.9073 (tttt) cc_final: 0.8849 (ttmm) REVERT: C 367 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8080 (tt) REVERT: C 434 PHE cc_start: 0.7910 (t80) cc_final: 0.7586 (m-80) REVERT: C 442 MET cc_start: 0.8839 (ttm) cc_final: 0.8520 (ttm) REVERT: C 519 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: C 522 HIS cc_start: 0.9064 (OUTLIER) cc_final: 0.7757 (t-90) REVERT: C 523 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8510 (p90) REVERT: C 536 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8779 (tt) REVERT: C 578 MET cc_start: 0.9119 (ttm) cc_final: 0.8819 (mtm) REVERT: C 604 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8917 (tm) REVERT: C 622 GLU cc_start: 0.8552 (mm-30) cc_final: 0.7974 (tp30) REVERT: D 54 LYS cc_start: 0.8482 (tptp) cc_final: 0.7998 (tptp) REVERT: D 71 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6866 (pmmt) REVERT: D 113 GLU cc_start: 0.8837 (tt0) cc_final: 0.7945 (tm-30) REVERT: D 164 GLU cc_start: 0.8278 (mp0) cc_final: 0.7466 (mp0) REVERT: D 177 GLU cc_start: 0.9234 (mp0) cc_final: 0.8924 (mp0) REVERT: D 215 MET cc_start: 0.8930 (ttp) cc_final: 0.8466 (tmm) REVERT: D 239 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.8443 (tm-30) REVERT: D 270 TYR cc_start: 0.8625 (t80) cc_final: 0.8305 (t80) REVERT: D 279 ASP cc_start: 0.8240 (t0) cc_final: 0.7655 (t0) REVERT: D 294 GLU cc_start: 0.8619 (tt0) cc_final: 0.8390 (tt0) REVERT: D 306 GLN cc_start: 0.9208 (tm-30) cc_final: 0.8276 (tm-30) REVERT: D 322 LYS cc_start: 0.9117 (tttt) cc_final: 0.8720 (ttmm) REVERT: D 345 MET cc_start: 0.8221 (tpp) cc_final: 0.7999 (mmt) REVERT: D 367 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7968 (tt) REVERT: D 474 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7539 (ttp) REVERT: D 522 HIS cc_start: 0.9114 (OUTLIER) cc_final: 0.7788 (t-90) REVERT: D 536 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8956 (tt) REVERT: D 546 ASN cc_start: 0.9347 (t0) cc_final: 0.9015 (t0) REVERT: D 578 MET cc_start: 0.9021 (ttm) cc_final: 0.8767 (mtp) REVERT: D 622 GLU cc_start: 0.8602 (mm-30) cc_final: 0.7800 (tp30) outliers start: 126 outliers final: 72 residues processed: 539 average time/residue: 0.2852 time to fit residues: 239.2691 Evaluate side-chains 528 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 436 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 377 TYR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 522 HIS Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 140 optimal weight: 0.0870 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 160 optimal weight: 0.0670 chunk 116 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20341 Z= 0.183 Angle : 0.776 15.963 27607 Z= 0.354 Chirality : 0.042 0.210 3118 Planarity : 0.004 0.042 3474 Dihedral : 5.563 46.624 2877 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 5.21 % Allowed : 24.06 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -1.49 (0.17), residues: 2448 helix: 0.33 (0.14), residues: 1372 sheet: -1.39 (0.64), residues: 56 loop : -2.93 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 613 HIS 0.008 0.001 HIS B 582 PHE 0.027 0.001 PHE C 553 TYR 0.019 0.001 TYR A 467 ARG 0.009 0.000 ARG C 323 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 472 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8111 (tt0) cc_final: 0.7783 (mm-30) REVERT: A 113 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8610 (tm-30) REVERT: A 150 THR cc_start: 0.9319 (p) cc_final: 0.9011 (p) REVERT: A 176 GLU cc_start: 0.8971 (pm20) cc_final: 0.8756 (pm20) REVERT: A 211 PHE cc_start: 0.8699 (m-80) cc_final: 0.8401 (m-80) REVERT: A 227 ASP cc_start: 0.6295 (m-30) cc_final: 0.5664 (t70) REVERT: A 239 GLN cc_start: 0.9423 (OUTLIER) cc_final: 0.9121 (tm-30) REVERT: A 279 ASP cc_start: 0.8176 (t0) cc_final: 0.7947 (t0) REVERT: A 306 GLN cc_start: 0.9240 (tm-30) cc_final: 0.8544 (tm-30) REVERT: A 322 LYS cc_start: 0.9129 (tttt) cc_final: 0.8871 (ttmm) REVERT: A 442 MET cc_start: 0.8793 (ttm) cc_final: 0.8493 (ttm) REVERT: A 489 ASP cc_start: 0.8393 (m-30) cc_final: 0.8060 (m-30) REVERT: A 536 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8785 (tt) REVERT: A 547 TYR cc_start: 0.9065 (m-10) cc_final: 0.8824 (m-10) REVERT: A 577 MET cc_start: 0.8847 (ptm) cc_final: 0.8327 (ptm) REVERT: A 605 GLU cc_start: 0.8677 (tt0) cc_final: 0.8136 (tt0) REVERT: A 622 GLU cc_start: 0.8552 (mm-30) cc_final: 0.7942 (tp30) REVERT: B 67 TYR cc_start: 0.6692 (m-80) cc_final: 0.6337 (m-80) REVERT: B 96 MET cc_start: 0.8720 (mmm) cc_final: 0.8250 (mmt) REVERT: B 113 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8511 (tm-30) REVERT: B 150 THR cc_start: 0.9247 (p) cc_final: 0.8881 (p) REVERT: B 195 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8944 (tm) REVERT: B 227 ASP cc_start: 0.6282 (m-30) cc_final: 0.5764 (t70) REVERT: B 239 GLN cc_start: 0.9444 (OUTLIER) cc_final: 0.9096 (tm-30) REVERT: B 279 ASP cc_start: 0.7968 (t70) cc_final: 0.7328 (t0) REVERT: B 294 GLU cc_start: 0.8281 (tt0) cc_final: 0.7632 (pt0) REVERT: B 303 GLU cc_start: 0.8642 (mp0) cc_final: 0.8441 (mp0) REVERT: B 306 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8354 (tm-30) REVERT: B 322 LYS cc_start: 0.9018 (tttt) cc_final: 0.8765 (ttmm) REVERT: B 363 ARG cc_start: 0.7646 (mmt180) cc_final: 0.7087 (mmp80) REVERT: B 434 PHE cc_start: 0.7980 (t80) cc_final: 0.7604 (m-80) REVERT: B 440 MET cc_start: 0.8817 (ptm) cc_final: 0.8607 (tmm) REVERT: B 442 MET cc_start: 0.8816 (ttm) cc_final: 0.8499 (ttm) REVERT: B 578 MET cc_start: 0.9126 (ttm) cc_final: 0.8681 (mtm) REVERT: B 605 GLU cc_start: 0.8716 (tt0) cc_final: 0.8147 (tt0) REVERT: B 622 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7980 (tp30) REVERT: C 113 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8443 (tm-30) REVERT: C 195 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8943 (tm) REVERT: C 227 ASP cc_start: 0.6431 (m-30) cc_final: 0.5901 (t70) REVERT: C 239 GLN cc_start: 0.9418 (OUTLIER) cc_final: 0.9075 (tm-30) REVERT: C 261 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8349 (mm-40) REVERT: C 279 ASP cc_start: 0.8054 (t70) cc_final: 0.7416 (t0) REVERT: C 294 GLU cc_start: 0.8367 (tt0) cc_final: 0.7650 (pt0) REVERT: C 306 GLN cc_start: 0.9280 (tm-30) cc_final: 0.8397 (tm-30) REVERT: C 322 LYS cc_start: 0.8982 (tttt) cc_final: 0.8738 (ttmm) REVERT: C 367 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8057 (tt) REVERT: C 434 PHE cc_start: 0.7928 (t80) cc_final: 0.7605 (m-80) REVERT: C 442 MET cc_start: 0.8846 (ttm) cc_final: 0.8521 (ttm) REVERT: C 497 MET cc_start: 0.8988 (tpp) cc_final: 0.8495 (ttm) REVERT: C 519 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: C 522 HIS cc_start: 0.9077 (OUTLIER) cc_final: 0.7683 (t-90) REVERT: C 536 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8749 (tt) REVERT: C 604 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8925 (tm) REVERT: C 622 GLU cc_start: 0.8549 (mm-30) cc_final: 0.7968 (tp30) REVERT: D 54 LYS cc_start: 0.8524 (tptp) cc_final: 0.8038 (tptp) REVERT: D 71 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6871 (pmmt) REVERT: D 113 GLU cc_start: 0.8848 (tt0) cc_final: 0.8000 (tm-30) REVERT: D 177 GLU cc_start: 0.9200 (mp0) cc_final: 0.8838 (mp0) REVERT: D 178 ILE cc_start: 0.9424 (mm) cc_final: 0.9222 (tt) REVERT: D 215 MET cc_start: 0.8949 (ttp) cc_final: 0.8452 (tmm) REVERT: D 239 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.8453 (tm-30) REVERT: D 270 TYR cc_start: 0.8606 (t80) cc_final: 0.8366 (t80) REVERT: D 279 ASP cc_start: 0.8232 (t0) cc_final: 0.7649 (t0) REVERT: D 294 GLU cc_start: 0.8611 (tt0) cc_final: 0.8394 (tt0) REVERT: D 306 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8400 (tm-30) REVERT: D 322 LYS cc_start: 0.9106 (tttt) cc_final: 0.8716 (ttmm) REVERT: D 367 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7979 (tt) REVERT: D 522 HIS cc_start: 0.9113 (OUTLIER) cc_final: 0.7650 (t-90) REVERT: D 536 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8963 (tt) REVERT: D 546 ASN cc_start: 0.9326 (t0) cc_final: 0.8959 (t0) REVERT: D 622 GLU cc_start: 0.8569 (mm-30) cc_final: 0.7772 (tp30) outliers start: 111 outliers final: 71 residues processed: 541 average time/residue: 0.2861 time to fit residues: 242.3005 Evaluate side-chains 533 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 445 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 377 TYR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 522 HIS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.8980 chunk 225 optimal weight: 0.9990 chunk 205 optimal weight: 8.9990 chunk 219 optimal weight: 2.9990 chunk 131 optimal weight: 0.0980 chunk 95 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 218 optimal weight: 8.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20341 Z= 0.171 Angle : 0.784 16.568 27607 Z= 0.356 Chirality : 0.042 0.218 3118 Planarity : 0.004 0.041 3474 Dihedral : 5.423 47.430 2877 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.89 % Allowed : 26.17 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -1.37 (0.17), residues: 2448 helix: 0.41 (0.14), residues: 1376 sheet: -1.26 (0.66), residues: 56 loop : -2.85 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 268 HIS 0.014 0.001 HIS B 582 PHE 0.027 0.001 PHE B 553 TYR 0.017 0.001 TYR A 467 ARG 0.008 0.000 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 478 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8075 (tt0) cc_final: 0.7762 (mm-30) REVERT: A 113 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8612 (tm-30) REVERT: A 150 THR cc_start: 0.9310 (p) cc_final: 0.9055 (p) REVERT: A 176 GLU cc_start: 0.8965 (pm20) cc_final: 0.8741 (pm20) REVERT: A 211 PHE cc_start: 0.8653 (m-80) cc_final: 0.8345 (m-80) REVERT: A 227 ASP cc_start: 0.6184 (m-30) cc_final: 0.5650 (t70) REVERT: A 239 GLN cc_start: 0.9394 (OUTLIER) cc_final: 0.9135 (tm-30) REVERT: A 279 ASP cc_start: 0.8162 (t0) cc_final: 0.7938 (t0) REVERT: A 306 GLN cc_start: 0.9218 (tm-30) cc_final: 0.8512 (tm-30) REVERT: A 322 LYS cc_start: 0.9043 (tttt) cc_final: 0.8793 (ttmm) REVERT: A 434 PHE cc_start: 0.7954 (t80) cc_final: 0.7574 (m-80) REVERT: A 454 MET cc_start: 0.8925 (tpp) cc_final: 0.8722 (tpp) REVERT: A 489 ASP cc_start: 0.8355 (m-30) cc_final: 0.8105 (m-30) REVERT: A 547 TYR cc_start: 0.9051 (m-10) cc_final: 0.8812 (m-10) REVERT: A 577 MET cc_start: 0.8803 (ptm) cc_final: 0.8355 (ptm) REVERT: A 605 GLU cc_start: 0.8671 (tt0) cc_final: 0.8137 (tt0) REVERT: A 622 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7942 (tp30) REVERT: B 96 MET cc_start: 0.8749 (mmm) cc_final: 0.8244 (mmt) REVERT: B 113 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8512 (tm-30) REVERT: B 150 THR cc_start: 0.9246 (p) cc_final: 0.8911 (p) REVERT: B 195 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8884 (tm) REVERT: B 227 ASP cc_start: 0.6128 (m-30) cc_final: 0.5673 (t70) REVERT: B 239 GLN cc_start: 0.9416 (OUTLIER) cc_final: 0.9071 (tm-30) REVERT: B 279 ASP cc_start: 0.7962 (t70) cc_final: 0.7326 (t0) REVERT: B 306 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8488 (tm-30) REVERT: B 434 PHE cc_start: 0.7958 (t80) cc_final: 0.7602 (m-80) REVERT: B 442 MET cc_start: 0.8806 (ttm) cc_final: 0.8491 (ttm) REVERT: B 536 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8819 (tt) REVERT: B 578 MET cc_start: 0.9136 (ttm) cc_final: 0.8650 (mtm) REVERT: B 605 GLU cc_start: 0.8695 (tt0) cc_final: 0.8139 (tt0) REVERT: B 622 GLU cc_start: 0.8525 (mm-30) cc_final: 0.7959 (tp30) REVERT: C 113 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8423 (tm-30) REVERT: C 195 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8881 (tm) REVERT: C 227 ASP cc_start: 0.6446 (m-30) cc_final: 0.6002 (t70) REVERT: C 239 GLN cc_start: 0.9414 (OUTLIER) cc_final: 0.9115 (tm-30) REVERT: C 261 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8408 (mm110) REVERT: C 279 ASP cc_start: 0.7993 (t70) cc_final: 0.7355 (t0) REVERT: C 306 GLN cc_start: 0.9266 (tm-30) cc_final: 0.8566 (tm-30) REVERT: C 321 TRP cc_start: 0.8803 (t60) cc_final: 0.8231 (t-100) REVERT: C 322 LYS cc_start: 0.8893 (tttt) cc_final: 0.8677 (tppp) REVERT: C 367 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.7940 (tt) REVERT: C 434 PHE cc_start: 0.7905 (t80) cc_final: 0.7589 (m-80) REVERT: C 442 MET cc_start: 0.8859 (ttm) cc_final: 0.8526 (ttm) REVERT: C 519 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: C 522 HIS cc_start: 0.8984 (OUTLIER) cc_final: 0.7698 (t-90) REVERT: C 523 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8369 (p90) REVERT: C 536 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8829 (tt) REVERT: C 622 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7995 (tp30) REVERT: D 27 GLU cc_start: 0.8715 (tp30) cc_final: 0.8264 (pm20) REVERT: D 54 LYS cc_start: 0.8545 (tptp) cc_final: 0.8074 (tptp) REVERT: D 71 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6716 (pmmt) REVERT: D 113 GLU cc_start: 0.8837 (tt0) cc_final: 0.8024 (tm-30) REVERT: D 164 GLU cc_start: 0.7878 (mp0) cc_final: 0.7561 (pm20) REVERT: D 178 ILE cc_start: 0.9402 (mm) cc_final: 0.9191 (tt) REVERT: D 193 ASP cc_start: 0.7917 (m-30) cc_final: 0.7675 (m-30) REVERT: D 239 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.8417 (tm-30) REVERT: D 279 ASP cc_start: 0.8217 (t0) cc_final: 0.7627 (t0) REVERT: D 294 GLU cc_start: 0.8660 (tt0) cc_final: 0.8426 (tt0) REVERT: D 306 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8347 (tm-30) REVERT: D 322 LYS cc_start: 0.9071 (tttt) cc_final: 0.8681 (ttmm) REVERT: D 367 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7999 (tt) REVERT: D 522 HIS cc_start: 0.9055 (OUTLIER) cc_final: 0.7540 (t-90) REVERT: D 536 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8934 (tt) REVERT: D 622 GLU cc_start: 0.8571 (mm-30) cc_final: 0.7726 (tp30) outliers start: 83 outliers final: 57 residues processed: 536 average time/residue: 0.2827 time to fit residues: 237.8448 Evaluate side-chains 534 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 460 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 377 TYR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 522 HIS Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 243 optimal weight: 4.9990 chunk 223 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20341 Z= 0.213 Angle : 0.797 16.424 27607 Z= 0.365 Chirality : 0.043 0.242 3118 Planarity : 0.004 0.042 3474 Dihedral : 5.428 46.190 2877 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.40 % Favored : 90.56 % Rotamer: Outliers : 4.08 % Allowed : 26.55 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -1.25 (0.17), residues: 2448 helix: 0.57 (0.14), residues: 1352 sheet: -1.31 (0.65), residues: 56 loop : -2.82 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 268 HIS 0.009 0.001 HIS B 582 PHE 0.025 0.001 PHE A 523 TYR 0.017 0.001 TYR A 467 ARG 0.005 0.000 ARG C 323 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 458 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8077 (tt0) cc_final: 0.7756 (mm-30) REVERT: A 113 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8577 (tm-30) REVERT: A 150 THR cc_start: 0.9293 (p) cc_final: 0.8971 (p) REVERT: A 176 GLU cc_start: 0.8947 (pm20) cc_final: 0.8739 (pm20) REVERT: A 211 PHE cc_start: 0.8709 (m-80) cc_final: 0.8422 (m-80) REVERT: A 227 ASP cc_start: 0.6254 (m-30) cc_final: 0.5710 (t70) REVERT: A 239 GLN cc_start: 0.9385 (OUTLIER) cc_final: 0.9143 (tm-30) REVERT: A 279 ASP cc_start: 0.8170 (t0) cc_final: 0.7938 (t0) REVERT: A 306 GLN cc_start: 0.9249 (tm-30) cc_final: 0.8545 (tm-30) REVERT: A 489 ASP cc_start: 0.8436 (m-30) cc_final: 0.8031 (m-30) REVERT: A 547 TYR cc_start: 0.9073 (m-10) cc_final: 0.8860 (m-10) REVERT: A 577 MET cc_start: 0.8826 (ptm) cc_final: 0.8293 (ptm) REVERT: A 605 GLU cc_start: 0.8689 (tt0) cc_final: 0.8142 (tt0) REVERT: A 622 GLU cc_start: 0.8546 (mm-30) cc_final: 0.7946 (tp30) REVERT: B 99 MET cc_start: 0.8220 (mtp) cc_final: 0.7948 (mtm) REVERT: B 113 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8519 (tm-30) REVERT: B 150 THR cc_start: 0.9241 (p) cc_final: 0.8892 (p) REVERT: B 195 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8944 (tm) REVERT: B 227 ASP cc_start: 0.6245 (m-30) cc_final: 0.5704 (t70) REVERT: B 239 GLN cc_start: 0.9428 (OUTLIER) cc_final: 0.9091 (tm-30) REVERT: B 279 ASP cc_start: 0.8030 (t70) cc_final: 0.7380 (t0) REVERT: B 284 ASP cc_start: 0.8473 (t0) cc_final: 0.8256 (t0) REVERT: B 294 GLU cc_start: 0.8307 (tt0) cc_final: 0.7641 (pt0) REVERT: B 306 GLN cc_start: 0.9203 (tm-30) cc_final: 0.8384 (tm-30) REVERT: B 434 PHE cc_start: 0.7969 (t80) cc_final: 0.7596 (m-80) REVERT: B 442 MET cc_start: 0.8845 (ttm) cc_final: 0.8534 (ttm) REVERT: B 536 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8834 (tt) REVERT: B 578 MET cc_start: 0.9134 (ttm) cc_final: 0.8715 (mtm) REVERT: B 605 GLU cc_start: 0.8742 (tt0) cc_final: 0.8147 (tt0) REVERT: B 622 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7980 (tp30) REVERT: C 67 TYR cc_start: 0.6538 (m-80) cc_final: 0.6147 (m-80) REVERT: C 113 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8446 (tm-30) REVERT: C 195 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8888 (tm) REVERT: C 227 ASP cc_start: 0.6387 (m-30) cc_final: 0.5929 (t70) REVERT: C 239 GLN cc_start: 0.9412 (OUTLIER) cc_final: 0.9114 (tm-30) REVERT: C 261 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8408 (mm110) REVERT: C 279 ASP cc_start: 0.8034 (t70) cc_final: 0.7398 (t0) REVERT: C 306 GLN cc_start: 0.9298 (tm-30) cc_final: 0.8580 (tm-30) REVERT: C 321 TRP cc_start: 0.8819 (t60) cc_final: 0.8102 (t-100) REVERT: C 367 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.7987 (tt) REVERT: C 434 PHE cc_start: 0.7946 (t80) cc_final: 0.7606 (m-80) REVERT: C 442 MET cc_start: 0.8845 (ttm) cc_final: 0.8512 (ttm) REVERT: C 519 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: C 522 HIS cc_start: 0.9014 (OUTLIER) cc_final: 0.7710 (t-90) REVERT: C 523 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8457 (p90) REVERT: C 536 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8751 (tt) REVERT: C 578 MET cc_start: 0.8678 (mtm) cc_final: 0.8432 (mtm) REVERT: C 622 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8026 (tp30) REVERT: D 54 LYS cc_start: 0.8541 (tptp) cc_final: 0.8098 (tptp) REVERT: D 71 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6656 (pmmt) REVERT: D 113 GLU cc_start: 0.8844 (tt0) cc_final: 0.8065 (tm-30) REVERT: D 164 GLU cc_start: 0.7964 (mp0) cc_final: 0.7490 (pm20) REVERT: D 193 ASP cc_start: 0.7864 (m-30) cc_final: 0.7559 (m-30) REVERT: D 208 ASN cc_start: 0.7906 (t0) cc_final: 0.7596 (t0) REVERT: D 234 LEU cc_start: 0.8874 (mt) cc_final: 0.8663 (mm) REVERT: D 239 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.8439 (tm-30) REVERT: D 279 ASP cc_start: 0.8228 (t0) cc_final: 0.7635 (t0) REVERT: D 294 GLU cc_start: 0.8705 (tt0) cc_final: 0.8473 (tt0) REVERT: D 306 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8383 (tm-30) REVERT: D 322 LYS cc_start: 0.9064 (tttt) cc_final: 0.8693 (ttmm) REVERT: D 367 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8042 (tt) REVERT: D 522 HIS cc_start: 0.9153 (OUTLIER) cc_final: 0.7699 (t-90) REVERT: D 536 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8959 (tt) REVERT: D 622 GLU cc_start: 0.8590 (mm-30) cc_final: 0.7811 (tp30) outliers start: 87 outliers final: 61 residues processed: 520 average time/residue: 0.3265 time to fit residues: 270.2054 Evaluate side-chains 527 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 449 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain B residue 45 TRP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 377 TYR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 522 HIS Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 522 HIS Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 604 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 199 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101727 restraints weight = 37356.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104844 restraints weight = 18630.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106979 restraints weight = 11650.117| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20341 Z= 0.313 Angle : 0.855 16.406 27607 Z= 0.398 Chirality : 0.046 0.231 3118 Planarity : 0.004 0.041 3474 Dihedral : 5.739 46.596 2877 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.95 % Favored : 88.93 % Rotamer: Outliers : 4.50 % Allowed : 26.08 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: -1.31 (0.17), residues: 2448 helix: 0.47 (0.14), residues: 1372 sheet: -1.19 (0.58), residues: 64 loop : -2.83 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 268 HIS 0.008 0.001 HIS B 582 PHE 0.027 0.002 PHE A 523 TYR 0.019 0.002 TYR C 216 ARG 0.006 0.000 ARG D 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5102.38 seconds wall clock time: 92 minutes 21.46 seconds (5541.46 seconds total)