Starting phenix.real_space_refine on Wed Apr 10 08:30:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo8_7120/04_2024/6bo8_7120.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo8_7120/04_2024/6bo8_7120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo8_7120/04_2024/6bo8_7120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo8_7120/04_2024/6bo8_7120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo8_7120/04_2024/6bo8_7120.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo8_7120/04_2024/6bo8_7120.pdb" } resolution = 3.6 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= 0.001 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 12304 2.51 5 N 3220 2.21 5 O 3368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 621": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 621": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C ARG 589": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 621": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 589": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 621": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19048 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "B" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "C" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Chain: "D" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Time building chain proxies: 9.70, per 1000 atoms: 0.51 Number of scatterers: 19048 At special positions: 0 Unit cell: (136.22, 136.22, 125.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 3368 8.00 N 3220 7.00 C 12304 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: 7.21 Conformation dependent library (CDL) restraints added in 3.5 seconds 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 62.6% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 4.014A pdb=" N ARG A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.569A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.553A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.646A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.755A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.528A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 222 removed outlier: 4.024A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.686A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.638A pdb=" N HIS A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.546A pdb=" N LEU A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.797A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.530A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 346 Processing helix chain 'A' and resid 380 through 403 removed outlier: 3.557A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 445 Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.774A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 460 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.685A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 493 through 512 removed outlier: 3.861A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.189A pdb=" N PHE A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.803A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 568 removed outlier: 4.009A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 587 Processing helix chain 'A' and resid 588 through 606 removed outlier: 3.559A pdb=" N LEU A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 47 removed outlier: 4.013A pdb=" N ARG B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.569A pdb=" N ASP B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 66 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.553A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.647A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.754A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.528A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 222 removed outlier: 4.023A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.687A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.636A pdb=" N HIS B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.546A pdb=" N LEU B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.797A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.531A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 346 Processing helix chain 'B' and resid 380 through 403 removed outlier: 3.556A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 445 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.774A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 460 " --> pdb=" O PHE B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.684A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 489 through 492 Processing helix chain 'B' and resid 493 through 512 removed outlier: 3.861A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 4.190A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 524' Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.802A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 568 removed outlier: 4.010A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 587 Processing helix chain 'B' and resid 588 through 606 removed outlier: 3.560A pdb=" N LEU B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 47 removed outlier: 4.014A pdb=" N ARG C 33 " --> pdb=" O TRP C 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.570A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.553A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.646A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.755A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.527A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 222 removed outlier: 4.023A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.688A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.638A pdb=" N HIS C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.546A pdb=" N LEU C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.796A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.530A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 346 Processing helix chain 'C' and resid 380 through 403 removed outlier: 3.556A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 445 Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.774A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 460 " --> pdb=" O PHE C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.684A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 489 through 492 Processing helix chain 'C' and resid 493 through 512 removed outlier: 3.861A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 4.189A pdb=" N PHE C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 524' Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.802A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 568 removed outlier: 4.009A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 568 " --> pdb=" O ILE C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 587 Processing helix chain 'C' and resid 588 through 606 removed outlier: 3.559A pdb=" N LEU C 592 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 47 removed outlier: 4.014A pdb=" N ARG D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN D 40 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.569A pdb=" N ASP D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.553A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.646A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.754A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.528A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 222 removed outlier: 4.024A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.687A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.637A pdb=" N HIS D 258 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.547A pdb=" N LEU D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 309 removed outlier: 3.796A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.530A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 346 Processing helix chain 'D' and resid 380 through 403 removed outlier: 3.557A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 445 Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.775A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 460 " --> pdb=" O PHE D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.684A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 489 through 492 Processing helix chain 'D' and resid 493 through 512 removed outlier: 3.861A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 4.189A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR D 524 " --> pdb=" O GLY D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 524' Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.802A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 568 removed outlier: 4.009A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 568 " --> pdb=" O ILE D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 587 Processing helix chain 'D' and resid 588 through 606 removed outlier: 3.560A pdb=" N LEU D 592 " --> pdb=" O GLU D 588 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 removed outlier: 3.526A pdb=" N THR A 276 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 270 removed outlier: 3.526A pdb=" N THR B 276 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 270 removed outlier: 3.526A pdb=" N THR C 276 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 269 through 270 removed outlier: 3.526A pdb=" N THR D 276 " --> pdb=" O VAL D 633 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2532 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: 5.90 Time building geometry restraints manager: 7.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5464 1.33 - 1.45: 3323 1.45 - 1.57: 10433 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 19484 Sorted by residual: bond pdb=" CA VAL C 452 " pdb=" CB VAL C 452 " ideal model delta sigma weight residual 1.534 1.550 -0.015 6.80e-03 2.16e+04 4.97e+00 bond pdb=" CA VAL A 452 " pdb=" CB VAL A 452 " ideal model delta sigma weight residual 1.534 1.550 -0.015 6.80e-03 2.16e+04 4.93e+00 bond pdb=" CA VAL D 452 " pdb=" CB VAL D 452 " ideal model delta sigma weight residual 1.534 1.549 -0.015 6.80e-03 2.16e+04 4.69e+00 bond pdb=" CA HIS C 265 " pdb=" CB HIS C 265 " ideal model delta sigma weight residual 1.522 1.494 0.027 1.27e-02 6.20e+03 4.63e+00 bond pdb=" CA VAL B 452 " pdb=" CB VAL B 452 " ideal model delta sigma weight residual 1.534 1.549 -0.015 6.80e-03 2.16e+04 4.63e+00 ... (remaining 19479 not shown) Histogram of bond angle deviations from ideal: 97.76 - 105.13: 423 105.13 - 112.51: 10061 112.51 - 119.88: 7131 119.88 - 127.26: 8556 127.26 - 134.63: 269 Bond angle restraints: 26440 Sorted by residual: angle pdb=" N LEU D 352 " pdb=" CA LEU D 352 " pdb=" C LEU D 352 " ideal model delta sigma weight residual 110.91 118.03 -7.12 1.17e+00 7.31e-01 3.70e+01 angle pdb=" N LEU A 352 " pdb=" CA LEU A 352 " pdb=" C LEU A 352 " ideal model delta sigma weight residual 110.91 118.03 -7.12 1.17e+00 7.31e-01 3.70e+01 angle pdb=" N LEU C 352 " pdb=" CA LEU C 352 " pdb=" C LEU C 352 " ideal model delta sigma weight residual 110.91 118.00 -7.09 1.17e+00 7.31e-01 3.67e+01 angle pdb=" N LEU B 352 " pdb=" CA LEU B 352 " pdb=" C LEU B 352 " ideal model delta sigma weight residual 110.91 117.99 -7.08 1.17e+00 7.31e-01 3.67e+01 angle pdb=" N SER D 112 " pdb=" CA SER D 112 " pdb=" C SER D 112 " ideal model delta sigma weight residual 108.79 117.52 -8.73 1.53e+00 4.27e-01 3.26e+01 ... (remaining 26435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 10858 15.42 - 30.85: 657 30.85 - 46.27: 157 46.27 - 61.69: 4 61.69 - 77.11: 12 Dihedral angle restraints: 11688 sinusoidal: 4728 harmonic: 6960 Sorted by residual: dihedral pdb=" CA ASP B 223 " pdb=" C ASP B 223 " pdb=" N ARG B 224 " pdb=" CA ARG B 224 " ideal model delta harmonic sigma weight residual -180.00 -149.04 -30.96 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA ASP A 223 " pdb=" C ASP A 223 " pdb=" N ARG A 224 " pdb=" CA ARG A 224 " ideal model delta harmonic sigma weight residual -180.00 -149.11 -30.89 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA ASP D 223 " pdb=" C ASP D 223 " pdb=" N ARG D 224 " pdb=" CA ARG D 224 " ideal model delta harmonic sigma weight residual -180.00 -149.11 -30.89 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 11685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2014 0.051 - 0.103: 827 0.103 - 0.154: 141 0.154 - 0.205: 19 0.205 - 0.256: 11 Chirality restraints: 3012 Sorted by residual: chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA THR B 311 " pdb=" N THR B 311 " pdb=" C THR B 311 " pdb=" CB THR B 311 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA THR D 311 " pdb=" N THR D 311 " pdb=" C THR D 311 " pdb=" CB THR D 311 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 3009 not shown) Planarity restraints: 3336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 223 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C ASP D 223 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP D 223 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG D 224 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 223 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C ASP C 223 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP C 223 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG C 224 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 223 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C ASP A 223 " 0.044 2.00e-02 2.50e+03 pdb=" O ASP A 223 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 224 " -0.015 2.00e-02 2.50e+03 ... (remaining 3333 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5470 2.81 - 3.33: 19064 3.33 - 3.85: 31397 3.85 - 4.38: 37260 4.38 - 4.90: 60177 Nonbonded interactions: 153368 Sorted by model distance: nonbonded pdb=" OH TYR B 161 " pdb=" OD2 ASP B 193 " model vdw 2.286 2.440 nonbonded pdb=" OH TYR A 161 " pdb=" OD2 ASP A 193 " model vdw 2.286 2.440 nonbonded pdb=" OH TYR D 161 " pdb=" OD2 ASP D 193 " model vdw 2.286 2.440 nonbonded pdb=" OH TYR C 161 " pdb=" OD2 ASP C 193 " model vdw 2.286 2.440 nonbonded pdb=" OH TYR D 339 " pdb=" O THR D 392 " model vdw 2.310 2.440 ... (remaining 153363 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' 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: 0.350 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: 0.010 Extract box with map and model: 2.940 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 49.230 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 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 : 0.008 0.065 19484 Z= 0.490 Angle : 1.192 18.330 26440 Z= 0.668 Chirality : 0.055 0.256 3012 Planarity : 0.007 0.049 3336 Dihedral : 10.831 77.114 7184 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 0.97 % Allowed : 2.13 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.49 (0.14), residues: 2356 helix: -2.68 (0.10), residues: 1344 sheet: -5.00 (0.44), residues: 56 loop : -3.13 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP D 629 HIS 0.017 0.003 HIS A 522 PHE 0.029 0.003 PHE D 169 TYR 0.026 0.003 TYR C 547 ARG 0.007 0.001 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 759 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 CYS cc_start: 0.7568 (m) cc_final: 0.6918 (p) REVERT: A 183 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7377 (mm) REVERT: A 246 LEU cc_start: 0.6794 (tp) cc_final: 0.6588 (tp) REVERT: A 252 ASN cc_start: 0.6715 (t0) cc_final: 0.6322 (t0) REVERT: A 262 LYS cc_start: 0.8358 (tptp) cc_final: 0.7767 (mttt) REVERT: A 382 ASP cc_start: 0.7143 (m-30) cc_final: 0.6723 (m-30) REVERT: A 383 ASP cc_start: 0.8301 (m-30) cc_final: 0.7916 (t0) REVERT: A 435 MET cc_start: 0.6735 (mmt) cc_final: 0.6409 (mmt) REVERT: A 464 ASN cc_start: 0.6570 (t160) cc_final: 0.6253 (m-40) REVERT: A 487 PHE cc_start: 0.7586 (m-80) cc_final: 0.7338 (m-10) REVERT: A 527 PRO cc_start: 0.8595 (Cg_exo) cc_final: 0.8103 (Cg_endo) REVERT: A 550 ASP cc_start: 0.8049 (t0) cc_final: 0.7022 (p0) REVERT: A 580 ASP cc_start: 0.6486 (t0) cc_final: 0.6159 (m-30) REVERT: A 590 ASP cc_start: 0.7360 (m-30) cc_final: 0.6874 (t0) REVERT: A 628 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7817 (mtp-110) REVERT: A 630 PHE cc_start: 0.6910 (m-80) cc_final: 0.6499 (m-80) REVERT: B 40 GLN cc_start: 0.7590 (tt0) cc_final: 0.7276 (tt0) REVERT: B 78 MET cc_start: 0.7142 (pmt) cc_final: 0.6848 (pmm) REVERT: B 80 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8255 (mt-10) REVERT: B 97 VAL cc_start: 0.8799 (t) cc_final: 0.8574 (t) REVERT: B 106 VAL cc_start: 0.8541 (t) cc_final: 0.8317 (p) REVERT: B 176 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7981 (mp0) REVERT: B 183 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7285 (mm) REVERT: B 235 VAL cc_start: 0.7909 (t) cc_final: 0.7603 (m) REVERT: B 252 ASN cc_start: 0.6490 (t0) cc_final: 0.6118 (t0) REVERT: B 262 LYS cc_start: 0.8342 (tptp) cc_final: 0.7816 (mttt) REVERT: B 328 TYR cc_start: 0.6103 (m-10) cc_final: 0.5805 (m-10) REVERT: B 332 LEU cc_start: 0.6211 (tp) cc_final: 0.5993 (mt) REVERT: B 435 MET cc_start: 0.6695 (mmt) cc_final: 0.6441 (mmt) REVERT: B 450 GLU cc_start: 0.6692 (pt0) cc_final: 0.6366 (pt0) REVERT: B 527 PRO cc_start: 0.8627 (Cg_exo) cc_final: 0.8212 (Cg_endo) REVERT: B 550 ASP cc_start: 0.7753 (t0) cc_final: 0.6641 (p0) REVERT: B 588 GLU cc_start: 0.7042 (pt0) cc_final: 0.6836 (pt0) REVERT: B 590 ASP cc_start: 0.6970 (m-30) cc_final: 0.6519 (t0) REVERT: B 628 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7660 (mtp-110) REVERT: B 630 PHE cc_start: 0.6582 (m-80) cc_final: 0.6141 (m-80) REVERT: C 40 GLN cc_start: 0.7669 (tt0) cc_final: 0.7412 (tt0) REVERT: C 78 MET cc_start: 0.7233 (pmt) cc_final: 0.6951 (pmm) REVERT: C 80 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8118 (mt-10) REVERT: C 97 VAL cc_start: 0.8824 (t) cc_final: 0.8596 (t) REVERT: C 160 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7906 (pp) REVERT: C 176 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8041 (mp0) REVERT: C 183 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7759 (mp) REVERT: C 202 ILE cc_start: 0.8042 (mm) cc_final: 0.7798 (mm) REVERT: C 214 GLN cc_start: 0.7430 (tt0) cc_final: 0.7115 (tm-30) REVERT: C 217 ASN cc_start: 0.7381 (m-40) cc_final: 0.6998 (m-40) REVERT: C 235 VAL cc_start: 0.8006 (t) cc_final: 0.7606 (m) REVERT: C 252 ASN cc_start: 0.6847 (t0) cc_final: 0.6589 (t0) REVERT: C 262 LYS cc_start: 0.8013 (tptp) cc_final: 0.7402 (mttt) REVERT: C 331 MET cc_start: 0.6016 (tmm) cc_final: 0.5798 (tmm) REVERT: C 435 MET cc_start: 0.6241 (mmt) cc_final: 0.5944 (mmt) REVERT: C 467 TYR cc_start: 0.7290 (t80) cc_final: 0.7081 (t80) REVERT: C 474 MET cc_start: 0.6346 (mmm) cc_final: 0.5995 (ptt) REVERT: C 482 ILE cc_start: 0.6419 (mm) cc_final: 0.6081 (mt) REVERT: C 550 ASP cc_start: 0.7377 (t0) cc_final: 0.6600 (p0) REVERT: C 565 ILE cc_start: 0.7459 (tp) cc_final: 0.7019 (mm) REVERT: C 580 ASP cc_start: 0.6441 (t0) cc_final: 0.5967 (m-30) REVERT: C 583 TRP cc_start: 0.6997 (t60) cc_final: 0.6172 (t60) REVERT: C 591 GLU cc_start: 0.6536 (tt0) cc_final: 0.6220 (tp30) REVERT: C 630 PHE cc_start: 0.6519 (m-80) cc_final: 0.6299 (m-80) REVERT: D 44 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7305 (mp) REVERT: D 78 MET cc_start: 0.7339 (pmt) cc_final: 0.7104 (pmm) REVERT: D 157 CYS cc_start: 0.7881 (m) cc_final: 0.7281 (p) REVERT: D 183 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7650 (mm) REVERT: D 214 GLN cc_start: 0.7416 (tt0) cc_final: 0.7033 (tm-30) REVERT: D 252 ASN cc_start: 0.6554 (t0) cc_final: 0.6155 (t0) REVERT: D 262 LYS cc_start: 0.8305 (tptp) cc_final: 0.7648 (mttt) REVERT: D 265 HIS cc_start: 0.6581 (t70) cc_final: 0.6369 (t70) REVERT: D 328 TYR cc_start: 0.6045 (m-10) cc_final: 0.5785 (m-10) REVERT: D 384 ILE cc_start: 0.7764 (mt) cc_final: 0.7527 (mp) REVERT: D 464 ASN cc_start: 0.6722 (t160) cc_final: 0.6374 (t0) REVERT: D 487 PHE cc_start: 0.7493 (m-80) cc_final: 0.7250 (m-10) REVERT: D 550 ASP cc_start: 0.7811 (t0) cc_final: 0.7168 (p0) REVERT: D 580 ASP cc_start: 0.6471 (t0) cc_final: 0.6163 (m-30) REVERT: D 590 ASP cc_start: 0.7208 (m-30) cc_final: 0.6883 (t0) REVERT: D 634 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8279 (mm-30) outliers start: 20 outliers final: 0 residues processed: 769 average time/residue: 0.3313 time to fit residues: 375.0690 Evaluate side-chains 472 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 466 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 183 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 184 optimal weight: 0.0030 chunk 71 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 214 optimal weight: 4.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 165 HIS A 206 GLN A 522 HIS B 118 GLN B 165 HIS B 206 GLN B 426 HIS ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 165 HIS C 206 GLN C 265 HIS C 464 ASN C 522 HIS ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS D 206 GLN ** D 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 HIS D 548 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19484 Z= 0.239 Angle : 0.746 11.985 26440 Z= 0.371 Chirality : 0.043 0.200 3012 Planarity : 0.005 0.046 3336 Dihedral : 5.992 41.975 2608 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.55 % Favored : 90.32 % Rotamer: Outliers : 3.10 % Allowed : 12.55 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.16), residues: 2356 helix: -0.44 (0.13), residues: 1356 sheet: -4.21 (0.52), residues: 56 loop : -2.67 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 629 HIS 0.005 0.001 HIS B 582 PHE 0.018 0.002 PHE B 478 TYR 0.015 0.001 TYR C 526 ARG 0.006 0.001 ARG C 584 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 524 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8314 (mp0) REVERT: A 96 MET cc_start: 0.8207 (mmp) cc_final: 0.7870 (ptt) REVERT: A 157 CYS cc_start: 0.7748 (m) cc_final: 0.7059 (p) REVERT: A 158 ASN cc_start: 0.7029 (m-40) cc_final: 0.6762 (m110) REVERT: A 235 VAL cc_start: 0.8062 (t) cc_final: 0.7819 (m) REVERT: A 252 ASN cc_start: 0.7002 (t0) cc_final: 0.6630 (t0) REVERT: A 262 LYS cc_start: 0.8166 (tptp) cc_final: 0.7588 (mttm) REVERT: A 324 TYR cc_start: 0.7502 (m-80) cc_final: 0.7191 (m-80) REVERT: A 383 ASP cc_start: 0.8534 (m-30) cc_final: 0.8197 (t0) REVERT: A 440 MET cc_start: 0.8239 (tmm) cc_final: 0.7989 (tmm) REVERT: A 550 ASP cc_start: 0.8034 (t0) cc_final: 0.6905 (p0) REVERT: A 580 ASP cc_start: 0.6376 (t0) cc_final: 0.6144 (m-30) REVERT: A 590 ASP cc_start: 0.7444 (m-30) cc_final: 0.7065 (t0) REVERT: A 628 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7884 (mtp-110) REVERT: A 630 PHE cc_start: 0.6511 (m-80) cc_final: 0.6141 (m-80) REVERT: B 78 MET cc_start: 0.7494 (pmt) cc_final: 0.7126 (pmm) REVERT: B 80 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8042 (mm-30) REVERT: B 96 MET cc_start: 0.8244 (mmm) cc_final: 0.7904 (mmm) REVERT: B 157 CYS cc_start: 0.7671 (m) cc_final: 0.7059 (p) REVERT: B 235 VAL cc_start: 0.8131 (t) cc_final: 0.7900 (m) REVERT: B 252 ASN cc_start: 0.6747 (t0) cc_final: 0.6465 (t0) REVERT: B 262 LYS cc_start: 0.8264 (tptp) cc_final: 0.7699 (mttm) REVERT: B 277 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7123 (mt) REVERT: B 435 MET cc_start: 0.6355 (mmt) cc_final: 0.6067 (mmt) REVERT: B 450 GLU cc_start: 0.7009 (pt0) cc_final: 0.6719 (pt0) REVERT: B 474 MET cc_start: 0.6631 (mmm) cc_final: 0.6252 (ptt) REVERT: B 528 MET cc_start: 0.6468 (tmm) cc_final: 0.5530 (tmm) REVERT: B 590 ASP cc_start: 0.7141 (m-30) cc_final: 0.6739 (t0) REVERT: C 78 MET cc_start: 0.7399 (pmt) cc_final: 0.6715 (pmm) REVERT: C 80 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7935 (mm-30) REVERT: C 96 MET cc_start: 0.8321 (mmp) cc_final: 0.7808 (ptt) REVERT: C 176 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8235 (mp0) REVERT: C 210 THR cc_start: 0.8206 (t) cc_final: 0.7809 (p) REVERT: C 235 VAL cc_start: 0.8277 (t) cc_final: 0.7944 (m) REVERT: C 250 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6263 (tm-30) REVERT: C 262 LYS cc_start: 0.7915 (tptp) cc_final: 0.7258 (mttm) REVERT: C 278 TYR cc_start: 0.7527 (m-80) cc_final: 0.7168 (m-80) REVERT: C 306 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7587 (mm110) REVERT: C 345 MET cc_start: 0.7072 (mmm) cc_final: 0.6831 (mmt) REVERT: C 474 MET cc_start: 0.6670 (mmm) cc_final: 0.6267 (ptt) REVERT: C 550 ASP cc_start: 0.7546 (t0) cc_final: 0.6602 (p0) REVERT: C 565 ILE cc_start: 0.7644 (tp) cc_final: 0.7134 (mm) REVERT: C 580 ASP cc_start: 0.6504 (t0) cc_final: 0.5955 (m-30) REVERT: C 628 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7872 (mtm110) REVERT: C 630 PHE cc_start: 0.6867 (m-80) cc_final: 0.6586 (m-80) REVERT: D 61 LEU cc_start: 0.7787 (mt) cc_final: 0.7570 (mp) REVERT: D 74 GLN cc_start: 0.7623 (mt0) cc_final: 0.7407 (mt0) REVERT: D 78 MET cc_start: 0.7637 (pmt) cc_final: 0.7398 (pmm) REVERT: D 157 CYS cc_start: 0.8095 (m) cc_final: 0.7501 (p) REVERT: D 214 GLN cc_start: 0.7360 (tt0) cc_final: 0.6987 (tm-30) REVERT: D 235 VAL cc_start: 0.7936 (t) cc_final: 0.7642 (m) REVERT: D 250 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6664 (tm-30) REVERT: D 262 LYS cc_start: 0.8220 (tptp) cc_final: 0.7658 (mttt) REVERT: D 265 HIS cc_start: 0.6773 (t70) cc_final: 0.6510 (t70) REVERT: D 374 GLN cc_start: 0.8019 (tp40) cc_final: 0.7784 (tp40) REVERT: D 487 PHE cc_start: 0.7415 (m-80) cc_final: 0.7186 (m-80) REVERT: D 550 ASP cc_start: 0.7784 (t0) cc_final: 0.7070 (p0) REVERT: D 590 ASP cc_start: 0.7303 (m-30) cc_final: 0.7046 (t0) outliers start: 64 outliers final: 39 residues processed: 569 average time/residue: 0.3077 time to fit residues: 272.2741 Evaluate side-chains 447 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 407 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 615 ARG Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 615 ARG Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 178 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 214 optimal weight: 0.9990 chunk 231 optimal weight: 7.9990 chunk 191 optimal weight: 0.8980 chunk 212 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN C 572 ASN D 258 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19484 Z= 0.220 Angle : 0.710 12.028 26440 Z= 0.346 Chirality : 0.042 0.231 3012 Planarity : 0.004 0.046 3336 Dihedral : 5.243 28.024 2596 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.88 % Allowed : 15.94 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2356 helix: 0.32 (0.14), residues: 1368 sheet: -3.90 (0.54), residues: 56 loop : -2.74 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 321 HIS 0.018 0.001 HIS C 265 PHE 0.016 0.001 PHE B 478 TYR 0.025 0.001 TYR C 324 ARG 0.007 0.000 ARG D 263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 465 time to evaluate : 2.246 Fit side-chains revert: symmetry clash REVERT: A 157 CYS cc_start: 0.7807 (m) cc_final: 0.7159 (p) REVERT: A 158 ASN cc_start: 0.6985 (m-40) cc_final: 0.6729 (m-40) REVERT: A 235 VAL cc_start: 0.8134 (t) cc_final: 0.7891 (m) REVERT: A 250 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6631 (tm-30) REVERT: A 262 LYS cc_start: 0.8321 (tptp) cc_final: 0.7692 (mttm) REVERT: A 324 TYR cc_start: 0.7467 (m-80) cc_final: 0.7223 (m-80) REVERT: A 383 ASP cc_start: 0.8547 (m-30) cc_final: 0.8277 (t0) REVERT: A 440 MET cc_start: 0.8245 (tmm) cc_final: 0.8018 (tmm) REVERT: A 531 PHE cc_start: 0.7170 (t80) cc_final: 0.6725 (t80) REVERT: A 550 ASP cc_start: 0.7998 (t0) cc_final: 0.6781 (p0) REVERT: A 580 ASP cc_start: 0.6441 (t0) cc_final: 0.6084 (m-30) REVERT: A 590 ASP cc_start: 0.7368 (m-30) cc_final: 0.7138 (t0) REVERT: A 628 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7780 (mtp-110) REVERT: A 630 PHE cc_start: 0.6857 (m-80) cc_final: 0.6630 (m-80) REVERT: B 78 MET cc_start: 0.7418 (pmt) cc_final: 0.7175 (pmm) REVERT: B 80 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8152 (mm-30) REVERT: B 96 MET cc_start: 0.8215 (mmm) cc_final: 0.7908 (mmm) REVERT: B 157 CYS cc_start: 0.7775 (m) cc_final: 0.7164 (p) REVERT: B 235 VAL cc_start: 0.8128 (t) cc_final: 0.7871 (m) REVERT: B 250 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6344 (tm-30) REVERT: B 262 LYS cc_start: 0.8293 (tptp) cc_final: 0.7666 (mttm) REVERT: B 435 MET cc_start: 0.6400 (mmt) cc_final: 0.6093 (mmt) REVERT: B 474 MET cc_start: 0.6513 (mmm) cc_final: 0.6184 (ptt) REVERT: B 550 ASP cc_start: 0.7952 (t0) cc_final: 0.6531 (p0) REVERT: C 78 MET cc_start: 0.7404 (pmt) cc_final: 0.7182 (pmm) REVERT: C 80 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7933 (mm-30) REVERT: C 96 MET cc_start: 0.8264 (mmp) cc_final: 0.7739 (ptt) REVERT: C 113 GLU cc_start: 0.7408 (tp30) cc_final: 0.7191 (tp30) REVERT: C 235 VAL cc_start: 0.8226 (t) cc_final: 0.7887 (m) REVERT: C 250 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6515 (tm-30) REVERT: C 262 LYS cc_start: 0.8144 (tptp) cc_final: 0.7523 (mttm) REVERT: C 278 TYR cc_start: 0.7452 (m-80) cc_final: 0.7175 (m-80) REVERT: C 306 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7700 (mm110) REVERT: C 324 TYR cc_start: 0.7982 (m-80) cc_final: 0.7747 (m-80) REVERT: C 345 MET cc_start: 0.6998 (mmm) cc_final: 0.6739 (mmt) REVERT: C 363 ARG cc_start: 0.7623 (ttp80) cc_final: 0.7360 (ptm160) REVERT: C 442 MET cc_start: 0.6911 (ttm) cc_final: 0.6700 (mtp) REVERT: C 515 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8001 (mm-30) REVERT: C 550 ASP cc_start: 0.7533 (t0) cc_final: 0.6625 (p0) REVERT: C 565 ILE cc_start: 0.7583 (tp) cc_final: 0.7311 (mm) REVERT: C 580 ASP cc_start: 0.6415 (t0) cc_final: 0.6010 (m-30) REVERT: C 628 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7707 (mtm110) REVERT: C 630 PHE cc_start: 0.7057 (m-80) cc_final: 0.6708 (m-80) REVERT: D 78 MET cc_start: 0.7523 (pmt) cc_final: 0.7310 (pmm) REVERT: D 157 CYS cc_start: 0.8129 (m) cc_final: 0.7489 (p) REVERT: D 158 ASN cc_start: 0.7033 (m-40) cc_final: 0.6796 (m-40) REVERT: D 214 GLN cc_start: 0.7259 (tt0) cc_final: 0.6986 (tm-30) REVERT: D 235 VAL cc_start: 0.7931 (t) cc_final: 0.7624 (m) REVERT: D 250 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6741 (tm-30) REVERT: D 262 LYS cc_start: 0.8329 (tptp) cc_final: 0.8092 (tmtt) REVERT: D 550 ASP cc_start: 0.7795 (t0) cc_final: 0.7034 (p0) REVERT: D 580 ASP cc_start: 0.6111 (t0) cc_final: 0.5719 (m-30) REVERT: D 590 ASP cc_start: 0.7440 (m-30) cc_final: 0.7196 (t0) outliers start: 80 outliers final: 47 residues processed: 512 average time/residue: 0.2801 time to fit residues: 224.5324 Evaluate side-chains 451 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 404 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 228 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 ASN B 267 GLN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 265 HIS D 265 HIS D 370 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19484 Z= 0.184 Angle : 0.669 11.913 26440 Z= 0.326 Chirality : 0.040 0.174 3012 Planarity : 0.004 0.046 3336 Dihedral : 5.003 28.303 2596 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 4.26 % Allowed : 16.91 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.18), residues: 2356 helix: 0.69 (0.14), residues: 1364 sheet: -3.62 (0.55), residues: 56 loop : -2.62 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 321 HIS 0.005 0.001 HIS D 265 PHE 0.015 0.001 PHE B 478 TYR 0.027 0.001 TYR D 324 ARG 0.005 0.000 ARG C 305 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 434 time to evaluate : 2.354 Fit side-chains revert: symmetry clash REVERT: A 118 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6499 (tt0) REVERT: A 157 CYS cc_start: 0.7870 (m) cc_final: 0.7197 (p) REVERT: A 158 ASN cc_start: 0.7083 (m-40) cc_final: 0.6828 (m110) REVERT: A 235 VAL cc_start: 0.7931 (t) cc_final: 0.7699 (m) REVERT: A 250 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6832 (tm-30) REVERT: A 262 LYS cc_start: 0.8295 (tptp) cc_final: 0.7694 (mttm) REVERT: A 383 ASP cc_start: 0.8554 (m-30) cc_final: 0.8340 (t0) REVERT: A 440 MET cc_start: 0.8261 (tmm) cc_final: 0.8037 (tmm) REVERT: A 474 MET cc_start: 0.6508 (mmm) cc_final: 0.6142 (ptt) REVERT: A 550 ASP cc_start: 0.7969 (t0) cc_final: 0.6744 (p0) REVERT: A 580 ASP cc_start: 0.6544 (t0) cc_final: 0.6174 (m-30) REVERT: A 630 PHE cc_start: 0.6958 (m-80) cc_final: 0.6629 (m-80) REVERT: B 96 MET cc_start: 0.8180 (mmm) cc_final: 0.7853 (mmm) REVERT: B 118 GLN cc_start: 0.6442 (OUTLIER) cc_final: 0.6166 (tt0) REVERT: B 157 CYS cc_start: 0.7866 (m) cc_final: 0.7227 (p) REVERT: B 235 VAL cc_start: 0.8089 (t) cc_final: 0.7846 (m) REVERT: B 250 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6353 (tm-30) REVERT: B 262 LYS cc_start: 0.8245 (tptp) cc_final: 0.7612 (mttm) REVERT: B 359 ARG cc_start: 0.6250 (ttm-80) cc_final: 0.6022 (ttm-80) REVERT: B 435 MET cc_start: 0.6319 (mmt) cc_final: 0.6064 (mmt) REVERT: B 550 ASP cc_start: 0.7871 (t0) cc_final: 0.6573 (p0) REVERT: C 37 ASN cc_start: 0.6255 (OUTLIER) cc_final: 0.5906 (t0) REVERT: C 78 MET cc_start: 0.7393 (pmt) cc_final: 0.6884 (pmm) REVERT: C 80 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7916 (mm-30) REVERT: C 96 MET cc_start: 0.8156 (mmp) cc_final: 0.7751 (ptt) REVERT: C 235 VAL cc_start: 0.8206 (t) cc_final: 0.7882 (m) REVERT: C 250 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6547 (tm-30) REVERT: C 262 LYS cc_start: 0.8200 (tptp) cc_final: 0.7535 (mttm) REVERT: C 306 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7693 (mm110) REVERT: C 345 MET cc_start: 0.6997 (mmm) cc_final: 0.6743 (mmt) REVERT: C 363 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7399 (ptm160) REVERT: C 474 MET cc_start: 0.6560 (mmm) cc_final: 0.6171 (ptt) REVERT: C 515 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8055 (mm-30) REVERT: C 550 ASP cc_start: 0.7551 (t0) cc_final: 0.6639 (p0) REVERT: C 565 ILE cc_start: 0.7492 (tp) cc_final: 0.7221 (mm) REVERT: C 580 ASP cc_start: 0.6510 (t0) cc_final: 0.6098 (m-30) REVERT: C 628 ARG cc_start: 0.8100 (mtm-85) cc_final: 0.7770 (mtm110) REVERT: C 630 PHE cc_start: 0.7176 (m-80) cc_final: 0.6767 (m-80) REVERT: D 157 CYS cc_start: 0.8169 (m) cc_final: 0.7514 (p) REVERT: D 158 ASN cc_start: 0.6985 (m-40) cc_final: 0.6774 (m110) REVERT: D 214 GLN cc_start: 0.7265 (tt0) cc_final: 0.6958 (tm-30) REVERT: D 250 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6753 (tm-30) REVERT: D 262 LYS cc_start: 0.8321 (tptp) cc_final: 0.7654 (mttm) REVERT: D 550 ASP cc_start: 0.7913 (t0) cc_final: 0.7189 (p0) REVERT: D 580 ASP cc_start: 0.6411 (t0) cc_final: 0.6050 (m-30) outliers start: 88 outliers final: 53 residues processed: 485 average time/residue: 0.2836 time to fit residues: 218.2687 Evaluate side-chains 453 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 397 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 265 HIS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 194 optimal weight: 0.0770 chunk 157 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 overall best weight: 2.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS D 267 GLN D 546 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19484 Z= 0.282 Angle : 0.710 11.889 26440 Z= 0.348 Chirality : 0.043 0.210 3012 Planarity : 0.004 0.047 3336 Dihedral : 4.994 28.236 2596 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 5.14 % Allowed : 16.76 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.18), residues: 2356 helix: 0.79 (0.14), residues: 1372 sheet: -3.42 (0.55), residues: 56 loop : -2.61 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 629 HIS 0.029 0.001 HIS D 265 PHE 0.016 0.002 PHE B 244 TYR 0.028 0.001 TYR A 324 ARG 0.006 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 413 time to evaluate : 2.281 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.7044 (pmm) cc_final: 0.6420 (pmm) REVERT: A 96 MET cc_start: 0.7671 (mmm) cc_final: 0.7431 (mmm) REVERT: A 250 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6818 (tm-30) REVERT: A 262 LYS cc_start: 0.8365 (tptp) cc_final: 0.7706 (mttm) REVERT: A 383 ASP cc_start: 0.8565 (m-30) cc_final: 0.8329 (t0) REVERT: A 440 MET cc_start: 0.8268 (tmm) cc_final: 0.8036 (tmm) REVERT: A 474 MET cc_start: 0.6438 (mmm) cc_final: 0.6193 (ptt) REVERT: A 550 ASP cc_start: 0.8053 (t0) cc_final: 0.6831 (p0) REVERT: B 68 GLU cc_start: 0.7215 (pt0) cc_final: 0.6680 (tm-30) REVERT: B 80 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7857 (mp0) REVERT: B 250 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6461 (tm-30) REVERT: B 262 LYS cc_start: 0.8305 (tptp) cc_final: 0.7598 (mttm) REVERT: B 359 ARG cc_start: 0.6340 (ttm-80) cc_final: 0.6068 (ttm-80) REVERT: B 474 MET cc_start: 0.6345 (mmm) cc_final: 0.6103 (ptt) REVERT: B 550 ASP cc_start: 0.7920 (t0) cc_final: 0.6738 (p0) REVERT: C 37 ASN cc_start: 0.6609 (OUTLIER) cc_final: 0.6097 (t0) REVERT: C 78 MET cc_start: 0.7420 (pmt) cc_final: 0.6916 (pmm) REVERT: C 80 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8178 (mm-30) REVERT: C 96 MET cc_start: 0.8098 (mmp) cc_final: 0.7812 (ptt) REVERT: C 250 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6658 (tm-30) REVERT: C 262 LYS cc_start: 0.8182 (tptp) cc_final: 0.7448 (mttm) REVERT: C 306 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7867 (mm110) REVERT: C 324 TYR cc_start: 0.7928 (m-80) cc_final: 0.7573 (m-80) REVERT: C 345 MET cc_start: 0.6991 (mmm) cc_final: 0.6734 (mmt) REVERT: C 363 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7508 (ptm160) REVERT: C 474 MET cc_start: 0.6618 (mmm) cc_final: 0.6264 (ptt) REVERT: C 515 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7795 (mm-30) REVERT: C 550 ASP cc_start: 0.7696 (t0) cc_final: 0.6782 (p0) REVERT: C 580 ASP cc_start: 0.6478 (t0) cc_final: 0.6062 (m-30) REVERT: D 80 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7503 (mt-10) REVERT: D 214 GLN cc_start: 0.7331 (tt0) cc_final: 0.6977 (tm-30) REVERT: D 250 GLU cc_start: 0.7400 (mm-30) cc_final: 0.6780 (tm-30) REVERT: D 262 LYS cc_start: 0.8396 (tptp) cc_final: 0.8124 (tmtt) REVERT: D 550 ASP cc_start: 0.7894 (t0) cc_final: 0.7129 (p0) outliers start: 106 outliers final: 61 residues processed: 486 average time/residue: 0.2857 time to fit residues: 217.3550 Evaluate side-chains 435 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 373 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 470 ARG Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 56 optimal weight: 0.0570 chunk 228 optimal weight: 0.6980 chunk 189 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN C 267 GLN C 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19484 Z= 0.176 Angle : 0.680 11.883 26440 Z= 0.326 Chirality : 0.041 0.201 3012 Planarity : 0.004 0.045 3336 Dihedral : 4.834 29.166 2596 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 4.02 % Allowed : 18.27 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.18), residues: 2356 helix: 0.99 (0.14), residues: 1376 sheet: -3.31 (0.54), residues: 56 loop : -2.55 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 629 HIS 0.014 0.001 HIS C 265 PHE 0.017 0.001 PHE A 478 TYR 0.025 0.001 TYR A 324 ARG 0.004 0.000 ARG D 305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 416 time to evaluate : 2.178 Fit side-chains REVERT: A 78 MET cc_start: 0.6970 (pmm) cc_final: 0.6314 (pmm) REVERT: A 118 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6698 (tt0) REVERT: A 250 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6701 (tm-30) REVERT: A 262 LYS cc_start: 0.8342 (tptp) cc_final: 0.7642 (mttm) REVERT: A 474 MET cc_start: 0.6345 (mmm) cc_final: 0.5985 (ptt) REVERT: A 550 ASP cc_start: 0.7938 (t0) cc_final: 0.6700 (p0) REVERT: B 80 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7790 (mp0) REVERT: B 100 GLU cc_start: 0.8325 (mp0) cc_final: 0.7933 (pm20) REVERT: B 118 GLN cc_start: 0.6573 (OUTLIER) cc_final: 0.6325 (tt0) REVERT: B 157 CYS cc_start: 0.8124 (m) cc_final: 0.7764 (p) REVERT: B 235 VAL cc_start: 0.8016 (t) cc_final: 0.7782 (m) REVERT: B 250 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6539 (tm-30) REVERT: B 262 LYS cc_start: 0.8261 (tptp) cc_final: 0.7559 (mttm) REVERT: B 359 ARG cc_start: 0.6316 (ttm-80) cc_final: 0.6017 (ttm-80) REVERT: B 474 MET cc_start: 0.6341 (mmm) cc_final: 0.6033 (ptt) REVERT: B 550 ASP cc_start: 0.7910 (t0) cc_final: 0.6769 (p0) REVERT: C 78 MET cc_start: 0.7408 (pmt) cc_final: 0.6926 (pmm) REVERT: C 100 GLU cc_start: 0.8283 (mp0) cc_final: 0.7816 (pm20) REVERT: C 118 GLN cc_start: 0.6906 (OUTLIER) cc_final: 0.6626 (tt0) REVERT: C 262 LYS cc_start: 0.8236 (tptp) cc_final: 0.7969 (tmtt) REVERT: C 302 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.5871 (tpp-160) REVERT: C 306 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7760 (mm110) REVERT: C 324 TYR cc_start: 0.7903 (m-80) cc_final: 0.7601 (m-80) REVERT: C 363 ARG cc_start: 0.7823 (ttp80) cc_final: 0.7534 (ptm160) REVERT: C 371 LYS cc_start: 0.7249 (mttt) cc_final: 0.6202 (mtmt) REVERT: C 515 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8051 (mm-30) REVERT: C 550 ASP cc_start: 0.7695 (t0) cc_final: 0.6685 (p0) REVERT: D 80 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7601 (mt-10) REVERT: D 214 GLN cc_start: 0.7358 (tt0) cc_final: 0.6988 (tm-30) REVERT: D 250 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6861 (tm-30) REVERT: D 262 LYS cc_start: 0.8303 (tptp) cc_final: 0.8047 (tmtt) REVERT: D 306 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7706 (mm-40) REVERT: D 550 ASP cc_start: 0.7780 (t0) cc_final: 0.6936 (p0) REVERT: D 588 GLU cc_start: 0.6981 (pt0) cc_final: 0.6760 (pt0) outliers start: 83 outliers final: 61 residues processed: 467 average time/residue: 0.2910 time to fit residues: 211.0250 Evaluate side-chains 448 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 383 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 470 ARG Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 166 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 142 optimal weight: 0.2980 chunk 138 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 265 HIS B 158 ASN B 267 GLN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19484 Z= 0.190 Angle : 0.681 13.682 26440 Z= 0.328 Chirality : 0.041 0.213 3012 Planarity : 0.004 0.046 3336 Dihedral : 4.703 28.124 2596 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 3.88 % Allowed : 18.94 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2356 helix: 1.09 (0.14), residues: 1368 sheet: -3.17 (0.54), residues: 56 loop : -2.57 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 629 HIS 0.007 0.001 HIS A 265 PHE 0.018 0.001 PHE A 478 TYR 0.026 0.001 TYR D 324 ARG 0.008 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 396 time to evaluate : 2.091 Fit side-chains REVERT: A 78 MET cc_start: 0.6816 (pmm) cc_final: 0.6536 (pmm) REVERT: A 96 MET cc_start: 0.8019 (mmp) cc_final: 0.7447 (mmm) REVERT: A 250 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6635 (tm-30) REVERT: A 262 LYS cc_start: 0.8359 (tptp) cc_final: 0.7650 (mttm) REVERT: A 440 MET cc_start: 0.8077 (tmm) cc_final: 0.7791 (tmm) REVERT: A 550 ASP cc_start: 0.7981 (t0) cc_final: 0.6875 (p0) REVERT: B 80 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7864 (mp0) REVERT: B 100 GLU cc_start: 0.8182 (mp0) cc_final: 0.7823 (pm20) REVERT: B 118 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.6406 (tt0) REVERT: B 157 CYS cc_start: 0.8201 (m) cc_final: 0.7800 (p) REVERT: B 235 VAL cc_start: 0.8023 (t) cc_final: 0.7797 (m) REVERT: B 250 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6470 (tm-30) REVERT: B 262 LYS cc_start: 0.8271 (tptp) cc_final: 0.7538 (mttm) REVERT: B 359 ARG cc_start: 0.6370 (ttm-80) cc_final: 0.6035 (ttm-80) REVERT: B 550 ASP cc_start: 0.7889 (t0) cc_final: 0.6778 (p0) REVERT: C 78 MET cc_start: 0.7333 (pmt) cc_final: 0.7017 (pmm) REVERT: C 100 GLU cc_start: 0.8211 (mp0) cc_final: 0.7759 (pm20) REVERT: C 118 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6766 (tt0) REVERT: C 262 LYS cc_start: 0.8244 (tptp) cc_final: 0.7982 (tmtt) REVERT: C 302 ARG cc_start: 0.6349 (OUTLIER) cc_final: 0.5781 (tpp-160) REVERT: C 306 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7717 (mm110) REVERT: C 324 TYR cc_start: 0.7860 (m-80) cc_final: 0.7585 (m-80) REVERT: C 363 ARG cc_start: 0.7861 (ttp80) cc_final: 0.7611 (ptm160) REVERT: C 474 MET cc_start: 0.6571 (mmm) cc_final: 0.6344 (ptt) REVERT: C 515 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7867 (mm-30) REVERT: C 550 ASP cc_start: 0.7647 (t0) cc_final: 0.6684 (p0) REVERT: C 580 ASP cc_start: 0.6157 (t0) cc_final: 0.5619 (m-30) REVERT: D 80 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7603 (mt-10) REVERT: D 96 MET cc_start: 0.8296 (mmp) cc_final: 0.7699 (mmm) REVERT: D 214 GLN cc_start: 0.7410 (tt0) cc_final: 0.7021 (tm-30) REVERT: D 250 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6893 (tm-30) REVERT: D 262 LYS cc_start: 0.8295 (tptp) cc_final: 0.8037 (tmtt) REVERT: D 456 PHE cc_start: 0.6423 (OUTLIER) cc_final: 0.6178 (m-80) REVERT: D 474 MET cc_start: 0.6399 (mmm) cc_final: 0.6093 (ptt) REVERT: D 550 ASP cc_start: 0.7775 (t0) cc_final: 0.6959 (p0) REVERT: D 580 ASP cc_start: 0.6105 (t0) cc_final: 0.5779 (m-30) REVERT: D 588 GLU cc_start: 0.6940 (pt0) cc_final: 0.6717 (pt0) outliers start: 80 outliers final: 60 residues processed: 447 average time/residue: 0.2869 time to fit residues: 199.6509 Evaluate side-chains 431 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 367 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 470 ARG Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 68 optimal weight: 0.0980 chunk 44 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 206 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN D 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19484 Z= 0.179 Angle : 0.692 13.061 26440 Z= 0.329 Chirality : 0.041 0.219 3012 Planarity : 0.004 0.045 3336 Dihedral : 4.651 28.775 2596 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 3.59 % Allowed : 19.86 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.18), residues: 2356 helix: 1.17 (0.14), residues: 1364 sheet: -3.11 (0.55), residues: 56 loop : -2.56 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 629 HIS 0.016 0.001 HIS A 265 PHE 0.015 0.001 PHE A 478 TYR 0.026 0.001 TYR D 324 ARG 0.008 0.000 ARG D 224 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 390 time to evaluate : 2.108 Fit side-chains REVERT: A 78 MET cc_start: 0.6804 (pmm) cc_final: 0.6264 (pmm) REVERT: A 96 MET cc_start: 0.8040 (mmp) cc_final: 0.7507 (mmm) REVERT: A 250 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6605 (tm-30) REVERT: A 262 LYS cc_start: 0.8352 (tptp) cc_final: 0.7660 (mttm) REVERT: A 440 MET cc_start: 0.8085 (tmm) cc_final: 0.7849 (tmm) REVERT: A 474 MET cc_start: 0.6337 (mmm) cc_final: 0.6136 (ptt) REVERT: A 550 ASP cc_start: 0.7854 (t0) cc_final: 0.6717 (p0) REVERT: B 100 GLU cc_start: 0.8168 (mp0) cc_final: 0.7801 (pm20) REVERT: B 118 GLN cc_start: 0.6650 (OUTLIER) cc_final: 0.6443 (tt0) REVERT: B 262 LYS cc_start: 0.8251 (tptp) cc_final: 0.8032 (tmtt) REVERT: B 359 ARG cc_start: 0.6410 (ttm-80) cc_final: 0.6030 (ttm-80) REVERT: B 474 MET cc_start: 0.5640 (ptt) cc_final: 0.5338 (mmm) REVERT: B 550 ASP cc_start: 0.7794 (t0) cc_final: 0.6679 (p0) REVERT: C 100 GLU cc_start: 0.8260 (mp0) cc_final: 0.7826 (pm20) REVERT: C 118 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6847 (tt0) REVERT: C 262 LYS cc_start: 0.8311 (tptp) cc_final: 0.8040 (tmtt) REVERT: C 302 ARG cc_start: 0.6364 (OUTLIER) cc_final: 0.5768 (tpp-160) REVERT: C 306 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7718 (mm110) REVERT: C 324 TYR cc_start: 0.7778 (m-80) cc_final: 0.7523 (m-80) REVERT: C 363 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7624 (ptm160) REVERT: C 371 LYS cc_start: 0.7200 (mttt) cc_final: 0.6200 (mtmt) REVERT: C 474 MET cc_start: 0.6575 (mmm) cc_final: 0.6324 (ptt) REVERT: C 515 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7762 (mm-30) REVERT: C 580 ASP cc_start: 0.6139 (t0) cc_final: 0.5778 (m-30) REVERT: D 80 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7669 (mt-10) REVERT: D 96 MET cc_start: 0.8308 (mmp) cc_final: 0.7827 (mmm) REVERT: D 130 MET cc_start: 0.8148 (mmt) cc_final: 0.7866 (tpt) REVERT: D 132 LEU cc_start: 0.8090 (mp) cc_final: 0.7685 (mp) REVERT: D 214 GLN cc_start: 0.7311 (tt0) cc_final: 0.6931 (tm-30) REVERT: D 250 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6837 (tm-30) REVERT: D 262 LYS cc_start: 0.8307 (tptp) cc_final: 0.8050 (tmtt) REVERT: D 456 PHE cc_start: 0.6299 (OUTLIER) cc_final: 0.6026 (m-80) REVERT: D 474 MET cc_start: 0.6456 (mmm) cc_final: 0.6070 (ptt) REVERT: D 550 ASP cc_start: 0.7714 (t0) cc_final: 0.6921 (p0) REVERT: D 580 ASP cc_start: 0.6181 (t0) cc_final: 0.5822 (m-30) REVERT: D 588 GLU cc_start: 0.6947 (pt0) cc_final: 0.6721 (pt0) outliers start: 74 outliers final: 56 residues processed: 434 average time/residue: 0.2866 time to fit residues: 194.2802 Evaluate side-chains 430 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 370 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 470 ARG Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 166 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 224 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN C 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19484 Z= 0.186 Angle : 0.696 12.448 26440 Z= 0.331 Chirality : 0.042 0.311 3012 Planarity : 0.004 0.082 3336 Dihedral : 4.571 28.046 2596 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 3.54 % Allowed : 20.25 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2356 helix: 1.23 (0.15), residues: 1344 sheet: -2.91 (0.56), residues: 56 loop : -2.57 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 629 HIS 0.004 0.001 HIS A 582 PHE 0.018 0.001 PHE A 478 TYR 0.027 0.001 TYR D 324 ARG 0.008 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 384 time to evaluate : 2.206 Fit side-chains REVERT: A 78 MET cc_start: 0.6766 (pmm) cc_final: 0.6518 (pmm) REVERT: A 250 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6552 (tm-30) REVERT: A 262 LYS cc_start: 0.8352 (tptp) cc_final: 0.8096 (tmtt) REVERT: A 440 MET cc_start: 0.8097 (tmm) cc_final: 0.7774 (tmm) REVERT: A 474 MET cc_start: 0.6394 (mmm) cc_final: 0.6094 (ptt) REVERT: A 550 ASP cc_start: 0.7735 (t0) cc_final: 0.6602 (p0) REVERT: B 118 GLN cc_start: 0.6678 (OUTLIER) cc_final: 0.6471 (tt0) REVERT: B 262 LYS cc_start: 0.8222 (tptp) cc_final: 0.8015 (tmtt) REVERT: B 359 ARG cc_start: 0.6368 (ttm-80) cc_final: 0.5995 (ttm-80) REVERT: B 371 LYS cc_start: 0.6998 (ttmm) cc_final: 0.6446 (mtmt) REVERT: B 550 ASP cc_start: 0.7702 (t0) cc_final: 0.6609 (p0) REVERT: C 97 VAL cc_start: 0.8678 (m) cc_final: 0.8301 (m) REVERT: C 100 GLU cc_start: 0.8261 (mp0) cc_final: 0.7814 (pm20) REVERT: C 118 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6966 (tt0) REVERT: C 262 LYS cc_start: 0.8282 (tptp) cc_final: 0.8022 (tmtt) REVERT: C 306 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7707 (mm-40) REVERT: C 324 TYR cc_start: 0.7769 (m-80) cc_final: 0.7541 (m-80) REVERT: C 363 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7638 (ptm160) REVERT: C 371 LYS cc_start: 0.7161 (mttt) cc_final: 0.6170 (mtmt) REVERT: C 474 MET cc_start: 0.6575 (mmm) cc_final: 0.6326 (ptt) REVERT: C 515 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7797 (mm-30) REVERT: C 580 ASP cc_start: 0.6228 (t0) cc_final: 0.5744 (m-30) REVERT: D 78 MET cc_start: 0.6912 (pmm) cc_final: 0.6512 (pmm) REVERT: D 80 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7732 (mt-10) REVERT: D 96 MET cc_start: 0.8300 (mmp) cc_final: 0.7987 (ptt) REVERT: D 214 GLN cc_start: 0.7231 (tt0) cc_final: 0.6888 (tm-30) REVERT: D 250 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6838 (tm-30) REVERT: D 262 LYS cc_start: 0.8262 (tptp) cc_final: 0.8017 (tmtt) REVERT: D 474 MET cc_start: 0.6570 (mmm) cc_final: 0.6225 (ptt) REVERT: D 550 ASP cc_start: 0.7636 (t0) cc_final: 0.6884 (p0) REVERT: D 580 ASP cc_start: 0.6138 (t0) cc_final: 0.5768 (m-30) REVERT: D 588 GLU cc_start: 0.6938 (pt0) cc_final: 0.6723 (pt0) outliers start: 73 outliers final: 58 residues processed: 426 average time/residue: 0.3013 time to fit residues: 197.5310 Evaluate side-chains 425 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 365 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 470 ARG Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 19 optimal weight: 0.1980 chunk 144 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 522 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19484 Z= 0.250 Angle : 0.725 13.323 26440 Z= 0.349 Chirality : 0.044 0.311 3012 Planarity : 0.004 0.075 3336 Dihedral : 4.666 27.263 2596 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 3.20 % Allowed : 20.54 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 2356 helix: 1.18 (0.15), residues: 1348 sheet: -2.73 (0.57), residues: 56 loop : -2.56 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 629 HIS 0.006 0.001 HIS A 582 PHE 0.020 0.002 PHE D 478 TYR 0.028 0.001 TYR A 324 ARG 0.010 0.000 ARG C 224 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 383 time to evaluate : 2.108 Fit side-chains REVERT: A 80 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8202 (mp0) REVERT: A 262 LYS cc_start: 0.8303 (tptp) cc_final: 0.8064 (tmtt) REVERT: A 474 MET cc_start: 0.6401 (mmm) cc_final: 0.6116 (ptt) REVERT: A 550 ASP cc_start: 0.7812 (t0) cc_final: 0.6737 (p0) REVERT: B 100 GLU cc_start: 0.8289 (mp0) cc_final: 0.7971 (pm20) REVERT: B 262 LYS cc_start: 0.8249 (tptp) cc_final: 0.8035 (tmtt) REVERT: B 359 ARG cc_start: 0.6469 (ttm-80) cc_final: 0.6072 (ttm-80) REVERT: B 371 LYS cc_start: 0.6814 (ttmm) cc_final: 0.6322 (mtmt) REVERT: B 550 ASP cc_start: 0.7670 (t0) cc_final: 0.6757 (p0) REVERT: C 100 GLU cc_start: 0.8336 (mp0) cc_final: 0.7796 (pm20) REVERT: C 262 LYS cc_start: 0.8243 (tptp) cc_final: 0.7965 (tmtt) REVERT: C 306 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7805 (mm110) REVERT: C 324 TYR cc_start: 0.7900 (m-80) cc_final: 0.7627 (m-80) REVERT: C 363 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7715 (ptm160) REVERT: C 371 LYS cc_start: 0.7232 (mttt) cc_final: 0.6318 (mtmm) REVERT: C 474 MET cc_start: 0.6544 (mmm) cc_final: 0.6342 (ptt) REVERT: C 515 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7772 (mm-30) REVERT: C 550 ASP cc_start: 0.7573 (t0) cc_final: 0.6667 (p0) REVERT: D 78 MET cc_start: 0.6863 (pmm) cc_final: 0.6482 (pmm) REVERT: D 96 MET cc_start: 0.8252 (mmp) cc_final: 0.7969 (ptt) REVERT: D 176 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8186 (mp0) REVERT: D 214 GLN cc_start: 0.7279 (tt0) cc_final: 0.6993 (tm-30) REVERT: D 250 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6714 (tm-30) REVERT: D 262 LYS cc_start: 0.8317 (tptp) cc_final: 0.8054 (tmtt) REVERT: D 474 MET cc_start: 0.6566 (mmm) cc_final: 0.6242 (ptt) REVERT: D 550 ASP cc_start: 0.7674 (t0) cc_final: 0.6993 (p0) REVERT: D 588 GLU cc_start: 0.6917 (pt0) cc_final: 0.6703 (pt0) outliers start: 66 outliers final: 58 residues processed: 424 average time/residue: 0.3012 time to fit residues: 196.2998 Evaluate side-chains 425 residues out of total 2064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 367 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 217 ASN Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 217 ASN Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 164 optimal weight: 0.0270 chunk 10 optimal weight: 0.7980 overall best weight: 1.1040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.150878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.121770 restraints weight = 28492.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.124724 restraints weight = 15642.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126617 restraints weight = 10780.443| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19484 Z= 0.204 Angle : 0.718 12.752 26440 Z= 0.344 Chirality : 0.043 0.295 3012 Planarity : 0.004 0.073 3336 Dihedral : 4.620 27.587 2596 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 3.05 % Allowed : 20.74 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.18), residues: 2356 helix: 1.20 (0.14), residues: 1352 sheet: -2.61 (0.56), residues: 56 loop : -2.48 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 629 HIS 0.004 0.001 HIS B 522 PHE 0.018 0.001 PHE A 244 TYR 0.028 0.001 TYR A 324 ARG 0.009 0.000 ARG C 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4449.77 seconds wall clock time: 93 minutes 9.89 seconds (5589.89 seconds total)