Starting phenix.real_space_refine on Sat Mar 23 19:05:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm5_30401/03_2024/7cm5_30401.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm5_30401/03_2024/7cm5_30401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm5_30401/03_2024/7cm5_30401.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm5_30401/03_2024/7cm5_30401.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm5_30401/03_2024/7cm5_30401.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm5_30401/03_2024/7cm5_30401.pdb" } resolution = 2.6 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= -0.000 sd= 0.004 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 184 5.16 5 C 24200 2.51 5 N 6896 2.21 5 O 7024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ARG 570": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ARG 159": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B ARG 468": "NH1" <-> "NH2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B ARG 570": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 157": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C ARG 468": "NH1" <-> "NH2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C ARG 570": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D ARG 434": "NH1" <-> "NH2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D ARG 468": "NH1" <-> "NH2" Residue "D ARG 517": "NH1" <-> "NH2" Residue "D ARG 543": "NH1" <-> "NH2" Residue "D ARG 570": "NH1" <-> "NH2" Residue "D ARG 615": "NH1" <-> "NH2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E ARG 159": "NH1" <-> "NH2" Residue "E ARG 201": "NH1" <-> "NH2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E ARG 322": "NH1" <-> "NH2" Residue "E ARG 338": "NH1" <-> "NH2" Residue "E ARG 434": "NH1" <-> "NH2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E ARG 468": "NH1" <-> "NH2" Residue "E ARG 517": "NH1" <-> "NH2" Residue "E ARG 543": "NH1" <-> "NH2" Residue "E ARG 570": "NH1" <-> "NH2" Residue "E ARG 615": "NH1" <-> "NH2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F ARG 201": "NH1" <-> "NH2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F ARG 322": "NH1" <-> "NH2" Residue "F ARG 338": "NH1" <-> "NH2" Residue "F ARG 434": "NH1" <-> "NH2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F ARG 468": "NH1" <-> "NH2" Residue "F ARG 517": "NH1" <-> "NH2" Residue "F ARG 543": "NH1" <-> "NH2" Residue "F ARG 570": "NH1" <-> "NH2" Residue "F ARG 615": "NH1" <-> "NH2" Residue "G ARG 86": "NH1" <-> "NH2" Residue "G ARG 121": "NH1" <-> "NH2" Residue "G ARG 146": "NH1" <-> "NH2" Residue "G ARG 157": "NH1" <-> "NH2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G ARG 201": "NH1" <-> "NH2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G ARG 322": "NH1" <-> "NH2" Residue "G ARG 338": "NH1" <-> "NH2" Residue "G ARG 434": "NH1" <-> "NH2" Residue "G ARG 465": "NH1" <-> "NH2" Residue "G ARG 468": "NH1" <-> "NH2" Residue "G ARG 517": "NH1" <-> "NH2" Residue "G ARG 543": "NH1" <-> "NH2" Residue "G ARG 570": "NH1" <-> "NH2" Residue "G ARG 615": "NH1" <-> "NH2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H ARG 121": "NH1" <-> "NH2" Residue "H ARG 146": "NH1" <-> "NH2" Residue "H ARG 157": "NH1" <-> "NH2" Residue "H ARG 159": "NH1" <-> "NH2" Residue "H ARG 201": "NH1" <-> "NH2" Residue "H ARG 244": "NH1" <-> "NH2" Residue "H ARG 322": "NH1" <-> "NH2" Residue "H ARG 338": "NH1" <-> "NH2" Residue "H ARG 434": "NH1" <-> "NH2" Residue "H ARG 465": "NH1" <-> "NH2" Residue "H ARG 468": "NH1" <-> "NH2" Residue "H ARG 517": "NH1" <-> "NH2" Residue "H ARG 543": "NH1" <-> "NH2" Residue "H ARG 570": "NH1" <-> "NH2" Residue "H ARG 615": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38304 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4788 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "B" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4788 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "C" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4788 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "D" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4788 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "E" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4788 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "F" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4788 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "G" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4788 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "H" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4788 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Time building chain proxies: 19.43, per 1000 atoms: 0.51 Number of scatterers: 38304 At special positions: 0 Unit cell: (214.165, 213.11, 83.345, 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 184 16.00 O 7024 8.00 N 6896 7.00 C 24200 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: 14.25 Conformation dependent library (CDL) restraints added in 6.2 seconds 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9120 Finding SS restraints... Secondary structure from input PDB file: 320 helices and 8 sheets defined 71.2% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'A' and resid 62 through 82 removed outlier: 3.581A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 85 through 104 removed outlier: 3.711A pdb=" N LEU A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.502A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 138 through 152 removed outlier: 3.675A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 removed outlier: 4.463A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 172 Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.529A pdb=" N ALA A 181 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.566A pdb=" N ALA A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.769A pdb=" N VAL A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 236 Processing helix chain 'A' and resid 238 through 248 removed outlier: 3.690A pdb=" N GLN A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 260 Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 283 through 291 Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.897A pdb=" N LEU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.605A pdb=" N PHE A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 338 through 359 removed outlier: 3.516A pdb=" N GLN A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.083A pdb=" N SER A 366 " --> pdb=" O THR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 removed outlier: 4.134A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 removed outlier: 3.513A pdb=" N SER A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 413 through 425 removed outlier: 3.636A pdb=" N VAL A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 429 through 435 removed outlier: 3.799A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 447 through 453 Processing helix chain 'A' and resid 459 through 476 removed outlier: 3.545A pdb=" N PHE A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.874A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.668A pdb=" N VAL A 518 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 525 Processing helix chain 'A' and resid 531 through 545 Processing helix chain 'A' and resid 573 through 586 Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 637 through 650 Processing helix chain 'A' and resid 669 through 678 removed outlier: 4.681A pdb=" N ALA A 674 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 675 " --> pdb=" O MET A 672 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 678 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'B' and resid 62 through 82 removed outlier: 3.582A pdb=" N GLU B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 85 through 104 removed outlier: 3.711A pdb=" N LEU B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 123 removed outlier: 3.501A pdb=" N VAL B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 138 through 152 removed outlier: 3.674A pdb=" N GLN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 removed outlier: 4.462A pdb=" N ARG B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 177 through 192 removed outlier: 3.528A pdb=" N ALA B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 removed outlier: 3.566A pdb=" N ALA B 205 " --> pdb=" O ARG B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.769A pdb=" N VAL B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 236 Processing helix chain 'B' and resid 238 through 248 removed outlier: 3.691A pdb=" N GLN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 260 Processing helix chain 'B' and resid 264 through 279 Processing helix chain 'B' and resid 283 through 291 Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.897A pdb=" N LEU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.604A pdb=" N PHE B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 338 through 359 removed outlier: 3.516A pdb=" N GLN B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.082A pdb=" N SER B 366 " --> pdb=" O THR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 removed outlier: 4.134A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 removed outlier: 3.513A pdb=" N SER B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 413 through 425 removed outlier: 3.636A pdb=" N VAL B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 429 through 435 removed outlier: 3.799A pdb=" N GLU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 459 through 476 removed outlier: 3.545A pdb=" N PHE B 476 " --> pdb=" O GLU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.873A pdb=" N TRP B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 500 No H-bonds generated for 'chain 'B' and resid 498 through 500' Processing helix chain 'B' and resid 501 through 507 Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.669A pdb=" N VAL B 518 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 525 Processing helix chain 'B' and resid 531 through 545 Processing helix chain 'B' and resid 573 through 586 Processing helix chain 'B' and resid 606 through 614 Processing helix chain 'B' and resid 637 through 650 Processing helix chain 'B' and resid 669 through 678 removed outlier: 4.680A pdb=" N ALA B 674 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 675 " --> pdb=" O MET B 672 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 678 " --> pdb=" O VAL B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 697 Processing helix chain 'C' and resid 62 through 82 removed outlier: 3.582A pdb=" N GLU C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Proline residue: C 70 - end of helix Processing helix chain 'C' and resid 85 through 104 removed outlier: 3.710A pdb=" N LEU C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 123 removed outlier: 3.501A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 133 Processing helix chain 'C' and resid 138 through 152 removed outlier: 3.675A pdb=" N GLN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 removed outlier: 4.462A pdb=" N ARG C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 172 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.529A pdb=" N ALA C 181 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.566A pdb=" N ALA C 205 " --> pdb=" O ARG C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.769A pdb=" N VAL C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 236 Processing helix chain 'C' and resid 238 through 248 removed outlier: 3.690A pdb=" N GLN C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 260 Processing helix chain 'C' and resid 264 through 279 Processing helix chain 'C' and resid 283 through 291 Processing helix chain 'C' and resid 295 through 303 removed outlier: 3.897A pdb=" N LEU C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.605A pdb=" N PHE C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 338 through 359 removed outlier: 3.516A pdb=" N GLN C 359 " --> pdb=" O ILE C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 removed outlier: 4.083A pdb=" N SER C 366 " --> pdb=" O THR C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 removed outlier: 4.133A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 397 removed outlier: 3.513A pdb=" N SER C 387 " --> pdb=" O ASN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 413 through 425 removed outlier: 3.635A pdb=" N VAL C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 429 through 435 removed outlier: 3.798A pdb=" N GLU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 447 through 453 Processing helix chain 'C' and resid 459 through 476 removed outlier: 3.545A pdb=" N PHE C 476 " --> pdb=" O GLU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 495 removed outlier: 3.874A pdb=" N TRP C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 500 No H-bonds generated for 'chain 'C' and resid 498 through 500' Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.668A pdb=" N VAL C 518 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 525 Processing helix chain 'C' and resid 531 through 545 Processing helix chain 'C' and resid 573 through 586 Processing helix chain 'C' and resid 606 through 614 Processing helix chain 'C' and resid 637 through 650 Processing helix chain 'C' and resid 669 through 678 removed outlier: 4.680A pdb=" N ALA C 674 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL C 675 " --> pdb=" O MET C 672 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE C 678 " --> pdb=" O VAL C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 697 Processing helix chain 'D' and resid 62 through 82 removed outlier: 3.582A pdb=" N GLU D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Proline residue: D 70 - end of helix Processing helix chain 'D' and resid 85 through 104 removed outlier: 3.711A pdb=" N LEU D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 123 removed outlier: 3.502A pdb=" N VAL D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 Processing helix chain 'D' and resid 138 through 152 removed outlier: 3.675A pdb=" N GLN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 removed outlier: 4.462A pdb=" N ARG D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 172 Processing helix chain 'D' and resid 177 through 192 removed outlier: 3.528A pdb=" N ALA D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.566A pdb=" N ALA D 205 " --> pdb=" O ARG D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.769A pdb=" N VAL D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 236 Processing helix chain 'D' and resid 238 through 248 removed outlier: 3.690A pdb=" N GLN D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 260 Processing helix chain 'D' and resid 264 through 279 Processing helix chain 'D' and resid 283 through 291 Processing helix chain 'D' and resid 295 through 303 removed outlier: 3.896A pdb=" N LEU D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.604A pdb=" N PHE D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 338 through 359 removed outlier: 3.515A pdb=" N GLN D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 369 removed outlier: 4.082A pdb=" N SER D 366 " --> pdb=" O THR D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 380 removed outlier: 4.133A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 removed outlier: 3.512A pdb=" N SER D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 412 Processing helix chain 'D' and resid 413 through 425 removed outlier: 3.636A pdb=" N VAL D 417 " --> pdb=" O LYS D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 428 No H-bonds generated for 'chain 'D' and resid 426 through 428' Processing helix chain 'D' and resid 429 through 435 removed outlier: 3.799A pdb=" N GLU D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 447 through 453 Processing helix chain 'D' and resid 459 through 476 removed outlier: 3.545A pdb=" N PHE D 476 " --> pdb=" O GLU D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 495 removed outlier: 3.874A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 500 No H-bonds generated for 'chain 'D' and resid 498 through 500' Processing helix chain 'D' and resid 501 through 507 Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.668A pdb=" N VAL D 518 " --> pdb=" O LEU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 525 Processing helix chain 'D' and resid 531 through 545 Processing helix chain 'D' and resid 573 through 586 Processing helix chain 'D' and resid 606 through 614 Processing helix chain 'D' and resid 637 through 650 Processing helix chain 'D' and resid 669 through 678 removed outlier: 4.681A pdb=" N ALA D 674 " --> pdb=" O ASP D 671 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 675 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE D 678 " --> pdb=" O VAL D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 697 Processing helix chain 'E' and resid 62 through 82 removed outlier: 3.583A pdb=" N GLU E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 85 through 104 removed outlier: 3.711A pdb=" N LEU E 104 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 123 removed outlier: 3.501A pdb=" N VAL E 112 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 133 Processing helix chain 'E' and resid 138 through 152 removed outlier: 3.674A pdb=" N GLN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 163 removed outlier: 4.462A pdb=" N ARG E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 172 Processing helix chain 'E' and resid 177 through 192 removed outlier: 3.529A pdb=" N ALA E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 3.567A pdb=" N ALA E 205 " --> pdb=" O ARG E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 215 removed outlier: 3.769A pdb=" N VAL E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 236 Processing helix chain 'E' and resid 238 through 248 removed outlier: 3.690A pdb=" N GLN E 242 " --> pdb=" O GLY E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 260 Processing helix chain 'E' and resid 264 through 279 Processing helix chain 'E' and resid 283 through 291 Processing helix chain 'E' and resid 295 through 303 removed outlier: 3.897A pdb=" N LEU E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 309 removed outlier: 3.605A pdb=" N PHE E 308 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 338 through 359 removed outlier: 3.516A pdb=" N GLN E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 369 removed outlier: 4.082A pdb=" N SER E 366 " --> pdb=" O THR E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 380 removed outlier: 4.133A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 removed outlier: 3.512A pdb=" N SER E 387 " --> pdb=" O ASN E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 413 through 425 removed outlier: 3.635A pdb=" N VAL E 417 " --> pdb=" O LYS E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 429 through 435 removed outlier: 3.797A pdb=" N GLU E 435 " --> pdb=" O GLU E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 447 through 453 Processing helix chain 'E' and resid 459 through 476 removed outlier: 3.544A pdb=" N PHE E 476 " --> pdb=" O GLU E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.874A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 500 No H-bonds generated for 'chain 'E' and resid 498 through 500' Processing helix chain 'E' and resid 501 through 507 Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.668A pdb=" N VAL E 518 " --> pdb=" O LEU E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 525 Processing helix chain 'E' and resid 531 through 545 Processing helix chain 'E' and resid 573 through 586 Processing helix chain 'E' and resid 606 through 614 Processing helix chain 'E' and resid 637 through 650 Processing helix chain 'E' and resid 669 through 678 removed outlier: 4.680A pdb=" N ALA E 674 " --> pdb=" O ASP E 671 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL E 675 " --> pdb=" O MET E 672 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE E 678 " --> pdb=" O VAL E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 697 Processing helix chain 'F' and resid 62 through 82 removed outlier: 3.582A pdb=" N GLU F 66 " --> pdb=" O GLN F 62 " (cutoff:3.500A) Proline residue: F 70 - end of helix Processing helix chain 'F' and resid 85 through 104 removed outlier: 3.711A pdb=" N LEU F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 123 removed outlier: 3.501A pdb=" N VAL F 112 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 133 Processing helix chain 'F' and resid 138 through 152 removed outlier: 3.674A pdb=" N GLN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 163 removed outlier: 4.463A pdb=" N ARG F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 172 Processing helix chain 'F' and resid 177 through 192 removed outlier: 3.528A pdb=" N ALA F 181 " --> pdb=" O PRO F 177 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.565A pdb=" N ALA F 205 " --> pdb=" O ARG F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 215 removed outlier: 3.769A pdb=" N VAL F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 236 Processing helix chain 'F' and resid 238 through 248 removed outlier: 3.690A pdb=" N GLN F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 260 Processing helix chain 'F' and resid 264 through 279 Processing helix chain 'F' and resid 283 through 291 Processing helix chain 'F' and resid 295 through 303 removed outlier: 3.896A pdb=" N LEU F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 309 removed outlier: 3.604A pdb=" N PHE F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 338 through 359 removed outlier: 3.515A pdb=" N GLN F 359 " --> pdb=" O ILE F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 369 removed outlier: 4.082A pdb=" N SER F 366 " --> pdb=" O THR F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 380 removed outlier: 4.133A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 removed outlier: 3.513A pdb=" N SER F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 412 Processing helix chain 'F' and resid 413 through 425 removed outlier: 3.636A pdb=" N VAL F 417 " --> pdb=" O LYS F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 428 No H-bonds generated for 'chain 'F' and resid 426 through 428' Processing helix chain 'F' and resid 429 through 435 removed outlier: 3.798A pdb=" N GLU F 435 " --> pdb=" O GLU F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 447 through 453 Processing helix chain 'F' and resid 459 through 476 removed outlier: 3.545A pdb=" N PHE F 476 " --> pdb=" O GLU F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 495 removed outlier: 3.873A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 500 No H-bonds generated for 'chain 'F' and resid 498 through 500' Processing helix chain 'F' and resid 501 through 507 Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.669A pdb=" N VAL F 518 " --> pdb=" O LEU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 525 Processing helix chain 'F' and resid 531 through 545 Processing helix chain 'F' and resid 573 through 586 Processing helix chain 'F' and resid 606 through 614 Processing helix chain 'F' and resid 637 through 650 Processing helix chain 'F' and resid 669 through 678 removed outlier: 4.681A pdb=" N ALA F 674 " --> pdb=" O ASP F 671 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL F 675 " --> pdb=" O MET F 672 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE F 678 " --> pdb=" O VAL F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 697 Processing helix chain 'G' and resid 62 through 82 removed outlier: 3.582A pdb=" N GLU G 66 " --> pdb=" O GLN G 62 " (cutoff:3.500A) Proline residue: G 70 - end of helix Processing helix chain 'G' and resid 85 through 104 removed outlier: 3.710A pdb=" N LEU G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 123 removed outlier: 3.502A pdb=" N VAL G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 133 Processing helix chain 'G' and resid 138 through 152 removed outlier: 3.674A pdb=" N GLN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 163 removed outlier: 4.462A pdb=" N ARG G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 172 Processing helix chain 'G' and resid 177 through 192 removed outlier: 3.529A pdb=" N ALA G 181 " --> pdb=" O PRO G 177 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.565A pdb=" N ALA G 205 " --> pdb=" O ARG G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 215 removed outlier: 3.769A pdb=" N VAL G 211 " --> pdb=" O GLY G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 236 Processing helix chain 'G' and resid 238 through 248 removed outlier: 3.691A pdb=" N GLN G 242 " --> pdb=" O GLY G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 260 Processing helix chain 'G' and resid 264 through 279 Processing helix chain 'G' and resid 283 through 291 Processing helix chain 'G' and resid 295 through 303 removed outlier: 3.897A pdb=" N LEU G 299 " --> pdb=" O LEU G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 309 removed outlier: 3.604A pdb=" N PHE G 308 " --> pdb=" O ASP G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 328 Processing helix chain 'G' and resid 338 through 359 removed outlier: 3.515A pdb=" N GLN G 359 " --> pdb=" O ILE G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 369 removed outlier: 4.083A pdb=" N SER G 366 " --> pdb=" O THR G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 380 removed outlier: 4.133A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 397 removed outlier: 3.512A pdb=" N SER G 387 " --> pdb=" O ASN G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 413 through 425 removed outlier: 3.636A pdb=" N VAL G 417 " --> pdb=" O LYS G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 428 No H-bonds generated for 'chain 'G' and resid 426 through 428' Processing helix chain 'G' and resid 429 through 435 removed outlier: 3.799A pdb=" N GLU G 435 " --> pdb=" O GLU G 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 444 Processing helix chain 'G' and resid 447 through 453 Processing helix chain 'G' and resid 459 through 476 removed outlier: 3.545A pdb=" N PHE G 476 " --> pdb=" O GLU G 472 " (cutoff:3.500A) Processing helix chain 'G' and resid 486 through 495 removed outlier: 3.874A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 500 No H-bonds generated for 'chain 'G' and resid 498 through 500' Processing helix chain 'G' and resid 501 through 507 Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.668A pdb=" N VAL G 518 " --> pdb=" O LEU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 525 Processing helix chain 'G' and resid 531 through 545 Processing helix chain 'G' and resid 573 through 586 Processing helix chain 'G' and resid 606 through 614 Processing helix chain 'G' and resid 637 through 650 Processing helix chain 'G' and resid 669 through 678 removed outlier: 4.680A pdb=" N ALA G 674 " --> pdb=" O ASP G 671 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL G 675 " --> pdb=" O MET G 672 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE G 678 " --> pdb=" O VAL G 675 " (cutoff:3.500A) Processing helix chain 'G' and resid 687 through 697 Processing helix chain 'H' and resid 62 through 82 removed outlier: 3.582A pdb=" N GLU H 66 " --> pdb=" O GLN H 62 " (cutoff:3.500A) Proline residue: H 70 - end of helix Processing helix chain 'H' and resid 85 through 104 removed outlier: 3.711A pdb=" N LEU H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 123 removed outlier: 3.501A pdb=" N VAL H 112 " --> pdb=" O VAL H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 138 through 152 removed outlier: 3.675A pdb=" N GLN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU H 152 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 163 removed outlier: 4.463A pdb=" N ARG H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 172 Processing helix chain 'H' and resid 177 through 192 removed outlier: 3.529A pdb=" N ALA H 181 " --> pdb=" O PRO H 177 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY H 186 " --> pdb=" O ARG H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 205 removed outlier: 3.565A pdb=" N ALA H 205 " --> pdb=" O ARG H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 215 removed outlier: 3.769A pdb=" N VAL H 211 " --> pdb=" O GLY H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 236 Processing helix chain 'H' and resid 238 through 248 removed outlier: 3.690A pdb=" N GLN H 242 " --> pdb=" O GLY H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 260 Processing helix chain 'H' and resid 264 through 279 Processing helix chain 'H' and resid 283 through 291 Processing helix chain 'H' and resid 295 through 303 removed outlier: 3.897A pdb=" N LEU H 299 " --> pdb=" O LEU H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 309 removed outlier: 3.605A pdb=" N PHE H 308 " --> pdb=" O ASP H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 328 Processing helix chain 'H' and resid 338 through 359 removed outlier: 3.516A pdb=" N GLN H 359 " --> pdb=" O ILE H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 369 removed outlier: 4.083A pdb=" N SER H 366 " --> pdb=" O THR H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 380 removed outlier: 4.134A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 397 removed outlier: 3.511A pdb=" N SER H 387 " --> pdb=" O ASN H 383 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 412 Processing helix chain 'H' and resid 413 through 425 removed outlier: 3.636A pdb=" N VAL H 417 " --> pdb=" O LYS H 413 " (cutoff:3.500A) Processing helix chain 'H' and resid 426 through 428 No H-bonds generated for 'chain 'H' and resid 426 through 428' Processing helix chain 'H' and resid 429 through 435 removed outlier: 3.799A pdb=" N GLU H 435 " --> pdb=" O GLU H 431 " (cutoff:3.500A) Processing helix chain 'H' and resid 439 through 444 Processing helix chain 'H' and resid 447 through 453 Processing helix chain 'H' and resid 459 through 476 removed outlier: 3.544A pdb=" N PHE H 476 " --> pdb=" O GLU H 472 " (cutoff:3.500A) Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.873A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 500 No H-bonds generated for 'chain 'H' and resid 498 through 500' Processing helix chain 'H' and resid 501 through 507 Processing helix chain 'H' and resid 514 through 518 removed outlier: 3.669A pdb=" N VAL H 518 " --> pdb=" O LEU H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 525 Processing helix chain 'H' and resid 531 through 545 Processing helix chain 'H' and resid 573 through 586 Processing helix chain 'H' and resid 606 through 614 Processing helix chain 'H' and resid 637 through 650 Processing helix chain 'H' and resid 669 through 678 removed outlier: 4.681A pdb=" N ALA H 674 " --> pdb=" O ASP H 671 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL H 675 " --> pdb=" O MET H 672 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE H 678 " --> pdb=" O VAL H 675 " (cutoff:3.500A) Processing helix chain 'H' and resid 687 through 697 Processing sheet with id=AA1, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.696A pdb=" N VAL A 564 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE A 565 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL A 620 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER A 567 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE A 681 " --> pdb=" O ILE A 653 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 591 through 592 removed outlier: 6.695A pdb=" N VAL B 564 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE B 565 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL B 620 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE B 681 " --> pdb=" O ILE B 653 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 591 through 592 removed outlier: 6.696A pdb=" N VAL C 564 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE C 565 " --> pdb=" O VAL C 618 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL C 620 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER C 567 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE C 681 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 591 through 592 removed outlier: 6.696A pdb=" N VAL D 564 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE D 565 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL D 620 " --> pdb=" O PHE D 565 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER D 567 " --> pdb=" O VAL D 620 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE D 681 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 591 through 592 removed outlier: 6.695A pdb=" N VAL E 564 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE E 565 " --> pdb=" O VAL E 618 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL E 620 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER E 567 " --> pdb=" O VAL E 620 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE E 681 " --> pdb=" O ILE E 653 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 591 through 592 removed outlier: 6.695A pdb=" N VAL F 564 " --> pdb=" O PHE F 592 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE F 565 " --> pdb=" O VAL F 618 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL F 620 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER F 567 " --> pdb=" O VAL F 620 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE F 681 " --> pdb=" O ILE F 653 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 591 through 592 removed outlier: 6.696A pdb=" N VAL G 564 " --> pdb=" O PHE G 592 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE G 565 " --> pdb=" O VAL G 618 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL G 620 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER G 567 " --> pdb=" O VAL G 620 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE G 681 " --> pdb=" O ILE G 653 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 591 through 592 removed outlier: 6.695A pdb=" N VAL H 564 " --> pdb=" O PHE H 592 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE H 565 " --> pdb=" O VAL H 618 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL H 620 " --> pdb=" O PHE H 565 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE H 681 " --> pdb=" O ILE H 653 " (cutoff:3.500A) 2048 hydrogen bonds defined for protein. 5976 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: 13.59 Time building geometry restraints manager: 15.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12970 1.34 - 1.46: 5381 1.46 - 1.58: 20337 1.58 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 38928 Sorted by residual: bond pdb=" N ASN C 337 " pdb=" CA ASN C 337 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.04e+00 bond pdb=" N ASN F 337 " pdb=" CA ASN F 337 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.00e+00 bond pdb=" N ASN B 337 " pdb=" CA ASN B 337 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.98e+00 bond pdb=" N ASN D 337 " pdb=" CA ASN D 337 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.89e+00 bond pdb=" N ASN H 337 " pdb=" CA ASN H 337 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.86e+00 ... (remaining 38923 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.13: 977 107.13 - 113.86: 21897 113.86 - 120.58: 16805 120.58 - 127.31: 12541 127.31 - 134.03: 388 Bond angle restraints: 52608 Sorted by residual: angle pdb=" C SER H 336 " pdb=" N ASN H 337 " pdb=" CA ASN H 337 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C SER B 336 " pdb=" N ASN B 337 " pdb=" CA ASN B 337 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C SER A 336 " pdb=" N ASN A 337 " pdb=" CA ASN A 337 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C SER G 336 " pdb=" N ASN G 337 " pdb=" CA ASN G 337 " ideal model delta sigma weight residual 121.54 130.21 -8.67 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C SER D 336 " pdb=" N ASN D 337 " pdb=" CA ASN D 337 " ideal model delta sigma weight residual 121.54 130.18 -8.64 1.91e+00 2.74e-01 2.05e+01 ... (remaining 52603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.08: 22969 15.08 - 30.16: 615 30.16 - 45.24: 120 45.24 - 60.32: 8 60.32 - 75.40: 16 Dihedral angle restraints: 23728 sinusoidal: 9680 harmonic: 14048 Sorted by residual: dihedral pdb=" CA GLU G 174 " pdb=" C GLU G 174 " pdb=" N ARG G 175 " pdb=" CA ARG G 175 " ideal model delta harmonic sigma weight residual -180.00 -162.51 -17.49 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA GLU B 174 " pdb=" C GLU B 174 " pdb=" N ARG B 175 " pdb=" CA ARG B 175 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA GLU E 174 " pdb=" C GLU E 174 " pdb=" N ARG E 175 " pdb=" CA ARG E 175 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 23725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4321 0.042 - 0.085: 1357 0.085 - 0.127: 298 0.127 - 0.170: 25 0.170 - 0.212: 23 Chirality restraints: 6024 Sorted by residual: chirality pdb=" CA ASN G 337 " pdb=" N ASN G 337 " pdb=" C ASN G 337 " pdb=" CB ASN G 337 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ASN A 337 " pdb=" N ASN A 337 " pdb=" C ASN A 337 " pdb=" CB ASN A 337 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ASN E 337 " pdb=" N ASN E 337 " pdb=" C ASN E 337 " pdb=" CB ASN E 337 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 6021 not shown) Planarity restraints: 6816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 283 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C VAL G 283 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL G 283 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU G 284 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 283 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" C VAL H 283 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL H 283 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU H 284 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 283 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C VAL D 283 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL D 283 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU D 284 " 0.014 2.00e-02 2.50e+03 ... (remaining 6813 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 11276 2.83 - 3.35: 33651 3.35 - 3.86: 60935 3.86 - 4.38: 71804 4.38 - 4.90: 123065 Nonbonded interactions: 300731 Sorted by model distance: nonbonded pdb=" OE1 GLN D 436 " pdb=" OG SER E 459 " model vdw 2.309 2.440 nonbonded pdb=" OE1 GLN C 436 " pdb=" OG SER D 459 " model vdw 2.313 2.440 nonbonded pdb=" OH TYR A 568 " pdb=" OD1 ASP A 594 " model vdw 2.331 2.440 nonbonded pdb=" OH TYR C 568 " pdb=" OD1 ASP C 594 " model vdw 2.331 2.440 nonbonded pdb=" OH TYR G 568 " pdb=" OD1 ASP G 594 " model vdw 2.331 2.440 ... (remaining 300726 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' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.180 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: 0.060 Extract box with map and model: 14.840 Check model and map are aligned: 0.540 Set scattering table: 0.340 Process input model: 93.710 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.240 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:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38928 Z= 0.220 Angle : 0.766 9.858 52608 Z= 0.440 Chirality : 0.044 0.212 6024 Planarity : 0.006 0.055 6816 Dihedral : 8.238 75.399 14608 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -3.70 (0.09), residues: 4824 helix: -2.56 (0.06), residues: 3160 sheet: -1.27 (0.43), residues: 152 loop : -1.85 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 214 HIS 0.010 0.002 HIS D 269 PHE 0.032 0.002 PHE C 192 TYR 0.009 0.001 TYR H 568 ARG 0.006 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1013 time to evaluate : 4.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8558 (tp) cc_final: 0.8348 (tm) REVERT: A 174 GLU cc_start: 0.7180 (tt0) cc_final: 0.6915 (tp30) REVERT: A 580 LEU cc_start: 0.8642 (mt) cc_final: 0.7824 (tm) REVERT: A 589 PHE cc_start: 0.7563 (m-10) cc_final: 0.7098 (m-80) REVERT: A 608 ILE cc_start: 0.6242 (mt) cc_final: 0.6030 (pp) REVERT: A 686 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7242 (tm-30) REVERT: A 694 LYS cc_start: 0.7984 (tttt) cc_final: 0.7668 (tptp) REVERT: B 114 GLN cc_start: 0.7543 (mt0) cc_final: 0.7110 (mm-40) REVERT: B 171 LEU cc_start: 0.7283 (mt) cc_final: 0.6964 (mt) REVERT: B 686 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6823 (tm-30) REVERT: B 694 LYS cc_start: 0.7846 (tttt) cc_final: 0.7601 (ttpt) REVERT: C 114 GLN cc_start: 0.7708 (mt0) cc_final: 0.7362 (tm-30) REVERT: C 117 CYS cc_start: 0.7607 (m) cc_final: 0.7235 (m) REVERT: C 580 LEU cc_start: 0.8542 (mt) cc_final: 0.7834 (tm) REVERT: C 608 ILE cc_start: 0.6300 (mt) cc_final: 0.6029 (pp) REVERT: C 643 ILE cc_start: 0.8160 (mt) cc_final: 0.7887 (tp) REVERT: C 686 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7240 (tt0) REVERT: C 694 LYS cc_start: 0.7929 (tttt) cc_final: 0.7588 (tptp) REVERT: C 696 ILE cc_start: 0.7931 (mt) cc_final: 0.7693 (pt) REVERT: D 98 LEU cc_start: 0.7914 (tt) cc_final: 0.7691 (tp) REVERT: D 694 LYS cc_start: 0.7868 (tttt) cc_final: 0.7607 (ttmt) REVERT: E 571 ASN cc_start: 0.7757 (m-40) cc_final: 0.7244 (t0) REVERT: E 580 LEU cc_start: 0.8404 (mt) cc_final: 0.7741 (tm) REVERT: E 696 ILE cc_start: 0.7893 (mt) cc_final: 0.7687 (pt) REVERT: F 580 LEU cc_start: 0.8850 (mt) cc_final: 0.8118 (tm) REVERT: F 686 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6756 (tm-30) REVERT: F 694 LYS cc_start: 0.7989 (tttt) cc_final: 0.7579 (ttmt) REVERT: G 114 GLN cc_start: 0.7783 (mt0) cc_final: 0.7578 (tm-30) REVERT: G 580 LEU cc_start: 0.8537 (mt) cc_final: 0.7808 (tm) REVERT: G 608 ILE cc_start: 0.6337 (mt) cc_final: 0.6069 (pp) REVERT: G 672 MET cc_start: 0.5110 (ptm) cc_final: 0.4833 (ppp) REVERT: G 694 LYS cc_start: 0.7941 (tttt) cc_final: 0.7654 (tptp) REVERT: G 696 ILE cc_start: 0.7934 (mt) cc_final: 0.7704 (pt) REVERT: H 114 GLN cc_start: 0.7504 (mt0) cc_final: 0.7147 (mm-40) REVERT: H 694 LYS cc_start: 0.7768 (tttt) cc_final: 0.7543 (ttpt) outliers start: 0 outliers final: 0 residues processed: 1013 average time/residue: 1.7248 time to fit residues: 2050.2237 Evaluate side-chains 372 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 4.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 412 optimal weight: 2.9990 chunk 369 optimal weight: 0.7980 chunk 205 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 249 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 382 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 232 optimal weight: 0.8980 chunk 284 optimal weight: 0.9980 chunk 443 optimal weight: 5.9990 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 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN A 609 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN B 143 GLN ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 GLN C 616 ASN D 143 GLN D 280 ASN E 452 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN F 170 ASN F 280 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 609 GLN G 616 ASN G 700 GLN H 97 GLN H 170 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 38928 Z= 0.192 Angle : 0.557 10.397 52608 Z= 0.280 Chirality : 0.039 0.147 6024 Planarity : 0.005 0.058 6816 Dihedral : 4.038 15.597 5312 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.53 % Allowed : 11.20 % Favored : 85.27 % 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: -1.22 (0.11), residues: 4824 helix: -0.57 (0.09), residues: 3240 sheet: -0.91 (0.42), residues: 152 loop : -0.98 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 412 HIS 0.004 0.001 HIS G 534 PHE 0.025 0.002 PHE A 433 TYR 0.018 0.002 TYR D 687 ARG 0.007 0.001 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 513 time to evaluate : 4.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: A 355 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7534 (mt) REVERT: A 580 LEU cc_start: 0.8476 (mt) cc_final: 0.7814 (tm) REVERT: A 694 LYS cc_start: 0.8065 (tttt) cc_final: 0.7573 (tptp) REVERT: B 98 LEU cc_start: 0.7680 (pp) cc_final: 0.7470 (pt) REVERT: B 580 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8397 (mm) REVERT: B 615 ARG cc_start: 0.7310 (ttt180) cc_final: 0.6975 (ttt-90) REVERT: B 655 PRO cc_start: 0.7887 (Cg_exo) cc_final: 0.7522 (Cg_endo) REVERT: B 694 LYS cc_start: 0.8006 (tttt) cc_final: 0.7694 (ttmt) REVERT: C 150 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7498 (tp40) REVERT: C 355 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7426 (mt) REVERT: C 367 ASP cc_start: 0.6734 (m-30) cc_final: 0.6429 (m-30) REVERT: C 414 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: C 615 ARG cc_start: 0.6586 (ttt180) cc_final: 0.6175 (ttt-90) REVERT: C 655 PRO cc_start: 0.7411 (Cg_exo) cc_final: 0.6998 (Cg_endo) REVERT: C 694 LYS cc_start: 0.8016 (tttt) cc_final: 0.7517 (tptp) REVERT: D 580 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8343 (mm) REVERT: D 615 ARG cc_start: 0.7162 (ttt180) cc_final: 0.6836 (ttt-90) REVERT: D 655 PRO cc_start: 0.7878 (Cg_exo) cc_final: 0.7506 (Cg_endo) REVERT: E 367 ASP cc_start: 0.6872 (m-30) cc_final: 0.6552 (m-30) REVERT: E 414 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: E 576 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8309 (tp) REVERT: E 580 LEU cc_start: 0.8497 (mt) cc_final: 0.7839 (tm) REVERT: E 615 ARG cc_start: 0.6387 (ttt180) cc_final: 0.5991 (ttt-90) REVERT: E 630 MET cc_start: 0.3527 (mmp) cc_final: 0.3110 (ppp) REVERT: E 655 PRO cc_start: 0.7395 (Cg_exo) cc_final: 0.7044 (Cg_endo) REVERT: E 672 MET cc_start: 0.5317 (ptm) cc_final: 0.5088 (ppp) REVERT: F 98 LEU cc_start: 0.7667 (pp) cc_final: 0.7288 (pp) REVERT: F 363 LYS cc_start: 0.7869 (tppt) cc_final: 0.7551 (tppp) REVERT: F 615 ARG cc_start: 0.7290 (ttt180) cc_final: 0.6780 (ttt-90) REVERT: F 655 PRO cc_start: 0.7822 (Cg_exo) cc_final: 0.7433 (Cg_endo) REVERT: F 686 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6869 (tm-30) REVERT: G 252 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: G 367 ASP cc_start: 0.6899 (m-30) cc_final: 0.6574 (m-30) REVERT: G 571 ASN cc_start: 0.7964 (m-40) cc_final: 0.7311 (t0) REVERT: G 655 PRO cc_start: 0.7330 (Cg_exo) cc_final: 0.6909 (Cg_endo) REVERT: G 694 LYS cc_start: 0.8065 (tttt) cc_final: 0.7564 (tptp) REVERT: H 98 LEU cc_start: 0.7683 (pp) cc_final: 0.7306 (pp) REVERT: H 138 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6932 (tm) REVERT: H 580 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8374 (mm) REVERT: H 615 ARG cc_start: 0.7257 (ttt180) cc_final: 0.6877 (ttt-90) REVERT: H 655 PRO cc_start: 0.7883 (Cg_exo) cc_final: 0.7514 (Cg_endo) REVERT: H 694 LYS cc_start: 0.7662 (tttt) cc_final: 0.7432 (ttpt) outliers start: 144 outliers final: 35 residues processed: 627 average time/residue: 1.6713 time to fit residues: 1245.2553 Evaluate side-chains 374 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 327 time to evaluate : 4.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 581 LYS Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 608 ILE Chi-restraints excluded: chain H residue 616 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 246 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 368 optimal weight: 7.9990 chunk 301 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 443 optimal weight: 0.9990 chunk 479 optimal weight: 5.9990 chunk 395 optimal weight: 2.9990 chunk 440 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 356 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN C 97 GLN C 575 GLN E 97 GLN E 437 GLN E 585 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 437 GLN G 575 GLN G 585 GLN H 452 GLN H 521 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 38928 Z= 0.388 Angle : 0.674 10.514 52608 Z= 0.334 Chirality : 0.044 0.146 6024 Planarity : 0.005 0.051 6816 Dihedral : 4.286 16.629 5312 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.85 % Allowed : 12.52 % Favored : 83.63 % 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: -0.55 (0.12), residues: 4824 helix: -0.09 (0.09), residues: 3336 sheet: -0.97 (0.39), residues: 152 loop : -0.62 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 214 HIS 0.008 0.002 HIS F 194 PHE 0.021 0.002 PHE H 433 TYR 0.015 0.003 TYR B 429 ARG 0.012 0.001 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 378 time to evaluate : 4.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7178 (mtp180) REVERT: A 694 LYS cc_start: 0.8075 (tttt) cc_final: 0.7619 (tptp) REVERT: B 363 LYS cc_start: 0.7914 (tppt) cc_final: 0.7596 (tppp) REVERT: B 543 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7264 (mtp180) REVERT: B 580 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8449 (mm) REVERT: B 615 ARG cc_start: 0.7324 (ttt180) cc_final: 0.6728 (ttt-90) REVERT: C 114 GLN cc_start: 0.7636 (mt0) cc_final: 0.7376 (tm-30) REVERT: C 118 ASP cc_start: 0.7761 (m-30) cc_final: 0.7490 (m-30) REVERT: C 149 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7202 (tm-30) REVERT: C 150 GLN cc_start: 0.7676 (tp40) cc_final: 0.7332 (tp40) REVERT: C 395 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7212 (mtp180) REVERT: C 399 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6332 (mp0) REVERT: C 414 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7429 (mt-10) REVERT: C 615 ARG cc_start: 0.6545 (ttt180) cc_final: 0.5943 (ttt-90) REVERT: C 694 LYS cc_start: 0.8079 (tttt) cc_final: 0.7602 (tptp) REVERT: D 97 GLN cc_start: 0.7207 (tm130) cc_final: 0.6972 (tm130) REVERT: D 363 LYS cc_start: 0.7899 (tppt) cc_final: 0.7619 (tppp) REVERT: D 445 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7816 (mtp85) REVERT: D 543 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7264 (mtp180) REVERT: D 580 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8470 (mm) REVERT: D 615 ARG cc_start: 0.7267 (ttt180) cc_final: 0.6564 (ttt-90) REVERT: D 655 PRO cc_start: 0.7823 (Cg_exo) cc_final: 0.7441 (Cg_endo) REVERT: E 118 ASP cc_start: 0.8087 (m-30) cc_final: 0.7883 (m-30) REVERT: E 337 ASN cc_start: 0.7996 (p0) cc_final: 0.7751 (p0) REVERT: E 399 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6323 (mp0) REVERT: E 403 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6973 (mtp180) REVERT: E 414 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: E 672 MET cc_start: 0.5156 (ptm) cc_final: 0.4890 (pp-130) REVERT: E 694 LYS cc_start: 0.8131 (ttmt) cc_final: 0.7343 (tptp) REVERT: F 130 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8171 (mm) REVERT: F 395 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7672 (mtp180) REVERT: F 543 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7258 (mtp180) REVERT: F 580 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8473 (mm) REVERT: F 615 ARG cc_start: 0.7184 (ttt180) cc_final: 0.6701 (ttt-90) REVERT: F 686 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7177 (tm-30) REVERT: G 116 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7472 (mp) REVERT: G 138 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6922 (tt) REVERT: G 399 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6450 (mp0) REVERT: G 580 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8232 (mm) REVERT: G 615 ARG cc_start: 0.6437 (mtp180) cc_final: 0.6141 (ttt-90) REVERT: G 694 LYS cc_start: 0.8129 (tttt) cc_final: 0.7613 (tptp) REVERT: H 245 MET cc_start: 0.8436 (mtp) cc_final: 0.8199 (mtp) REVERT: H 363 LYS cc_start: 0.7958 (tppt) cc_final: 0.7655 (tppp) REVERT: H 395 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7698 (mtp180) REVERT: H 543 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7253 (mtp180) REVERT: H 580 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8520 (mm) REVERT: H 615 ARG cc_start: 0.7290 (ttt180) cc_final: 0.6599 (ttt-90) REVERT: H 655 PRO cc_start: 0.7864 (Cg_exo) cc_final: 0.7533 (Cg_endo) REVERT: H 694 LYS cc_start: 0.7818 (tttt) cc_final: 0.7453 (tmmt) outliers start: 157 outliers final: 56 residues processed: 514 average time/residue: 1.7150 time to fit residues: 1043.7687 Evaluate side-chains 403 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 324 time to evaluate : 4.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 543 ARG Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 403 ARG Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 643 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 286 GLU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 395 ARG Chi-restraints excluded: chain F residue 543 ARG Chi-restraints excluded: chain F residue 580 LEU Chi-restraints excluded: chain F residue 608 ILE Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 286 GLU Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 399 GLU Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 169 LEU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 286 GLU Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 543 ARG Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 608 ILE Chi-restraints excluded: chain H residue 616 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 438 optimal weight: 1.9990 chunk 333 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 211 optimal weight: 0.9980 chunk 298 optimal weight: 0.0060 chunk 445 optimal weight: 2.9990 chunk 471 optimal weight: 0.6980 chunk 232 optimal weight: 1.9990 chunk 422 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 38928 Z= 0.193 Angle : 0.537 10.344 52608 Z= 0.265 Chirality : 0.039 0.141 6024 Planarity : 0.004 0.050 6816 Dihedral : 3.923 14.662 5312 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.38 % Allowed : 13.70 % Favored : 82.92 % 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: 0.21 (0.12), residues: 4824 helix: 0.46 (0.09), residues: 3352 sheet: -0.62 (0.41), residues: 152 loop : -0.27 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 103 HIS 0.004 0.001 HIS F 269 PHE 0.017 0.001 PHE D 96 TYR 0.012 0.001 TYR A 687 ARG 0.012 0.000 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 356 time to evaluate : 4.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ARG cc_start: 0.7255 (mtm110) cc_final: 0.7055 (ptm-80) REVERT: A 285 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7218 (mmt-90) REVERT: A 399 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.5954 (mp0) REVERT: A 414 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: A 580 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8116 (mm) REVERT: A 694 LYS cc_start: 0.8073 (tttt) cc_final: 0.7609 (tptp) REVERT: B 138 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7087 (tm) REVERT: B 307 ARG cc_start: 0.7652 (ttp80) cc_final: 0.7357 (ttp80) REVERT: B 395 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7653 (mtp180) REVERT: B 454 ASP cc_start: 0.8336 (m-30) cc_final: 0.8069 (m-30) REVERT: B 543 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7283 (mtp180) REVERT: B 580 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8502 (mm) REVERT: B 615 ARG cc_start: 0.7209 (ttt180) cc_final: 0.6671 (ttt-90) REVERT: B 655 PRO cc_start: 0.7828 (Cg_exo) cc_final: 0.7453 (Cg_endo) REVERT: B 669 PRO cc_start: 0.6003 (Cg_exo) cc_final: 0.5605 (Cg_endo) REVERT: B 694 LYS cc_start: 0.7943 (tttt) cc_final: 0.7701 (ttmt) REVERT: C 116 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7312 (mp) REVERT: C 150 GLN cc_start: 0.7854 (tp40) cc_final: 0.7479 (tp-100) REVERT: C 414 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: C 580 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8175 (mm) REVERT: C 615 ARG cc_start: 0.6639 (ttt180) cc_final: 0.6017 (ttt-90) REVERT: C 669 PRO cc_start: 0.6307 (Cg_exo) cc_final: 0.6077 (Cg_endo) REVERT: C 694 LYS cc_start: 0.8078 (tttt) cc_final: 0.7561 (tptp) REVERT: D 97 GLN cc_start: 0.7196 (tm130) cc_final: 0.6882 (tm130) REVERT: D 138 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7037 (tm) REVERT: D 143 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7360 (tp-100) REVERT: D 363 LYS cc_start: 0.7856 (tppt) cc_final: 0.7598 (tppp) REVERT: D 395 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7656 (mtp180) REVERT: D 454 ASP cc_start: 0.8334 (m-30) cc_final: 0.8068 (m-30) REVERT: D 543 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7260 (mtp180) REVERT: D 580 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8554 (mm) REVERT: D 615 ARG cc_start: 0.7217 (ttt180) cc_final: 0.6596 (ttt-90) REVERT: D 655 PRO cc_start: 0.7815 (Cg_exo) cc_final: 0.7443 (Cg_endo) REVERT: E 114 GLN cc_start: 0.7613 (tm-30) cc_final: 0.7086 (tm-30) REVERT: E 395 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7307 (mtp180) REVERT: E 399 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6150 (mp0) REVERT: E 414 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7416 (mt-10) REVERT: E 580 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8168 (mm) REVERT: E 630 MET cc_start: 0.4765 (mmm) cc_final: 0.3915 (ppp) REVERT: E 694 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7862 (tmmm) REVERT: F 130 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8233 (mm) REVERT: F 454 ASP cc_start: 0.8342 (m-30) cc_final: 0.8071 (m-30) REVERT: F 543 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7266 (mtp180) REVERT: F 580 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8450 (mm) REVERT: F 615 ARG cc_start: 0.7107 (ttt180) cc_final: 0.6641 (ttt-90) REVERT: F 630 MET cc_start: 0.4357 (mmm) cc_final: 0.3723 (pp-130) REVERT: F 686 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7226 (tm-30) REVERT: G 138 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.7035 (tt) REVERT: G 150 GLN cc_start: 0.7851 (tp40) cc_final: 0.7582 (tp-100) REVERT: G 358 LEU cc_start: 0.7570 (tt) cc_final: 0.7252 (tp) REVERT: G 395 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7315 (mtp180) REVERT: G 399 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: G 571 ASN cc_start: 0.8089 (m-40) cc_final: 0.7368 (t0) REVERT: G 615 ARG cc_start: 0.6523 (mtp180) cc_final: 0.6109 (ttt-90) REVERT: G 694 LYS cc_start: 0.8086 (tttt) cc_final: 0.7583 (tptp) REVERT: H 97 GLN cc_start: 0.7284 (pp30) cc_final: 0.6887 (tm130) REVERT: H 138 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6935 (tm) REVERT: H 454 ASP cc_start: 0.8330 (m-30) cc_final: 0.8087 (m-30) REVERT: H 543 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7267 (mtp180) REVERT: H 580 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8534 (mm) REVERT: H 615 ARG cc_start: 0.7158 (ttt180) cc_final: 0.6578 (ttt-90) REVERT: H 655 PRO cc_start: 0.7717 (Cg_exo) cc_final: 0.7375 (Cg_endo) REVERT: H 669 PRO cc_start: 0.5892 (Cg_exo) cc_final: 0.5649 (Cg_endo) REVERT: H 694 LYS cc_start: 0.7793 (tttt) cc_final: 0.7443 (ttmt) REVERT: H 696 ILE cc_start: 0.8242 (tp) cc_final: 0.7799 (pt) outliers start: 138 outliers final: 54 residues processed: 476 average time/residue: 1.6393 time to fit residues: 929.6323 Evaluate side-chains 401 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 318 time to evaluate : 4.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 543 ARG Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 652 ASN Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 543 ARG Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 580 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 355 ILE Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 399 GLU Chi-restraints excluded: chain G residue 544 GLU Chi-restraints excluded: chain G residue 581 LYS Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 543 ARG Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 608 ILE Chi-restraints excluded: chain H residue 616 ASN Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain H residue 652 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 392 optimal weight: 4.9990 chunk 267 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 351 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 402 optimal weight: 0.9990 chunk 326 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 240 optimal weight: 0.8980 chunk 423 optimal weight: 0.0050 chunk 119 optimal weight: 8.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 616 ASN B 97 GLN B 143 GLN C 143 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38928 Z= 0.169 Angle : 0.520 12.252 52608 Z= 0.255 Chirality : 0.038 0.184 6024 Planarity : 0.004 0.050 6816 Dihedral : 3.720 13.803 5312 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.38 % Allowed : 14.49 % Favored : 82.13 % 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: 0.74 (0.12), residues: 4824 helix: 0.85 (0.09), residues: 3352 sheet: -0.12 (0.43), residues: 152 loop : -0.11 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 103 HIS 0.004 0.001 HIS F 269 PHE 0.018 0.001 PHE G 96 TYR 0.011 0.001 TYR A 687 ARG 0.009 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 341 time to evaluate : 4.635 Fit side-chains revert: symmetry clash REVERT: A 399 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5927 (mp0) REVERT: A 580 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8114 (mm) REVERT: A 694 LYS cc_start: 0.8081 (tttt) cc_final: 0.7625 (tptp) REVERT: B 138 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7035 (tm) REVERT: B 143 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7382 (tp40) REVERT: B 150 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: B 307 ARG cc_start: 0.7771 (ttp80) cc_final: 0.7420 (ttp80) REVERT: B 363 LYS cc_start: 0.7951 (tptm) cc_final: 0.7740 (tppp) REVERT: B 367 ASP cc_start: 0.7158 (m-30) cc_final: 0.6860 (m-30) REVERT: B 395 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7632 (mtp180) REVERT: B 454 ASP cc_start: 0.8321 (m-30) cc_final: 0.8078 (m-30) REVERT: B 543 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7227 (mtp180) REVERT: B 580 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8536 (mm) REVERT: B 615 ARG cc_start: 0.7171 (ttt180) cc_final: 0.6718 (ttt-90) REVERT: B 669 PRO cc_start: 0.6078 (Cg_exo) cc_final: 0.5858 (Cg_endo) REVERT: B 694 LYS cc_start: 0.7898 (tttt) cc_final: 0.7637 (ttmt) REVERT: B 696 ILE cc_start: 0.8166 (tt) cc_final: 0.7745 (pt) REVERT: C 403 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.6387 (tmm160) REVERT: C 580 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8152 (mm) REVERT: C 589 PHE cc_start: 0.7795 (m-10) cc_final: 0.7224 (m-80) REVERT: C 615 ARG cc_start: 0.6486 (ttt180) cc_final: 0.5834 (ttt-90) REVERT: C 669 PRO cc_start: 0.6396 (Cg_exo) cc_final: 0.6104 (Cg_endo) REVERT: C 694 LYS cc_start: 0.8117 (tttt) cc_final: 0.7580 (tptp) REVERT: D 97 GLN cc_start: 0.7228 (tm130) cc_final: 0.7000 (tm130) REVERT: D 138 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7026 (tm) REVERT: D 395 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7637 (mtp180) REVERT: D 454 ASP cc_start: 0.8331 (m-30) cc_final: 0.8092 (m-30) REVERT: D 543 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7201 (mtp180) REVERT: D 580 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8484 (mm) REVERT: D 615 ARG cc_start: 0.7178 (ttt180) cc_final: 0.6620 (ttt-90) REVERT: E 114 GLN cc_start: 0.7774 (tm-30) cc_final: 0.7205 (tm-30) REVERT: E 395 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7321 (mtp180) REVERT: E 399 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.6064 (mp0) REVERT: E 580 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8133 (mm) REVERT: E 586 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8195 (mm) REVERT: E 630 MET cc_start: 0.4247 (mmm) cc_final: 0.3827 (ppp) REVERT: E 694 LYS cc_start: 0.8146 (ttmt) cc_final: 0.7875 (tmmm) REVERT: F 97 GLN cc_start: 0.7220 (pp30) cc_final: 0.6902 (tm130) REVERT: F 130 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8229 (mm) REVERT: F 363 LYS cc_start: 0.7927 (tppt) cc_final: 0.7634 (tppp) REVERT: F 454 ASP cc_start: 0.8322 (m-30) cc_final: 0.8078 (m-30) REVERT: F 543 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7266 (mtp180) REVERT: F 630 MET cc_start: 0.4083 (mmm) cc_final: 0.3480 (pp-130) REVERT: F 686 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7248 (tm-30) REVERT: G 358 LEU cc_start: 0.7584 (tt) cc_final: 0.7248 (tp) REVERT: G 395 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7331 (mtp180) REVERT: G 571 ASN cc_start: 0.8018 (m-40) cc_final: 0.7310 (t0) REVERT: G 580 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8137 (mm) REVERT: G 589 PHE cc_start: 0.7747 (m-10) cc_final: 0.7214 (m-80) REVERT: G 694 LYS cc_start: 0.8067 (tttt) cc_final: 0.7576 (tptp) REVERT: H 130 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8342 (mm) REVERT: H 138 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6931 (tm) REVERT: H 146 ARG cc_start: 0.7395 (mtm110) cc_final: 0.7192 (ttp80) REVERT: H 307 ARG cc_start: 0.7796 (ttp80) cc_final: 0.7363 (ttp80) REVERT: H 454 ASP cc_start: 0.8324 (m-30) cc_final: 0.8109 (m-30) REVERT: H 543 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7279 (mtp180) REVERT: H 580 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8541 (mm) REVERT: H 615 ARG cc_start: 0.7030 (ttt180) cc_final: 0.6539 (ttt-90) REVERT: H 655 PRO cc_start: 0.7733 (Cg_exo) cc_final: 0.7396 (Cg_endo) REVERT: H 669 PRO cc_start: 0.5782 (Cg_exo) cc_final: 0.5332 (Cg_endo) REVERT: H 694 LYS cc_start: 0.7813 (tttt) cc_final: 0.7530 (ttpt) REVERT: H 696 ILE cc_start: 0.8253 (tp) cc_final: 0.7883 (pt) outliers start: 138 outliers final: 44 residues processed: 450 average time/residue: 1.6612 time to fit residues: 889.8469 Evaluate side-chains 390 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 320 time to evaluate : 4.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 543 ARG Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 695 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 543 ARG Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 544 GLU Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 543 ARG Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 608 ILE Chi-restraints excluded: chain H residue 616 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 158 optimal weight: 0.5980 chunk 424 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 472 optimal weight: 0.4980 chunk 391 optimal weight: 10.0000 chunk 218 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 247 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 700 GLN G 97 GLN G 143 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38928 Z= 0.172 Angle : 0.522 13.861 52608 Z= 0.255 Chirality : 0.038 0.201 6024 Planarity : 0.004 0.055 6816 Dihedral : 3.651 13.493 5312 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.24 % Allowed : 14.71 % Favored : 82.06 % 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: 1.08 (0.12), residues: 4824 helix: 1.10 (0.09), residues: 3360 sheet: 0.30 (0.45), residues: 152 loop : 0.02 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 103 HIS 0.004 0.001 HIS F 269 PHE 0.021 0.001 PHE E 96 TYR 0.011 0.001 TYR A 687 ARG 0.010 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 342 time to evaluate : 3.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7386 (mp) REVERT: A 259 PHE cc_start: 0.8366 (t80) cc_final: 0.8032 (t80) REVERT: A 395 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7382 (mtp180) REVERT: A 399 GLU cc_start: 0.6235 (OUTLIER) cc_final: 0.5899 (mp0) REVERT: A 580 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8136 (mm) REVERT: A 694 LYS cc_start: 0.8066 (tttt) cc_final: 0.7560 (tptp) REVERT: B 97 GLN cc_start: 0.7207 (pp30) cc_final: 0.6901 (tm130) REVERT: B 150 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: B 307 ARG cc_start: 0.7753 (ttp80) cc_final: 0.7419 (ttp80) REVERT: B 363 LYS cc_start: 0.7989 (tptm) cc_final: 0.7649 (tppp) REVERT: B 395 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7652 (mtp180) REVERT: B 454 ASP cc_start: 0.8322 (m-30) cc_final: 0.8084 (m-30) REVERT: B 543 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7253 (mtp180) REVERT: B 576 LEU cc_start: 0.8856 (tp) cc_final: 0.8612 (tm) REVERT: B 580 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8421 (mm) REVERT: B 615 ARG cc_start: 0.7148 (ttt180) cc_final: 0.6772 (ttt-90) REVERT: B 652 ASN cc_start: 0.5750 (OUTLIER) cc_final: 0.5181 (t0) REVERT: B 669 PRO cc_start: 0.6104 (Cg_exo) cc_final: 0.5620 (Cg_endo) REVERT: B 694 LYS cc_start: 0.7896 (tttt) cc_final: 0.7617 (ttmt) REVERT: B 696 ILE cc_start: 0.8045 (tt) cc_final: 0.7673 (pt) REVERT: C 259 PHE cc_start: 0.8327 (t80) cc_final: 0.8025 (t80) REVERT: C 395 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7330 (mtp180) REVERT: C 580 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8129 (mm) REVERT: C 589 PHE cc_start: 0.7747 (m-10) cc_final: 0.7200 (m-80) REVERT: C 615 ARG cc_start: 0.6531 (ttt180) cc_final: 0.5845 (ttt-90) REVERT: C 669 PRO cc_start: 0.6336 (Cg_exo) cc_final: 0.6043 (Cg_endo) REVERT: C 694 LYS cc_start: 0.8125 (tttt) cc_final: 0.7604 (tptp) REVERT: D 150 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: D 395 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7639 (mtp180) REVERT: D 454 ASP cc_start: 0.8326 (m-30) cc_final: 0.8087 (m-30) REVERT: D 543 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7185 (mtp180) REVERT: D 580 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8473 (mm) REVERT: D 615 ARG cc_start: 0.7066 (ttt180) cc_final: 0.6591 (ttt-90) REVERT: D 696 ILE cc_start: 0.8059 (tt) cc_final: 0.7679 (pt) REVERT: E 114 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7197 (tm-30) REVERT: E 259 PHE cc_start: 0.8431 (t80) cc_final: 0.8126 (t80) REVERT: E 395 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7318 (mtp180) REVERT: E 399 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.6199 (mp0) REVERT: E 580 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8134 (mm) REVERT: E 612 MET cc_start: 0.6375 (OUTLIER) cc_final: 0.6173 (mpp) REVERT: E 630 MET cc_start: 0.4254 (mmm) cc_final: 0.3836 (ppp) REVERT: E 694 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7851 (tmmm) REVERT: F 97 GLN cc_start: 0.7180 (pp30) cc_final: 0.6883 (tm130) REVERT: F 130 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8104 (mm) REVERT: F 363 LYS cc_start: 0.7890 (tppt) cc_final: 0.7650 (tppp) REVERT: F 395 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7667 (mtp180) REVERT: F 454 ASP cc_start: 0.8311 (m-30) cc_final: 0.8060 (m-30) REVERT: F 543 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7187 (mtp180) REVERT: F 580 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8424 (mm) REVERT: F 630 MET cc_start: 0.3926 (mmm) cc_final: 0.3353 (pp-130) REVERT: F 686 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7213 (tm-30) REVERT: G 259 PHE cc_start: 0.8364 (t80) cc_final: 0.7989 (t80) REVERT: G 395 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7356 (mtp180) REVERT: G 399 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6226 (mp0) REVERT: G 571 ASN cc_start: 0.8072 (m-40) cc_final: 0.7351 (t0) REVERT: G 580 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8132 (mm) REVERT: G 630 MET cc_start: 0.3870 (mmt) cc_final: 0.3440 (ppp) REVERT: G 694 LYS cc_start: 0.8065 (tttt) cc_final: 0.7578 (tptp) REVERT: H 97 GLN cc_start: 0.7247 (pp30) cc_final: 0.6859 (tm130) REVERT: H 130 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8311 (mm) REVERT: H 138 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6973 (tm) REVERT: H 395 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7614 (mtp180) REVERT: H 454 ASP cc_start: 0.8329 (m-30) cc_final: 0.8128 (m-30) REVERT: H 543 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7255 (mtp180) REVERT: H 580 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8530 (mm) REVERT: H 615 ARG cc_start: 0.7002 (ttt180) cc_final: 0.6504 (ttt-90) REVERT: H 694 LYS cc_start: 0.7788 (tttt) cc_final: 0.7506 (ttpt) REVERT: H 696 ILE cc_start: 0.8235 (tp) cc_final: 0.7872 (pt) outliers start: 132 outliers final: 53 residues processed: 442 average time/residue: 1.6560 time to fit residues: 869.0103 Evaluate side-chains 410 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 326 time to evaluate : 4.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 445 ARG Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 543 ARG Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 612 MET Chi-restraints excluded: chain E residue 695 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 395 ARG Chi-restraints excluded: chain F residue 543 ARG Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 580 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 399 GLU Chi-restraints excluded: chain G residue 445 ARG Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 543 ARG Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 608 ILE Chi-restraints excluded: chain H residue 616 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 455 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 chunk 344 optimal weight: 0.9980 chunk 267 optimal weight: 0.2980 chunk 397 optimal weight: 3.9990 chunk 263 optimal weight: 0.2980 chunk 470 optimal weight: 0.8980 chunk 294 optimal weight: 0.4980 chunk 286 optimal weight: 0.6980 chunk 217 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN H 150 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 38928 Z= 0.146 Angle : 0.508 16.463 52608 Z= 0.248 Chirality : 0.038 0.183 6024 Planarity : 0.004 0.061 6816 Dihedral : 3.542 13.572 5312 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.84 % Allowed : 15.37 % Favored : 81.79 % 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: 1.39 (0.13), residues: 4824 helix: 1.31 (0.09), residues: 3360 sheet: 0.65 (0.46), residues: 152 loop : 0.14 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 103 HIS 0.003 0.001 HIS F 269 PHE 0.018 0.001 PHE E 96 TYR 0.011 0.001 TYR B 687 ARG 0.012 0.000 ARG C 131 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 346 time to evaluate : 4.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 PHE cc_start: 0.8240 (t80) cc_final: 0.7940 (t80) REVERT: A 395 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7427 (mtp180) REVERT: A 399 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.6006 (mp0) REVERT: A 580 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7716 (tm) REVERT: A 694 LYS cc_start: 0.8054 (tttt) cc_final: 0.7577 (tptp) REVERT: B 97 GLN cc_start: 0.7221 (pp30) cc_final: 0.6872 (tm130) REVERT: B 252 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: B 307 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7408 (ttp80) REVERT: B 395 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7651 (mtp180) REVERT: B 576 LEU cc_start: 0.8848 (tp) cc_final: 0.8592 (tm) REVERT: B 580 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8417 (mm) REVERT: B 615 ARG cc_start: 0.6968 (ttt180) cc_final: 0.6541 (ttt-90) REVERT: B 630 MET cc_start: 0.3817 (mmt) cc_final: 0.3152 (ppp) REVERT: B 652 ASN cc_start: 0.5662 (OUTLIER) cc_final: 0.5209 (t0) REVERT: B 696 ILE cc_start: 0.8006 (tt) cc_final: 0.7640 (pt) REVERT: C 131 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7441 (mtm-85) REVERT: C 259 PHE cc_start: 0.8255 (t80) cc_final: 0.8052 (t80) REVERT: C 395 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7354 (mtp180) REVERT: C 580 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8127 (mm) REVERT: C 589 PHE cc_start: 0.7735 (m-10) cc_final: 0.7227 (m-80) REVERT: C 615 ARG cc_start: 0.6628 (ttt180) cc_final: 0.5910 (ttt-90) REVERT: C 669 PRO cc_start: 0.6281 (Cg_exo) cc_final: 0.5997 (Cg_endo) REVERT: C 694 LYS cc_start: 0.8088 (tttt) cc_final: 0.7588 (tptp) REVERT: D 150 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: D 395 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7626 (mtp180) REVERT: D 576 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8599 (tm) REVERT: D 580 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8431 (mm) REVERT: D 615 ARG cc_start: 0.6990 (ttt180) cc_final: 0.6686 (ttt-90) REVERT: D 696 ILE cc_start: 0.8004 (tt) cc_final: 0.7620 (pt) REVERT: E 98 LEU cc_start: 0.7179 (pt) cc_final: 0.6973 (pt) REVERT: E 114 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7204 (tm-30) REVERT: E 131 ARG cc_start: 0.7742 (mtm110) cc_final: 0.7406 (mtm-85) REVERT: E 151 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7694 (tp) REVERT: E 259 PHE cc_start: 0.8365 (t80) cc_final: 0.8116 (t80) REVERT: E 395 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7424 (mtp180) REVERT: E 399 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.6144 (mp0) REVERT: E 580 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8069 (mm) REVERT: E 612 MET cc_start: 0.6379 (OUTLIER) cc_final: 0.6177 (mpp) REVERT: E 630 MET cc_start: 0.4322 (mmm) cc_final: 0.4021 (mtm) REVERT: E 672 MET cc_start: 0.5365 (ptm) cc_final: 0.5007 (pp-130) REVERT: E 694 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7776 (tmmm) REVERT: F 97 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6940 (tm130) REVERT: F 130 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8086 (mm) REVERT: F 395 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7658 (mtp180) REVERT: F 454 ASP cc_start: 0.8307 (m-30) cc_final: 0.8090 (m-30) REVERT: F 630 MET cc_start: 0.3845 (mmm) cc_final: 0.3241 (pp-130) REVERT: F 686 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7248 (tm-30) REVERT: G 131 ARG cc_start: 0.7807 (mtm110) cc_final: 0.7474 (mtm-85) REVERT: G 137 GLU cc_start: 0.6114 (mp0) cc_final: 0.5824 (mp0) REVERT: G 151 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7732 (tp) REVERT: G 259 PHE cc_start: 0.8261 (t80) cc_final: 0.8010 (t80) REVERT: G 395 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7431 (mtp180) REVERT: G 399 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6235 (mp0) REVERT: G 571 ASN cc_start: 0.8070 (m-40) cc_final: 0.7341 (t0) REVERT: G 580 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8131 (mm) REVERT: G 630 MET cc_start: 0.4111 (mmt) cc_final: 0.3708 (ppp) REVERT: G 694 LYS cc_start: 0.8084 (tttt) cc_final: 0.7609 (tptp) REVERT: H 97 GLN cc_start: 0.7175 (pp30) cc_final: 0.6820 (tm130) REVERT: H 143 GLN cc_start: 0.7514 (mt0) cc_final: 0.7192 (mm-40) REVERT: H 162 ARG cc_start: 0.7265 (mtp85) cc_final: 0.7045 (mmt-90) REVERT: H 307 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7343 (ttp80) REVERT: H 395 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7650 (mtp180) REVERT: H 576 LEU cc_start: 0.8873 (tp) cc_final: 0.8638 (tm) REVERT: H 580 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8462 (mm) REVERT: H 652 ASN cc_start: 0.5681 (OUTLIER) cc_final: 0.5148 (t0) REVERT: H 655 PRO cc_start: 0.7756 (Cg_exo) cc_final: 0.7352 (Cg_endo) REVERT: H 694 LYS cc_start: 0.7845 (tttt) cc_final: 0.7564 (ttpt) REVERT: H 696 ILE cc_start: 0.8234 (tp) cc_final: 0.7878 (pt) outliers start: 116 outliers final: 42 residues processed: 435 average time/residue: 1.6967 time to fit residues: 887.2822 Evaluate side-chains 394 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 324 time to evaluate : 3.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 445 ARG Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 576 LEU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 612 MET Chi-restraints excluded: chain E residue 695 ILE Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 395 ARG Chi-restraints excluded: chain F residue 608 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 399 GLU Chi-restraints excluded: chain G residue 445 ARG Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 608 ILE Chi-restraints excluded: chain H residue 652 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 290 optimal weight: 2.9990 chunk 187 optimal weight: 0.0770 chunk 280 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 299 optimal weight: 20.0000 chunk 320 optimal weight: 7.9990 chunk 232 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 369 optimal weight: 0.7980 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 616 ASN H 700 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 38928 Z= 0.162 Angle : 0.517 15.140 52608 Z= 0.254 Chirality : 0.038 0.173 6024 Planarity : 0.004 0.057 6816 Dihedral : 3.548 13.369 5312 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.55 % Allowed : 15.88 % Favored : 81.57 % 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: 1.54 (0.13), residues: 4824 helix: 1.42 (0.09), residues: 3360 sheet: 0.75 (0.46), residues: 152 loop : 0.21 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 103 HIS 0.003 0.001 HIS H 269 PHE 0.016 0.001 PHE G 96 TYR 0.010 0.001 TYR B 687 ARG 0.010 0.000 ARG G 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 329 time to evaluate : 5.091 Fit side-chains revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7444 (mtp180) REVERT: A 399 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.6036 (mp0) REVERT: A 576 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8404 (tp) REVERT: A 580 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7708 (tm) REVERT: A 694 LYS cc_start: 0.8052 (tttt) cc_final: 0.7582 (tptp) REVERT: B 97 GLN cc_start: 0.7240 (pp30) cc_final: 0.6935 (tm130) REVERT: B 252 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: B 395 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7663 (mtp180) REVERT: B 576 LEU cc_start: 0.8798 (tp) cc_final: 0.8544 (tm) REVERT: B 580 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8416 (mm) REVERT: B 615 ARG cc_start: 0.6912 (ttt180) cc_final: 0.6494 (ttt-90) REVERT: B 630 MET cc_start: 0.3821 (mmt) cc_final: 0.3143 (ppp) REVERT: B 652 ASN cc_start: 0.5644 (OUTLIER) cc_final: 0.5226 (t0) REVERT: B 696 ILE cc_start: 0.8002 (tt) cc_final: 0.7631 (pt) REVERT: C 395 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7370 (mtp180) REVERT: C 580 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8131 (mm) REVERT: C 589 PHE cc_start: 0.7699 (m-10) cc_final: 0.7197 (m-80) REVERT: C 615 ARG cc_start: 0.6730 (ttt180) cc_final: 0.5965 (ttt-90) REVERT: C 694 LYS cc_start: 0.8069 (tttt) cc_final: 0.7576 (tptp) REVERT: D 150 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: D 367 ASP cc_start: 0.7383 (m-30) cc_final: 0.7140 (m-30) REVERT: D 395 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7638 (mtp180) REVERT: D 576 LEU cc_start: 0.8869 (tp) cc_final: 0.8568 (tm) REVERT: D 580 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8419 (mm) REVERT: D 615 ARG cc_start: 0.7001 (ttt180) cc_final: 0.6687 (ttt-90) REVERT: D 696 ILE cc_start: 0.7997 (tt) cc_final: 0.7616 (pt) REVERT: E 114 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7172 (tm-30) REVERT: E 137 GLU cc_start: 0.6148 (mp0) cc_final: 0.5880 (mp0) REVERT: E 151 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7659 (tp) REVERT: E 395 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7455 (mtp180) REVERT: E 399 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.6230 (mp0) REVERT: E 580 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8114 (mm) REVERT: E 630 MET cc_start: 0.4428 (mmm) cc_final: 0.4043 (ppp) REVERT: E 672 MET cc_start: 0.5431 (ptm) cc_final: 0.5057 (pp-130) REVERT: E 694 LYS cc_start: 0.8072 (ttmt) cc_final: 0.7794 (tmmm) REVERT: F 97 GLN cc_start: 0.7198 (pp30) cc_final: 0.6915 (tm130) REVERT: F 130 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8024 (mm) REVERT: F 307 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7045 (ttt90) REVERT: F 395 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7670 (mtp180) REVERT: F 454 ASP cc_start: 0.8298 (m-30) cc_final: 0.8076 (m-30) REVERT: F 630 MET cc_start: 0.3848 (mmm) cc_final: 0.3216 (pp-130) REVERT: F 686 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7232 (tm-30) REVERT: G 97 GLN cc_start: 0.6925 (OUTLIER) cc_final: 0.6562 (tm130) REVERT: G 151 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7754 (tp) REVERT: G 395 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7438 (mtp180) REVERT: G 399 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6158 (mp0) REVERT: G 571 ASN cc_start: 0.8074 (m-40) cc_final: 0.7341 (t0) REVERT: G 580 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8130 (mm) REVERT: G 694 LYS cc_start: 0.8047 (tttt) cc_final: 0.7584 (tptp) REVERT: H 97 GLN cc_start: 0.7206 (pp30) cc_final: 0.6888 (tm130) REVERT: H 143 GLN cc_start: 0.7581 (mt0) cc_final: 0.7214 (mm-40) REVERT: H 395 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7661 (mtp180) REVERT: H 576 LEU cc_start: 0.8877 (tp) cc_final: 0.8625 (tm) REVERT: H 580 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8465 (mm) REVERT: H 652 ASN cc_start: 0.5660 (OUTLIER) cc_final: 0.5210 (t0) REVERT: H 655 PRO cc_start: 0.7754 (Cg_exo) cc_final: 0.7379 (Cg_endo) REVERT: H 696 ILE cc_start: 0.8229 (tp) cc_final: 0.7880 (pt) outliers start: 104 outliers final: 43 residues processed: 406 average time/residue: 1.6218 time to fit residues: 787.3332 Evaluate side-chains 383 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 312 time to evaluate : 4.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 445 ARG Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 695 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 307 ARG Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 395 ARG Chi-restraints excluded: chain F residue 608 ILE Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 399 GLU Chi-restraints excluded: chain G residue 445 ARG Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 608 ILE Chi-restraints excluded: chain H residue 652 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 427 optimal weight: 20.0000 chunk 450 optimal weight: 3.9990 chunk 411 optimal weight: 2.9990 chunk 438 optimal weight: 0.5980 chunk 263 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 344 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 396 optimal weight: 0.9990 chunk 414 optimal weight: 6.9990 chunk 436 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN ** D 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 38928 Z= 0.274 Angle : 0.591 14.653 52608 Z= 0.292 Chirality : 0.041 0.191 6024 Planarity : 0.004 0.061 6816 Dihedral : 3.820 13.964 5312 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.33 % Allowed : 16.42 % Favored : 81.25 % 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: 1.31 (0.12), residues: 4824 helix: 1.23 (0.09), residues: 3360 sheet: 0.61 (0.46), residues: 152 loop : 0.19 (0.19), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 103 HIS 0.006 0.001 HIS H 269 PHE 0.019 0.002 PHE H 96 TYR 0.011 0.002 TYR F 429 ARG 0.013 0.001 ARG G 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 321 time to evaluate : 4.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 GLU cc_start: 0.6511 (mp0) cc_final: 0.6301 (mp0) REVERT: A 151 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7697 (tp) REVERT: A 285 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7350 (mmt-90) REVERT: A 395 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7313 (mtp180) REVERT: A 580 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8159 (mm) REVERT: A 694 LYS cc_start: 0.8117 (tttt) cc_final: 0.7649 (tptp) REVERT: B 97 GLN cc_start: 0.7210 (pp30) cc_final: 0.6937 (tm130) REVERT: B 252 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: B 307 ARG cc_start: 0.7815 (ttp80) cc_final: 0.7418 (ttp80) REVERT: B 395 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7706 (mtp180) REVERT: B 576 LEU cc_start: 0.8808 (tp) cc_final: 0.8579 (tm) REVERT: B 580 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8435 (mm) REVERT: B 615 ARG cc_start: 0.7006 (ttt180) cc_final: 0.6545 (ttt-90) REVERT: B 630 MET cc_start: 0.3707 (mmt) cc_final: 0.3150 (ppp) REVERT: B 652 ASN cc_start: 0.5708 (OUTLIER) cc_final: 0.5300 (t0) REVERT: B 696 ILE cc_start: 0.8017 (tt) cc_final: 0.7638 (pt) REVERT: C 131 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7527 (mtm-85) REVERT: C 137 GLU cc_start: 0.6183 (mp0) cc_final: 0.5893 (mp0) REVERT: C 146 ARG cc_start: 0.7302 (mtm110) cc_final: 0.7072 (ttp-170) REVERT: C 395 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7317 (mtp180) REVERT: C 580 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8164 (mm) REVERT: C 589 PHE cc_start: 0.7707 (m-10) cc_final: 0.7205 (m-80) REVERT: C 694 LYS cc_start: 0.8079 (tttt) cc_final: 0.7623 (tptp) REVERT: D 395 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7709 (mtp180) REVERT: D 576 LEU cc_start: 0.8796 (tp) cc_final: 0.8520 (tm) REVERT: D 580 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8436 (mm) REVERT: D 615 ARG cc_start: 0.6986 (ttt180) cc_final: 0.6660 (ttt-90) REVERT: D 696 ILE cc_start: 0.8017 (tt) cc_final: 0.7629 (pt) REVERT: E 114 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7187 (tm-30) REVERT: E 131 ARG cc_start: 0.7878 (mtm110) cc_final: 0.7505 (mtm-85) REVERT: E 137 GLU cc_start: 0.6163 (mp0) cc_final: 0.5904 (mp0) REVERT: E 395 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7273 (mtp180) REVERT: E 399 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6343 (mp0) REVERT: E 580 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8133 (mm) REVERT: E 630 MET cc_start: 0.4303 (mmm) cc_final: 0.3847 (ppp) REVERT: E 672 MET cc_start: 0.5279 (ptm) cc_final: 0.4935 (pp-130) REVERT: E 694 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7836 (tmmm) REVERT: F 97 GLN cc_start: 0.7212 (pp30) cc_final: 0.6931 (tm130) REVERT: F 307 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7142 (ttt90) REVERT: F 367 ASP cc_start: 0.7384 (m-30) cc_final: 0.7140 (m-30) REVERT: F 395 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7648 (mtp180) REVERT: F 630 MET cc_start: 0.3779 (mmm) cc_final: 0.3208 (ppp) REVERT: G 97 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6539 (tm130) REVERT: G 98 LEU cc_start: 0.7240 (pt) cc_final: 0.7033 (pt) REVERT: G 131 ARG cc_start: 0.7833 (mtm110) cc_final: 0.7446 (mtm-85) REVERT: G 151 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7756 (tp) REVERT: G 395 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7332 (mtp180) REVERT: G 571 ASN cc_start: 0.8105 (m-40) cc_final: 0.7364 (t0) REVERT: G 580 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8133 (mm) REVERT: G 694 LYS cc_start: 0.8083 (tttt) cc_final: 0.7631 (tptp) REVERT: H 97 GLN cc_start: 0.7152 (pp30) cc_final: 0.6836 (tm130) REVERT: H 395 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7641 (mtp180) REVERT: H 576 LEU cc_start: 0.8804 (tp) cc_final: 0.8586 (tm) REVERT: H 580 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8459 (mm) REVERT: H 696 ILE cc_start: 0.8218 (tp) cc_final: 0.7854 (pt) outliers start: 95 outliers final: 43 residues processed: 403 average time/residue: 1.5970 time to fit residues: 772.1991 Evaluate side-chains 369 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 303 time to evaluate : 4.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 695 ILE Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 307 ARG Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 395 ARG Chi-restraints excluded: chain F residue 608 ILE Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 399 GLU Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 580 LEU Chi-restraints excluded: chain H residue 608 ILE Chi-restraints excluded: chain H residue 652 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 287 optimal weight: 1.9990 chunk 463 optimal weight: 0.9990 chunk 282 optimal weight: 0.8980 chunk 219 optimal weight: 0.0040 chunk 322 optimal weight: 1.9990 chunk 486 optimal weight: 0.1980 chunk 447 optimal weight: 0.8980 chunk 387 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 299 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 38928 Z= 0.154 Angle : 0.532 15.277 52608 Z= 0.262 Chirality : 0.038 0.187 6024 Planarity : 0.004 0.061 6816 Dihedral : 3.580 13.223 5312 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.74 % Allowed : 17.28 % Favored : 80.98 % 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: 1.69 (0.13), residues: 4824 helix: 1.51 (0.09), residues: 3352 sheet: 0.83 (0.47), residues: 152 loop : 0.34 (0.19), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 103 HIS 0.003 0.001 HIS F 269 PHE 0.024 0.001 PHE G 96 TYR 0.014 0.001 TYR B 687 ARG 0.012 0.000 ARG E 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 317 time to evaluate : 4.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7472 (mtp180) REVERT: A 399 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5860 (mp0) REVERT: A 580 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8122 (mm) REVERT: A 694 LYS cc_start: 0.8073 (tttt) cc_final: 0.7601 (tptp) REVERT: B 97 GLN cc_start: 0.7216 (pp30) cc_final: 0.6973 (tm130) REVERT: B 252 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: B 395 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7657 (mtp180) REVERT: B 615 ARG cc_start: 0.6910 (ttt180) cc_final: 0.6598 (ttt-90) REVERT: B 630 MET cc_start: 0.3987 (mmt) cc_final: 0.3327 (ppp) REVERT: B 696 ILE cc_start: 0.8015 (tt) cc_final: 0.7658 (pt) REVERT: C 131 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7441 (mtm-85) REVERT: C 137 GLU cc_start: 0.6154 (mp0) cc_final: 0.5878 (mp0) REVERT: C 395 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7414 (mtp180) REVERT: C 580 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8141 (mm) REVERT: C 589 PHE cc_start: 0.7648 (m-10) cc_final: 0.7158 (m-80) REVERT: C 694 LYS cc_start: 0.8070 (tttt) cc_final: 0.7578 (tptp) REVERT: D 325 ASP cc_start: 0.7140 (p0) cc_final: 0.6875 (p0) REVERT: D 395 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7660 (mtp180) REVERT: D 615 ARG cc_start: 0.7113 (ttt180) cc_final: 0.6772 (ttt-90) REVERT: D 696 ILE cc_start: 0.8000 (tt) cc_final: 0.7638 (pt) REVERT: E 98 LEU cc_start: 0.7276 (pt) cc_final: 0.7066 (pt) REVERT: E 114 GLN cc_start: 0.7586 (tm-30) cc_final: 0.7020 (tm-30) REVERT: E 131 ARG cc_start: 0.7796 (mtm110) cc_final: 0.7443 (mtm-85) REVERT: E 137 GLU cc_start: 0.6109 (mp0) cc_final: 0.5849 (mp0) REVERT: E 395 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7393 (mtp180) REVERT: E 399 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: E 580 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8078 (mm) REVERT: E 630 MET cc_start: 0.4411 (mmm) cc_final: 0.4191 (mtm) REVERT: E 672 MET cc_start: 0.5636 (ptm) cc_final: 0.5214 (pp-130) REVERT: E 694 LYS cc_start: 0.8050 (ttmt) cc_final: 0.7767 (tmmm) REVERT: F 97 GLN cc_start: 0.7247 (pp30) cc_final: 0.6966 (tm130) REVERT: F 307 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.7040 (ttt90) REVERT: F 395 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7690 (mtp180) REVERT: F 454 ASP cc_start: 0.8321 (m-30) cc_final: 0.8068 (m-30) REVERT: F 615 ARG cc_start: 0.7543 (ttm170) cc_final: 0.7005 (ttt-90) REVERT: F 630 MET cc_start: 0.3716 (mmm) cc_final: 0.3218 (pp-130) REVERT: F 686 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7372 (tm-30) REVERT: G 131 ARG cc_start: 0.7835 (mtm110) cc_final: 0.7469 (mtm-85) REVERT: G 137 GLU cc_start: 0.6492 (mp0) cc_final: 0.6244 (mp0) REVERT: G 151 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7742 (tp) REVERT: G 395 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7374 (mtp180) REVERT: G 399 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.6135 (mp0) REVERT: G 571 ASN cc_start: 0.8079 (m-40) cc_final: 0.7346 (t0) REVERT: G 580 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8147 (mm) REVERT: G 630 MET cc_start: 0.4235 (mmt) cc_final: 0.3604 (ppp) REVERT: G 694 LYS cc_start: 0.8070 (tttt) cc_final: 0.7616 (tptp) REVERT: H 97 GLN cc_start: 0.7081 (pp30) cc_final: 0.6787 (tm130) REVERT: H 395 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7680 (mtp180) REVERT: H 615 ARG cc_start: 0.7497 (ttm170) cc_final: 0.7136 (ttt-90) REVERT: H 630 MET cc_start: 0.3714 (mmt) cc_final: 0.3105 (ppp) REVERT: H 652 ASN cc_start: 0.5669 (OUTLIER) cc_final: 0.5340 (t0) REVERT: H 655 PRO cc_start: 0.7539 (Cg_exo) cc_final: 0.7160 (Cg_endo) REVERT: H 696 ILE cc_start: 0.8190 (tp) cc_final: 0.7859 (pt) outliers start: 71 outliers final: 32 residues processed: 378 average time/residue: 1.6080 time to fit residues: 728.2872 Evaluate side-chains 350 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 299 time to evaluate : 4.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 395 ARG Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 395 ARG Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 361 LYS Chi-restraints excluded: chain E residue 395 ARG Chi-restraints excluded: chain E residue 399 GLU Chi-restraints excluded: chain E residue 543 ARG Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 695 ILE Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 307 ARG Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 395 ARG Chi-restraints excluded: chain F residue 608 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 158 ASP Chi-restraints excluded: chain G residue 344 ILE Chi-restraints excluded: chain G residue 361 LYS Chi-restraints excluded: chain G residue 395 ARG Chi-restraints excluded: chain G residue 399 GLU Chi-restraints excluded: chain G residue 580 LEU Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain H residue 344 ILE Chi-restraints excluded: chain H residue 395 ARG Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 608 ILE Chi-restraints excluded: chain H residue 652 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 307 optimal weight: 6.9990 chunk 412 optimal weight: 4.9990 chunk 118 optimal weight: 30.0000 chunk 356 optimal weight: 1.9990 chunk 57 optimal weight: 30.0000 chunk 107 optimal weight: 2.9990 chunk 387 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 398 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.159283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097051 restraints weight = 51200.727| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.92 r_work: 0.3041 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 38928 Z= 0.326 Angle : 0.622 14.889 52608 Z= 0.307 Chirality : 0.042 0.177 6024 Planarity : 0.005 0.061 6816 Dihedral : 3.901 14.206 5312 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.94 % Allowed : 17.16 % Favored : 80.91 % 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: 1.30 (0.12), residues: 4824 helix: 1.20 (0.09), residues: 3360 sheet: 0.68 (0.47), residues: 152 loop : 0.24 (0.19), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 214 HIS 0.007 0.001 HIS H 194 PHE 0.022 0.002 PHE G 96 TYR 0.015 0.002 TYR B 687 ARG 0.012 0.001 ARG G 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16064.64 seconds wall clock time: 286 minutes 15.07 seconds (17175.07 seconds total)