Starting phenix.real_space_refine on Sat Mar 7 09:05:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7anw_11834/03_2026/7anw_11834.cif Found real_map, /net/cci-nas-00/data/ceres_data/7anw_11834/03_2026/7anw_11834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7anw_11834/03_2026/7anw_11834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7anw_11834/03_2026/7anw_11834.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7anw_11834/03_2026/7anw_11834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7anw_11834/03_2026/7anw_11834.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 192 5.16 5 C 25496 2.51 5 N 7264 2.21 5 O 7552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40520 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5021 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 24, 'TRANS': 620} Chain: "B" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5021 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 24, 'TRANS': 620} Chain: "C" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5021 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 24, 'TRANS': 620} Chain: "D" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5021 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 24, 'TRANS': 620} Chain: "E" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5021 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 24, 'TRANS': 620} Chain: "F" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5021 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 24, 'TRANS': 620} Chain: "G" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5021 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 24, 'TRANS': 620} Chain: "H" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5021 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 24, 'TRANS': 620} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.48, per 1000 atoms: 0.21 Number of scatterers: 40520 At special positions: 0 Unit cell: (210.885, 210.885, 84.354, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 192 16.00 P 16 15.00 O 7552 8.00 N 7264 7.00 C 25496 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 - 3.00 Amino acid : True - 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: 4.90 Conformation dependent library (CDL) restraints added in 1.9 seconds 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9568 Finding SS restraints... Secondary structure from input PDB file: 336 helices and 8 sheets defined 68.9% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 56 through 79 removed outlier: 3.690A pdb=" N ARG A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 85 through 104 removed outlier: 3.654A pdb=" N ALA A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 122 Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.599A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.903A pdb=" N ILE A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.781A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.682A pdb=" N VAL A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 237 Processing helix chain 'A' and resid 237 through 248 removed outlier: 4.043A pdb=" N VAL A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 263 through 279 removed outlier: 3.851A pdb=" N ARG A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 289 removed outlier: 3.518A pdb=" N ARG A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 330 through 334 Processing helix chain 'A' and resid 338 through 360 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 369 through 375 removed outlier: 3.617A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 413 through 424 removed outlier: 3.536A pdb=" N VAL A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.710A pdb=" N GLN A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.682A pdb=" N LEU A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 461 through 477 removed outlier: 3.550A pdb=" N ARG A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 475 " --> pdb=" O THR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 495 removed outlier: 3.651A pdb=" N SER A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 4.466A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.831A pdb=" N LEU A 515 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 531 through 548 removed outlier: 3.569A pdb=" N GLU A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 587 Processing helix chain 'A' and resid 605 through 614 removed outlier: 3.724A pdb=" N GLN A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 650 Processing helix chain 'A' and resid 664 through 668 Processing helix chain 'A' and resid 669 through 674 removed outlier: 4.346A pdb=" N ALA A 674 " --> pdb=" O GLU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 678 Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.651A pdb=" N PHE A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 79 removed outlier: 3.690A pdb=" N ARG B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 85 through 104 removed outlier: 3.654A pdb=" N ALA B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 122 Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.599A pdb=" N GLN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 164 Processing helix chain 'B' and resid 164 through 172 removed outlier: 3.902A pdb=" N ILE B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 192 removed outlier: 3.780A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 207 through 212 removed outlier: 3.682A pdb=" N VAL B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 237 Processing helix chain 'B' and resid 237 through 248 removed outlier: 4.043A pdb=" N VAL B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 253 Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 263 through 279 removed outlier: 3.850A pdb=" N ARG B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 289 removed outlier: 3.518A pdb=" N ARG B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 304 through 309 Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 338 through 360 Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 369 through 375 removed outlier: 3.617A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 413 through 424 removed outlier: 3.535A pdb=" N VAL B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.710A pdb=" N GLN B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 444 removed outlier: 3.682A pdb=" N LEU B 444 " --> pdb=" O GLY B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 461 through 477 removed outlier: 3.550A pdb=" N ARG B 468 " --> pdb=" O LYS B 464 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 removed outlier: 3.650A pdb=" N SER B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 removed outlier: 4.465A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 507 Processing helix chain 'B' and resid 511 through 515 removed outlier: 3.829A pdb=" N LEU B 515 " --> pdb=" O ARG B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 531 through 548 removed outlier: 3.569A pdb=" N GLU B 544 " --> pdb=" O THR B 540 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 546 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 587 Processing helix chain 'B' and resid 605 through 614 removed outlier: 3.723A pdb=" N GLN B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 650 Processing helix chain 'B' and resid 664 through 668 Processing helix chain 'B' and resid 669 through 674 removed outlier: 4.346A pdb=" N ALA B 674 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 678 Processing helix chain 'B' and resid 687 through 699 removed outlier: 3.652A pdb=" N PHE B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 79 removed outlier: 3.689A pdb=" N ARG C 67 " --> pdb=" O ASP C 63 " (cutoff:3.500A) Proline residue: C 70 - end of helix Processing helix chain 'C' and resid 85 through 104 removed outlier: 3.654A pdb=" N ALA C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 122 Processing helix chain 'C' and resid 126 through 133 Processing helix chain 'C' and resid 137 through 150 removed outlier: 3.599A pdb=" N GLN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.903A pdb=" N ILE C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.781A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.682A pdb=" N VAL C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 237 Processing helix chain 'C' and resid 237 through 248 removed outlier: 4.043A pdb=" N VAL C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 253 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 263 through 279 removed outlier: 3.851A pdb=" N ARG C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 289 removed outlier: 3.518A pdb=" N ARG C 289 " --> pdb=" O ARG C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 304 through 309 Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 338 through 360 Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 369 through 375 removed outlier: 3.617A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 397 Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 413 through 424 removed outlier: 3.536A pdb=" N VAL C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.710A pdb=" N GLN C 436 " --> pdb=" O SER C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.682A pdb=" N LEU C 444 " --> pdb=" O GLY C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 454 Processing helix chain 'C' and resid 461 through 477 removed outlier: 3.550A pdb=" N ARG C 468 " --> pdb=" O LYS C 464 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 475 " --> pdb=" O THR C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 495 removed outlier: 3.651A pdb=" N SER C 493 " --> pdb=" O ASP C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 500 removed outlier: 4.465A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 511 through 515 removed outlier: 3.830A pdb=" N LEU C 515 " --> pdb=" O ARG C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 531 through 548 removed outlier: 3.569A pdb=" N GLU C 544 " --> pdb=" O THR C 540 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 546 " --> pdb=" O ALA C 542 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS C 547 " --> pdb=" O ARG C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 587 Processing helix chain 'C' and resid 605 through 614 removed outlier: 3.724A pdb=" N GLN C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 650 Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 669 through 674 removed outlier: 4.346A pdb=" N ALA C 674 " --> pdb=" O GLU C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 678 Processing helix chain 'C' and resid 687 through 699 removed outlier: 3.651A pdb=" N PHE C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 699 " --> pdb=" O ILE C 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 79 removed outlier: 3.690A pdb=" N ARG D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) Proline residue: D 70 - end of helix Processing helix chain 'D' and resid 85 through 104 removed outlier: 3.654A pdb=" N ALA D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 122 Processing helix chain 'D' and resid 126 through 133 Processing helix chain 'D' and resid 137 through 150 removed outlier: 3.599A pdb=" N GLN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.903A pdb=" N ILE D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 192 removed outlier: 3.780A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 Processing helix chain 'D' and resid 207 through 212 removed outlier: 3.683A pdb=" N VAL D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 237 Processing helix chain 'D' and resid 237 through 248 removed outlier: 4.043A pdb=" N VAL D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 253 Processing helix chain 'D' and resid 254 through 259 Processing helix chain 'D' and resid 263 through 279 removed outlier: 3.851A pdb=" N ARG D 267 " --> pdb=" O ASP D 263 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 289 removed outlier: 3.519A pdb=" N ARG D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 303 Processing helix chain 'D' and resid 304 through 309 Processing helix chain 'D' and resid 330 through 334 Processing helix chain 'D' and resid 338 through 360 Processing helix chain 'D' and resid 363 through 368 Processing helix chain 'D' and resid 369 through 375 removed outlier: 3.617A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 408 through 412 Processing helix chain 'D' and resid 413 through 424 removed outlier: 3.535A pdb=" N VAL D 417 " --> pdb=" O LYS D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 436 removed outlier: 3.710A pdb=" N GLN D 436 " --> pdb=" O SER D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 removed outlier: 3.683A pdb=" N LEU D 444 " --> pdb=" O GLY D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'D' and resid 461 through 477 removed outlier: 3.551A pdb=" N ARG D 468 " --> pdb=" O LYS D 464 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR D 475 " --> pdb=" O THR D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 495 removed outlier: 3.651A pdb=" N SER D 493 " --> pdb=" O ASP D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 500 removed outlier: 4.465A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 507 Processing helix chain 'D' and resid 511 through 515 removed outlier: 3.831A pdb=" N LEU D 515 " --> pdb=" O ARG D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 531 through 548 removed outlier: 3.569A pdb=" N GLU D 544 " --> pdb=" O THR D 540 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 546 " --> pdb=" O ALA D 542 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS D 547 " --> pdb=" O ARG D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 587 Processing helix chain 'D' and resid 605 through 614 removed outlier: 3.723A pdb=" N GLN D 609 " --> pdb=" O ASP D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 650 Processing helix chain 'D' and resid 664 through 668 Processing helix chain 'D' and resid 669 through 674 removed outlier: 4.347A pdb=" N ALA D 674 " --> pdb=" O GLU D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 678 Processing helix chain 'D' and resid 687 through 699 removed outlier: 3.651A pdb=" N PHE D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 699 " --> pdb=" O ILE D 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 79 removed outlier: 3.689A pdb=" N ARG E 67 " --> pdb=" O ASP E 63 " (cutoff:3.500A) Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 85 through 104 removed outlier: 3.654A pdb=" N ALA E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 122 Processing helix chain 'E' and resid 126 through 133 Processing helix chain 'E' and resid 137 through 150 removed outlier: 3.597A pdb=" N GLN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 164 through 172 removed outlier: 3.903A pdb=" N ILE E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 192 removed outlier: 3.781A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 207 through 212 removed outlier: 3.682A pdb=" N VAL E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 237 Processing helix chain 'E' and resid 237 through 248 removed outlier: 4.043A pdb=" N VAL E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 253 Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 263 through 279 removed outlier: 3.851A pdb=" N ARG E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 289 removed outlier: 3.518A pdb=" N ARG E 289 " --> pdb=" O ARG E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 303 Processing helix chain 'E' and resid 304 through 309 Processing helix chain 'E' and resid 330 through 334 Processing helix chain 'E' and resid 338 through 360 Processing helix chain 'E' and resid 363 through 368 Processing helix chain 'E' and resid 369 through 375 removed outlier: 3.617A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 413 through 424 removed outlier: 3.536A pdb=" N VAL E 417 " --> pdb=" O LYS E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 436 removed outlier: 3.710A pdb=" N GLN E 436 " --> pdb=" O SER E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 removed outlier: 3.682A pdb=" N LEU E 444 " --> pdb=" O GLY E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 454 Processing helix chain 'E' and resid 461 through 477 removed outlier: 3.550A pdb=" N ARG E 468 " --> pdb=" O LYS E 464 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR E 475 " --> pdb=" O THR E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 495 removed outlier: 3.651A pdb=" N SER E 493 " --> pdb=" O ASP E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 500 removed outlier: 4.464A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 507 Processing helix chain 'E' and resid 511 through 515 removed outlier: 3.830A pdb=" N LEU E 515 " --> pdb=" O ARG E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 526 Processing helix chain 'E' and resid 531 through 548 removed outlier: 3.569A pdb=" N GLU E 544 " --> pdb=" O THR E 540 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 546 " --> pdb=" O ALA E 542 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS E 547 " --> pdb=" O ARG E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 587 Processing helix chain 'E' and resid 605 through 614 removed outlier: 3.723A pdb=" N GLN E 609 " --> pdb=" O ASP E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 650 Processing helix chain 'E' and resid 664 through 668 Processing helix chain 'E' and resid 669 through 674 removed outlier: 4.346A pdb=" N ALA E 674 " --> pdb=" O GLU E 670 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 678 Processing helix chain 'E' and resid 687 through 699 removed outlier: 3.651A pdb=" N PHE E 698 " --> pdb=" O LYS E 694 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 699 " --> pdb=" O ILE E 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 79 removed outlier: 3.690A pdb=" N ARG F 67 " --> pdb=" O ASP F 63 " (cutoff:3.500A) Proline residue: F 70 - end of helix Processing helix chain 'F' and resid 85 through 104 removed outlier: 3.654A pdb=" N ALA F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 126 through 133 Processing helix chain 'F' and resid 137 through 150 removed outlier: 3.599A pdb=" N GLN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 164 through 172 removed outlier: 3.902A pdb=" N ILE F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 192 removed outlier: 3.780A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 Processing helix chain 'F' and resid 207 through 212 removed outlier: 3.682A pdb=" N VAL F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 237 Processing helix chain 'F' and resid 237 through 248 removed outlier: 4.043A pdb=" N VAL F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 253 Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'F' and resid 263 through 279 removed outlier: 3.850A pdb=" N ARG F 267 " --> pdb=" O ASP F 263 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL F 274 " --> pdb=" O ALA F 270 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR F 279 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 289 removed outlier: 3.518A pdb=" N ARG F 289 " --> pdb=" O ARG F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 303 Processing helix chain 'F' and resid 304 through 309 Processing helix chain 'F' and resid 330 through 334 Processing helix chain 'F' and resid 338 through 360 Processing helix chain 'F' and resid 363 through 368 Processing helix chain 'F' and resid 369 through 375 removed outlier: 3.617A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 408 through 412 Processing helix chain 'F' and resid 413 through 424 removed outlier: 3.535A pdb=" N VAL F 417 " --> pdb=" O LYS F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 436 removed outlier: 3.710A pdb=" N GLN F 436 " --> pdb=" O SER F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 removed outlier: 3.682A pdb=" N LEU F 444 " --> pdb=" O GLY F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 454 Processing helix chain 'F' and resid 461 through 477 removed outlier: 3.550A pdb=" N ARG F 468 " --> pdb=" O LYS F 464 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR F 475 " --> pdb=" O THR F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 487 through 495 removed outlier: 3.651A pdb=" N SER F 493 " --> pdb=" O ASP F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 removed outlier: 4.465A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 507 Processing helix chain 'F' and resid 511 through 515 removed outlier: 3.831A pdb=" N LEU F 515 " --> pdb=" O ARG F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 526 Processing helix chain 'F' and resid 531 through 548 removed outlier: 3.569A pdb=" N GLU F 544 " --> pdb=" O THR F 540 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU F 546 " --> pdb=" O ALA F 542 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS F 547 " --> pdb=" O ARG F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 587 Processing helix chain 'F' and resid 605 through 614 removed outlier: 3.723A pdb=" N GLN F 609 " --> pdb=" O ASP F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 650 Processing helix chain 'F' and resid 664 through 668 Processing helix chain 'F' and resid 669 through 674 removed outlier: 4.347A pdb=" N ALA F 674 " --> pdb=" O GLU F 670 " (cutoff:3.500A) Processing helix chain 'F' and resid 675 through 678 Processing helix chain 'F' and resid 687 through 699 removed outlier: 3.651A pdb=" N PHE F 698 " --> pdb=" O LYS F 694 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 699 " --> pdb=" O ILE F 695 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 79 removed outlier: 3.690A pdb=" N ARG G 67 " --> pdb=" O ASP G 63 " (cutoff:3.500A) Proline residue: G 70 - end of helix Processing helix chain 'G' and resid 85 through 104 removed outlier: 3.654A pdb=" N ALA G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 122 Processing helix chain 'G' and resid 126 through 133 Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.599A pdb=" N GLN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 164 through 172 removed outlier: 3.903A pdb=" N ILE G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 192 removed outlier: 3.780A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 Processing helix chain 'G' and resid 207 through 212 removed outlier: 3.683A pdb=" N VAL G 211 " --> pdb=" O GLY G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 237 Processing helix chain 'G' and resid 237 through 248 removed outlier: 4.043A pdb=" N VAL G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 253 Processing helix chain 'G' and resid 254 through 259 Processing helix chain 'G' and resid 263 through 279 removed outlier: 3.851A pdb=" N ARG G 267 " --> pdb=" O ASP G 263 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR G 279 " --> pdb=" O ALA G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 289 removed outlier: 3.518A pdb=" N ARG G 289 " --> pdb=" O ARG G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 303 Processing helix chain 'G' and resid 304 through 309 Processing helix chain 'G' and resid 330 through 334 Processing helix chain 'G' and resid 338 through 360 Processing helix chain 'G' and resid 363 through 368 Processing helix chain 'G' and resid 369 through 375 removed outlier: 3.617A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 397 Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 413 through 424 removed outlier: 3.536A pdb=" N VAL G 417 " --> pdb=" O LYS G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 436 removed outlier: 3.710A pdb=" N GLN G 436 " --> pdb=" O SER G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 444 removed outlier: 3.682A pdb=" N LEU G 444 " --> pdb=" O GLY G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 447 through 454 Processing helix chain 'G' and resid 461 through 477 removed outlier: 3.550A pdb=" N ARG G 468 " --> pdb=" O LYS G 464 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR G 475 " --> pdb=" O THR G 471 " (cutoff:3.500A) Processing helix chain 'G' and resid 487 through 495 removed outlier: 3.651A pdb=" N SER G 493 " --> pdb=" O ASP G 489 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 500 removed outlier: 4.464A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) Processing helix chain 'G' and resid 501 through 507 Processing helix chain 'G' and resid 511 through 515 removed outlier: 3.830A pdb=" N LEU G 515 " --> pdb=" O ARG G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 526 Processing helix chain 'G' and resid 531 through 548 removed outlier: 3.569A pdb=" N GLU G 544 " --> pdb=" O THR G 540 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU G 546 " --> pdb=" O ALA G 542 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS G 547 " --> pdb=" O ARG G 543 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 587 Processing helix chain 'G' and resid 605 through 614 removed outlier: 3.724A pdb=" N GLN G 609 " --> pdb=" O ASP G 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 637 through 650 Processing helix chain 'G' and resid 664 through 668 Processing helix chain 'G' and resid 669 through 674 removed outlier: 4.346A pdb=" N ALA G 674 " --> pdb=" O GLU G 670 " (cutoff:3.500A) Processing helix chain 'G' and resid 675 through 678 Processing helix chain 'G' and resid 687 through 699 removed outlier: 3.651A pdb=" N PHE G 698 " --> pdb=" O LYS G 694 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU G 699 " --> pdb=" O ILE G 695 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 79 removed outlier: 3.689A pdb=" N ARG H 67 " --> pdb=" O ASP H 63 " (cutoff:3.500A) Proline residue: H 70 - end of helix Processing helix chain 'H' and resid 85 through 104 removed outlier: 3.654A pdb=" N ALA H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 122 Processing helix chain 'H' and resid 126 through 133 Processing helix chain 'H' and resid 137 through 150 removed outlier: 3.599A pdb=" N GLN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 164 through 172 removed outlier: 3.902A pdb=" N ILE H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 192 removed outlier: 3.780A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 205 Processing helix chain 'H' and resid 207 through 212 removed outlier: 3.683A pdb=" N VAL H 211 " --> pdb=" O GLY H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 237 Processing helix chain 'H' and resid 237 through 248 removed outlier: 4.043A pdb=" N VAL H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 253 Processing helix chain 'H' and resid 254 through 259 Processing helix chain 'H' and resid 263 through 279 removed outlier: 3.850A pdb=" N ARG H 267 " --> pdb=" O ASP H 263 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL H 274 " --> pdb=" O ALA H 270 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR H 279 " --> pdb=" O ALA H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 289 removed outlier: 3.519A pdb=" N ARG H 289 " --> pdb=" O ARG H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 303 Processing helix chain 'H' and resid 304 through 309 Processing helix chain 'H' and resid 330 through 334 Processing helix chain 'H' and resid 338 through 360 Processing helix chain 'H' and resid 363 through 368 Processing helix chain 'H' and resid 369 through 375 removed outlier: 3.617A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 397 Processing helix chain 'H' and resid 408 through 412 Processing helix chain 'H' and resid 413 through 424 removed outlier: 3.535A pdb=" N VAL H 417 " --> pdb=" O LYS H 413 " (cutoff:3.500A) Processing helix chain 'H' and resid 429 through 436 removed outlier: 3.710A pdb=" N GLN H 436 " --> pdb=" O SER H 432 " (cutoff:3.500A) Processing helix chain 'H' and resid 439 through 444 removed outlier: 3.682A pdb=" N LEU H 444 " --> pdb=" O GLY H 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 454 Processing helix chain 'H' and resid 461 through 477 removed outlier: 3.550A pdb=" N ARG H 468 " --> pdb=" O LYS H 464 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR H 475 " --> pdb=" O THR H 471 " (cutoff:3.500A) Processing helix chain 'H' and resid 487 through 495 removed outlier: 3.651A pdb=" N SER H 493 " --> pdb=" O ASP H 489 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 500 removed outlier: 4.465A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) Processing helix chain 'H' and resid 501 through 507 Processing helix chain 'H' and resid 511 through 515 removed outlier: 3.831A pdb=" N LEU H 515 " --> pdb=" O ARG H 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 526 Processing helix chain 'H' and resid 531 through 548 removed outlier: 3.569A pdb=" N GLU H 544 " --> pdb=" O THR H 540 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU H 546 " --> pdb=" O ALA H 542 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS H 547 " --> pdb=" O ARG H 543 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 587 Processing helix chain 'H' and resid 605 through 614 removed outlier: 3.723A pdb=" N GLN H 609 " --> pdb=" O ASP H 605 " (cutoff:3.500A) Processing helix chain 'H' and resid 637 through 650 Processing helix chain 'H' and resid 664 through 668 Processing helix chain 'H' and resid 669 through 674 removed outlier: 4.347A pdb=" N ALA H 674 " --> pdb=" O GLU H 670 " (cutoff:3.500A) Processing helix chain 'H' and resid 675 through 678 Processing helix chain 'H' and resid 687 through 699 removed outlier: 3.651A pdb=" N PHE H 698 " --> pdb=" O LYS H 694 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU H 699 " --> pdb=" O ILE H 695 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 591 through 593 removed outlier: 6.695A pdb=" N VAL A 564 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE A 617 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE A 656 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU A 619 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 8.352A 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 593 removed outlier: 6.695A pdb=" N VAL B 564 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE B 617 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE B 656 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU B 619 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 8.352A 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 593 removed outlier: 6.695A pdb=" N VAL C 564 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE C 617 " --> pdb=" O VAL C 654 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE C 656 " --> pdb=" O PHE C 617 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU C 619 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 8.352A 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 593 removed outlier: 6.695A pdb=" N VAL D 564 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE D 617 " --> pdb=" O VAL D 654 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE D 656 " --> pdb=" O PHE D 617 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU D 619 " --> pdb=" O ILE D 656 " (cutoff:3.500A) removed outlier: 8.353A 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 593 removed outlier: 6.695A pdb=" N VAL E 564 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE E 617 " --> pdb=" O VAL E 654 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE E 656 " --> pdb=" O PHE E 617 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU E 619 " --> pdb=" O ILE E 656 " (cutoff:3.500A) removed outlier: 8.352A 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 593 removed outlier: 6.695A pdb=" N VAL F 564 " --> pdb=" O PHE F 592 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE F 617 " --> pdb=" O VAL F 654 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE F 656 " --> pdb=" O PHE F 617 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU F 619 " --> pdb=" O ILE F 656 " (cutoff:3.500A) removed outlier: 8.353A 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 593 removed outlier: 6.695A pdb=" N VAL G 564 " --> pdb=" O PHE G 592 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE G 617 " --> pdb=" O VAL G 654 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE G 656 " --> pdb=" O PHE G 617 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU G 619 " --> pdb=" O ILE G 656 " (cutoff:3.500A) removed outlier: 8.352A 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 593 removed outlier: 6.695A pdb=" N VAL H 564 " --> pdb=" O PHE H 592 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE H 617 " --> pdb=" O VAL H 654 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE H 656 " --> pdb=" O PHE H 617 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU H 619 " --> pdb=" O ILE H 656 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ILE H 681 " --> pdb=" O ILE H 653 " (cutoff:3.500A) 2057 hydrogen bonds defined for protein. 5931 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: 8.04 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9060 1.33 - 1.45: 11270 1.45 - 1.58: 20621 1.58 - 1.71: 33 1.71 - 1.83: 248 Bond restraints: 41232 Sorted by residual: bond pdb=" CD ARG A 484 " pdb=" NE ARG A 484 " ideal model delta sigma weight residual 1.458 1.590 -0.132 1.40e-02 5.10e+03 8.83e+01 bond pdb=" CG ARG A 484 " pdb=" CD ARG A 484 " ideal model delta sigma weight residual 1.520 1.305 0.215 3.00e-02 1.11e+03 5.14e+01 bond pdb=" CA SER E 381 " pdb=" CB SER E 381 " ideal model delta sigma weight residual 1.530 1.460 0.069 1.55e-02 4.16e+03 2.00e+01 bond pdb=" CA SER H 381 " pdb=" CB SER H 381 " ideal model delta sigma weight residual 1.530 1.461 0.069 1.55e-02 4.16e+03 1.98e+01 bond pdb=" CA SER B 381 " pdb=" CB SER B 381 " ideal model delta sigma weight residual 1.530 1.461 0.069 1.55e-02 4.16e+03 1.98e+01 ... (remaining 41227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 51142 3.34 - 6.68: 4183 6.68 - 10.02: 425 10.02 - 13.36: 65 13.36 - 16.70: 17 Bond angle restraints: 55832 Sorted by residual: angle pdb=" C LYS E 375 " pdb=" CA LYS E 375 " pdb=" CB LYS E 375 " ideal model delta sigma weight residual 111.22 99.77 11.45 1.23e+00 6.61e-01 8.66e+01 angle pdb=" C LYS D 375 " pdb=" CA LYS D 375 " pdb=" CB LYS D 375 " ideal model delta sigma weight residual 111.22 99.78 11.44 1.23e+00 6.61e-01 8.64e+01 angle pdb=" C LYS B 375 " pdb=" CA LYS B 375 " pdb=" CB LYS B 375 " ideal model delta sigma weight residual 111.22 99.78 11.44 1.23e+00 6.61e-01 8.64e+01 angle pdb=" C LYS F 375 " pdb=" CA LYS F 375 " pdb=" CB LYS F 375 " ideal model delta sigma weight residual 111.22 99.78 11.44 1.23e+00 6.61e-01 8.64e+01 angle pdb=" C LYS A 375 " pdb=" CA LYS A 375 " pdb=" CB LYS A 375 " ideal model delta sigma weight residual 111.22 99.80 11.42 1.23e+00 6.61e-01 8.62e+01 ... (remaining 55827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.78: 21845 19.78 - 39.56: 2627 39.56 - 59.35: 576 59.35 - 79.13: 200 79.13 - 98.91: 96 Dihedral angle restraints: 25344 sinusoidal: 10552 harmonic: 14792 Sorted by residual: dihedral pdb=" C LYS E 375 " pdb=" N LYS E 375 " pdb=" CA LYS E 375 " pdb=" CB LYS E 375 " ideal model delta harmonic sigma weight residual -122.60 -106.93 -15.67 0 2.50e+00 1.60e-01 3.93e+01 dihedral pdb=" C LYS B 375 " pdb=" N LYS B 375 " pdb=" CA LYS B 375 " pdb=" CB LYS B 375 " ideal model delta harmonic sigma weight residual -122.60 -106.93 -15.67 0 2.50e+00 1.60e-01 3.93e+01 dihedral pdb=" C LYS F 375 " pdb=" N LYS F 375 " pdb=" CA LYS F 375 " pdb=" CB LYS F 375 " ideal model delta harmonic sigma weight residual -122.60 -106.93 -15.67 0 2.50e+00 1.60e-01 3.93e+01 ... (remaining 25341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.936: 6360 0.936 - 1.873: 0 1.873 - 2.809: 0 2.809 - 3.745: 0 3.745 - 4.681: 8 Chirality restraints: 6368 Sorted by residual: chirality pdb=" C1B NAD B 801 " pdb=" C2B NAD B 801 " pdb=" N9A NAD B 801 " pdb=" O4B NAD B 801 " both_signs ideal model delta sigma weight residual False 2.35 -2.33 4.68 2.00e-01 2.50e+01 5.48e+02 chirality pdb=" C1B NAD G 801 " pdb=" C2B NAD G 801 " pdb=" N9A NAD G 801 " pdb=" O4B NAD G 801 " both_signs ideal model delta sigma weight residual False 2.35 -2.33 4.68 2.00e-01 2.50e+01 5.48e+02 chirality pdb=" C1B NAD F 801 " pdb=" C2B NAD F 801 " pdb=" N9A NAD F 801 " pdb=" O4B NAD F 801 " both_signs ideal model delta sigma weight residual False 2.35 -2.33 4.68 2.00e-01 2.50e+01 5.47e+02 ... (remaining 6365 not shown) Planarity restraints: 7224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 801 " -0.248 2.00e-02 2.50e+03 1.57e-01 4.92e+02 pdb=" C2N NAD B 801 " 0.223 2.00e-02 2.50e+03 pdb=" C3N NAD B 801 " -0.007 2.00e-02 2.50e+03 pdb=" C4N NAD B 801 " -0.220 2.00e-02 2.50e+03 pdb=" C5N NAD B 801 " 0.015 2.00e-02 2.50e+03 pdb=" C6N NAD B 801 " 0.173 2.00e-02 2.50e+03 pdb=" C7N NAD B 801 " -0.017 2.00e-02 2.50e+03 pdb=" N1N NAD B 801 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD F 801 " 0.248 2.00e-02 2.50e+03 1.57e-01 4.92e+02 pdb=" C2N NAD F 801 " -0.223 2.00e-02 2.50e+03 pdb=" C3N NAD F 801 " 0.007 2.00e-02 2.50e+03 pdb=" C4N NAD F 801 " 0.220 2.00e-02 2.50e+03 pdb=" C5N NAD F 801 " -0.015 2.00e-02 2.50e+03 pdb=" C6N NAD F 801 " -0.173 2.00e-02 2.50e+03 pdb=" C7N NAD F 801 " 0.017 2.00e-02 2.50e+03 pdb=" N1N NAD F 801 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD C 801 " 0.248 2.00e-02 2.50e+03 1.57e-01 4.91e+02 pdb=" C2N NAD C 801 " -0.223 2.00e-02 2.50e+03 pdb=" C3N NAD C 801 " 0.006 2.00e-02 2.50e+03 pdb=" C4N NAD C 801 " 0.221 2.00e-02 2.50e+03 pdb=" C5N NAD C 801 " -0.016 2.00e-02 2.50e+03 pdb=" C6N NAD C 801 " -0.172 2.00e-02 2.50e+03 pdb=" C7N NAD C 801 " 0.017 2.00e-02 2.50e+03 pdb=" N1N NAD C 801 " -0.081 2.00e-02 2.50e+03 ... (remaining 7221 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9636 2.81 - 3.33: 39646 3.33 - 3.86: 69155 3.86 - 4.38: 90809 4.38 - 4.90: 138187 Nonbonded interactions: 347433 Sorted by model distance: nonbonded pdb=" OG SER A 381 " pdb=" OG SER A 387 " model vdw 2.288 3.040 nonbonded pdb=" OG SER E 381 " pdb=" OG SER E 387 " model vdw 2.288 3.040 nonbonded pdb=" OG SER C 381 " pdb=" OG SER C 387 " model vdw 2.288 3.040 nonbonded pdb=" OG SER G 381 " pdb=" OG SER G 387 " model vdw 2.288 3.040 nonbonded pdb=" OG SER H 381 " pdb=" OG SER H 387 " model vdw 2.288 3.040 ... (remaining 347428 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 34.290 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.080 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9230 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.215 41232 Z= 0.624 Angle : 1.981 16.703 55832 Z= 1.315 Chirality : 0.199 4.681 6368 Planarity : 0.009 0.157 7224 Dihedral : 19.395 98.908 15776 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 6.45 % Allowed : 14.67 % Favored : 78.88 % Cbeta Deviations : 1.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.69 (0.08), residues: 5144 helix: -3.91 (0.05), residues: 3504 sheet: -3.30 (0.28), residues: 120 loop : -2.77 (0.13), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.002 ARG A 484 TYR 0.041 0.009 TYR A 380 PHE 0.055 0.009 PHE D 466 TRP 0.047 0.009 TRP D 420 HIS 0.019 0.004 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00967 (41232) covalent geometry : angle 1.98134 (55832) hydrogen bonds : bond 0.21895 ( 2057) hydrogen bonds : angle 8.78054 ( 5931) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 276 poor density : 144 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8625 (p) REVERT: A 608 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8838 (mp) REVERT: A 672 MET cc_start: 0.8400 (ptm) cc_final: 0.8057 (ptp) REVERT: B 590 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8622 (p) REVERT: C 590 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8621 (p) REVERT: C 608 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8837 (mp) REVERT: C 672 MET cc_start: 0.8398 (ptm) cc_final: 0.8058 (ptp) REVERT: D 590 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8622 (p) REVERT: E 590 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8624 (p) REVERT: E 608 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8837 (mp) REVERT: E 672 MET cc_start: 0.8382 (ptm) cc_final: 0.8035 (ptp) REVERT: F 590 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8622 (p) REVERT: G 590 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8622 (p) REVERT: G 608 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8831 (mp) REVERT: G 672 MET cc_start: 0.8397 (ptm) cc_final: 0.8055 (ptp) REVERT: H 590 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8623 (p) outliers start: 276 outliers final: 48 residues processed: 420 average time/residue: 0.7583 time to fit residues: 383.7645 Evaluate side-chains 137 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 77 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 350 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 350 CYS Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 482 CYS Chi-restraints excluded: chain D residue 590 SER Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 297 GLU Chi-restraints excluded: chain E residue 350 CYS Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 482 CYS Chi-restraints excluded: chain E residue 590 SER Chi-restraints excluded: chain E residue 608 ILE Chi-restraints excluded: chain F residue 297 GLU Chi-restraints excluded: chain F residue 350 CYS Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 482 CYS Chi-restraints excluded: chain F residue 590 SER Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain G residue 297 GLU Chi-restraints excluded: chain G residue 350 CYS Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 590 SER Chi-restraints excluded: chain G residue 608 ILE Chi-restraints excluded: chain H residue 297 GLU Chi-restraints excluded: chain H residue 350 CYS Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 590 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 265 optimal weight: 7.9990 chunk 497 optimal weight: 30.0000 chunk 414 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 6.9990 chunk 223 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 150 GLN A 239 GLN A 328 GLN A 359 GLN A 516 HIS A 616 ASN B 150 GLN B 239 GLN B 359 GLN B 516 HIS B 616 ASN C 97 GLN C 150 GLN C 239 GLN C 328 GLN C 359 GLN C 516 HIS C 616 ASN D 150 GLN D 239 GLN D 359 GLN D 516 HIS D 616 ASN ** D 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 150 GLN E 239 GLN E 328 GLN E 359 GLN E 516 HIS E 616 ASN F 150 GLN F 239 GLN F 359 GLN F 516 HIS F 616 ASN ** F 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 150 GLN G 239 GLN G 328 GLN G 359 GLN G 516 HIS G 616 ASN H 150 GLN H 239 GLN H 359 GLN H 516 HIS H 616 ASN ** H 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.070540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.043940 restraints weight = 155139.928| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.48 r_work: 0.2758 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 41232 Z= 0.178 Angle : 0.659 9.898 55832 Z= 0.340 Chirality : 0.040 0.210 6368 Planarity : 0.004 0.032 7224 Dihedral : 10.271 83.055 6128 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.99 % Allowed : 15.93 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.11), residues: 5144 helix: -1.39 (0.08), residues: 3536 sheet: -2.05 (0.34), residues: 120 loop : -1.35 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 376 TYR 0.008 0.001 TYR F 687 PHE 0.019 0.002 PHE A 308 TRP 0.019 0.001 TRP C 420 HIS 0.004 0.001 HIS G 640 Details of bonding type rmsd covalent geometry : bond 0.00404 (41232) covalent geometry : angle 0.65851 (55832) hydrogen bonds : bond 0.04134 ( 2057) hydrogen bonds : angle 4.63495 ( 5931) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 113 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASN cc_start: 0.9319 (m-40) cc_final: 0.9024 (p0) REVERT: B 337 ASN cc_start: 0.9331 (m-40) cc_final: 0.9050 (p0) REVERT: C 337 ASN cc_start: 0.9321 (m-40) cc_final: 0.9021 (p0) REVERT: D 337 ASN cc_start: 0.9326 (m-40) cc_final: 0.9049 (p0) REVERT: E 337 ASN cc_start: 0.9327 (m-40) cc_final: 0.9027 (p0) REVERT: F 337 ASN cc_start: 0.9330 (m-40) cc_final: 0.9050 (p0) REVERT: G 337 ASN cc_start: 0.9324 (m-40) cc_final: 0.9028 (p0) REVERT: H 337 ASN cc_start: 0.9324 (m-40) cc_final: 0.9049 (p0) outliers start: 85 outliers final: 28 residues processed: 186 average time/residue: 0.6704 time to fit residues: 154.8363 Evaluate side-chains 125 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain D residue 607 LEU Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain E residue 667 VAL Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 607 LEU Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain G residue 453 THR Chi-restraints excluded: chain G residue 481 THR Chi-restraints excluded: chain G residue 607 LEU Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain H residue 453 THR Chi-restraints excluded: chain H residue 607 LEU Chi-restraints excluded: chain H residue 667 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 406 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 162 optimal weight: 30.0000 chunk 334 optimal weight: 0.9980 chunk 280 optimal weight: 4.9990 chunk 227 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 511 optimal weight: 10.0000 chunk 408 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN A 616 ASN A 631 GLN A 642 GLN B 616 ASN B 642 GLN C 328 GLN C 616 ASN C 631 GLN C 642 GLN D 616 ASN D 642 GLN E 328 GLN E 616 ASN E 631 GLN E 642 GLN F 616 ASN F 642 GLN G 328 GLN G 616 ASN G 631 GLN G 642 GLN H 616 ASN H 642 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.069009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.042520 restraints weight = 155379.029| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.46 r_work: 0.2722 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41232 Z= 0.186 Angle : 0.561 6.243 55832 Z= 0.292 Chirality : 0.038 0.165 6368 Planarity : 0.004 0.036 7224 Dihedral : 8.995 82.974 6052 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.43 % Allowed : 16.66 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.12), residues: 5144 helix: -0.19 (0.09), residues: 3568 sheet: -1.47 (0.37), residues: 120 loop : -0.77 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 376 TYR 0.008 0.001 TYR C 687 PHE 0.017 0.001 PHE A 308 TRP 0.014 0.001 TRP A 420 HIS 0.004 0.001 HIS C 640 Details of bonding type rmsd covalent geometry : bond 0.00430 (41232) covalent geometry : angle 0.56145 (55832) hydrogen bonds : bond 0.03625 ( 2057) hydrogen bonds : angle 3.99559 ( 5931) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 97 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASN cc_start: 0.9321 (m-40) cc_final: 0.9015 (p0) REVERT: B 337 ASN cc_start: 0.9345 (m-40) cc_final: 0.9025 (p0) REVERT: C 337 ASN cc_start: 0.9332 (m-40) cc_final: 0.9029 (p0) REVERT: D 337 ASN cc_start: 0.9350 (m-40) cc_final: 0.9027 (p0) REVERT: E 337 ASN cc_start: 0.9343 (m-40) cc_final: 0.9034 (p0) REVERT: F 337 ASN cc_start: 0.9347 (m-40) cc_final: 0.9027 (p0) REVERT: G 337 ASN cc_start: 0.9334 (m-40) cc_final: 0.9021 (p0) REVERT: H 337 ASN cc_start: 0.9344 (m-40) cc_final: 0.9028 (p0) REVERT: H 672 MET cc_start: 0.7096 (ptt) cc_final: 0.6891 (ptt) outliers start: 61 outliers final: 24 residues processed: 154 average time/residue: 0.7420 time to fit residues: 139.8037 Evaluate side-chains 111 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 607 LEU Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 667 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 607 LEU Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 607 LEU Chi-restraints excluded: chain H residue 667 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 338 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 457 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 61 optimal weight: 50.0000 chunk 230 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 370 optimal weight: 0.9990 chunk 401 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN B 616 ASN C 616 ASN D 616 ASN E 616 ASN F 616 ASN G 616 ASN H 616 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.069293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.042869 restraints weight = 154553.005| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.44 r_work: 0.2735 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41232 Z= 0.148 Angle : 0.510 6.999 55832 Z= 0.261 Chirality : 0.037 0.176 6368 Planarity : 0.003 0.040 7224 Dihedral : 8.841 87.785 6048 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.86 % Allowed : 17.22 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.12), residues: 5144 helix: 0.43 (0.09), residues: 3568 sheet: -0.85 (0.40), residues: 120 loop : -0.45 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 86 TYR 0.005 0.001 TYR A 503 PHE 0.020 0.001 PHE A 308 TRP 0.010 0.001 TRP A 420 HIS 0.004 0.001 HIS H 640 Details of bonding type rmsd covalent geometry : bond 0.00345 (41232) covalent geometry : angle 0.50980 (55832) hydrogen bonds : bond 0.03284 ( 2057) hydrogen bonds : angle 3.74521 ( 5931) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.9180 (mmm160) cc_final: 0.8928 (mmp80) REVERT: A 337 ASN cc_start: 0.9336 (m-40) cc_final: 0.9034 (p0) REVERT: A 672 MET cc_start: 0.7726 (ptm) cc_final: 0.7518 (ptm) REVERT: B 337 ASN cc_start: 0.9349 (m-40) cc_final: 0.9019 (p0) REVERT: C 86 ARG cc_start: 0.9181 (mmm160) cc_final: 0.8928 (mmp80) REVERT: C 337 ASN cc_start: 0.9332 (m-40) cc_final: 0.9030 (p0) REVERT: C 672 MET cc_start: 0.7736 (ptm) cc_final: 0.7527 (ptm) REVERT: D 337 ASN cc_start: 0.9346 (m-40) cc_final: 0.9018 (p0) REVERT: E 86 ARG cc_start: 0.9178 (mmm160) cc_final: 0.8926 (mmp80) REVERT: E 337 ASN cc_start: 0.9344 (m-40) cc_final: 0.9039 (p0) REVERT: E 672 MET cc_start: 0.7732 (ptm) cc_final: 0.7524 (ptm) REVERT: F 337 ASN cc_start: 0.9341 (m-40) cc_final: 0.9017 (p0) REVERT: G 86 ARG cc_start: 0.9177 (mmm160) cc_final: 0.8925 (mmp80) REVERT: G 337 ASN cc_start: 0.9347 (m-40) cc_final: 0.9034 (p0) REVERT: G 672 MET cc_start: 0.7731 (ptm) cc_final: 0.7522 (ptm) REVERT: H 337 ASN cc_start: 0.9350 (m-40) cc_final: 0.9020 (p0) outliers start: 37 outliers final: 12 residues processed: 134 average time/residue: 0.8239 time to fit residues: 132.6849 Evaluate side-chains 92 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 667 VAL Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain H residue 667 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 357 optimal weight: 0.4980 chunk 479 optimal weight: 0.9980 chunk 354 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 293 optimal weight: 0.8980 chunk 340 optimal weight: 0.8980 chunk 35 optimal weight: 0.0870 chunk 125 optimal weight: 20.0000 chunk 227 optimal weight: 0.7980 chunk 382 optimal weight: 30.0000 chunk 44 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN A 616 ASN B 585 GLN B 616 ASN C 585 GLN C 616 ASN D 585 GLN D 616 ASN E 585 GLN E 616 ASN F 585 GLN F 616 ASN G 585 GLN G 616 ASN H 585 GLN H 616 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.070643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.044536 restraints weight = 153859.632| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.46 r_work: 0.2798 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 41232 Z= 0.088 Angle : 0.460 5.902 55832 Z= 0.233 Chirality : 0.036 0.162 6368 Planarity : 0.003 0.042 7224 Dihedral : 8.510 81.032 6048 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.40 % Allowed : 16.66 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.13), residues: 5144 helix: 0.89 (0.09), residues: 3560 sheet: -0.34 (0.43), residues: 120 loop : -0.21 (0.18), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 86 TYR 0.004 0.001 TYR C 503 PHE 0.020 0.001 PHE B 308 TRP 0.006 0.001 TRP A 420 HIS 0.003 0.001 HIS H 640 Details of bonding type rmsd covalent geometry : bond 0.00203 (41232) covalent geometry : angle 0.46039 (55832) hydrogen bonds : bond 0.02789 ( 2057) hydrogen bonds : angle 3.47809 ( 5931) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 96 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 672 MET cc_start: 0.7697 (ptm) cc_final: 0.7485 (ptm) REVERT: B 337 ASN cc_start: 0.9326 (m-40) cc_final: 0.8949 (p0) REVERT: C 672 MET cc_start: 0.7703 (ptm) cc_final: 0.7489 (ptm) REVERT: D 337 ASN cc_start: 0.9326 (m-40) cc_final: 0.8948 (p0) REVERT: E 672 MET cc_start: 0.7697 (ptm) cc_final: 0.7487 (ptm) REVERT: F 337 ASN cc_start: 0.9323 (m-40) cc_final: 0.8945 (p0) REVERT: G 672 MET cc_start: 0.7699 (ptm) cc_final: 0.7488 (ptm) REVERT: H 337 ASN cc_start: 0.9328 (m-40) cc_final: 0.8947 (p0) outliers start: 60 outliers final: 12 residues processed: 152 average time/residue: 0.6014 time to fit residues: 116.3599 Evaluate side-chains 92 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 667 VAL Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain H residue 667 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 92 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 99 optimal weight: 0.0770 chunk 450 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 295 optimal weight: 9.9990 chunk 236 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 488 optimal weight: 3.9990 chunk 349 optimal weight: 0.9980 chunk 304 optimal weight: 4.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN B 616 ASN C 616 ASN D 616 ASN E 616 ASN F 616 ASN G 616 ASN H 616 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.069545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.043149 restraints weight = 155436.355| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.45 r_work: 0.2758 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41232 Z= 0.131 Angle : 0.483 7.624 55832 Z= 0.245 Chirality : 0.037 0.157 6368 Planarity : 0.003 0.042 7224 Dihedral : 8.336 79.660 6048 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.00 % Allowed : 16.64 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.13), residues: 5144 helix: 1.16 (0.09), residues: 3544 sheet: 0.20 (0.46), residues: 120 loop : -0.07 (0.18), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 86 TYR 0.007 0.001 TYR D 687 PHE 0.015 0.001 PHE A 308 TRP 0.007 0.001 TRP C 420 HIS 0.004 0.001 HIS F 640 Details of bonding type rmsd covalent geometry : bond 0.00310 (41232) covalent geometry : angle 0.48297 (55832) hydrogen bonds : bond 0.03033 ( 2057) hydrogen bonds : angle 3.46987 ( 5931) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 84 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 337 ASN cc_start: 0.9354 (m-40) cc_final: 0.8966 (p0) REVERT: B 672 MET cc_start: 0.6706 (ptt) cc_final: 0.6419 (ptt) REVERT: D 337 ASN cc_start: 0.9344 (m-40) cc_final: 0.8960 (p0) REVERT: D 672 MET cc_start: 0.6707 (ptt) cc_final: 0.6421 (ptt) REVERT: F 337 ASN cc_start: 0.9341 (m-40) cc_final: 0.8956 (p0) REVERT: H 337 ASN cc_start: 0.9346 (m-40) cc_final: 0.8961 (p0) REVERT: H 672 MET cc_start: 0.6775 (ptt) cc_final: 0.6525 (ptt) outliers start: 43 outliers final: 20 residues processed: 127 average time/residue: 0.6771 time to fit residues: 106.9979 Evaluate side-chains 100 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 604 GLU Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 667 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 604 GLU Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 604 GLU Chi-restraints excluded: chain H residue 667 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 371 optimal weight: 2.9990 chunk 432 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 242 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 332 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 186 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 190 HIS A 616 ASN B 134 GLN B 190 HIS B 616 ASN C 134 GLN C 190 HIS C 616 ASN D 134 GLN D 190 HIS D 616 ASN D 631 GLN E 134 GLN E 190 HIS E 616 ASN F 134 GLN F 190 HIS F 616 ASN G 190 HIS G 616 ASN H 134 GLN H 190 HIS H 616 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.067915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041474 restraints weight = 156382.915| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.40 r_work: 0.2697 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 41232 Z= 0.253 Angle : 0.569 9.057 55832 Z= 0.286 Chirality : 0.040 0.159 6368 Planarity : 0.004 0.048 7224 Dihedral : 8.483 82.568 6048 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.24 % Allowed : 16.68 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.12), residues: 5144 helix: 1.09 (0.09), residues: 3584 sheet: 0.29 (0.46), residues: 120 loop : -0.08 (0.18), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 86 TYR 0.007 0.001 TYR F 503 PHE 0.018 0.001 PHE A 308 TRP 0.008 0.001 TRP C 420 HIS 0.004 0.001 HIS B 640 Details of bonding type rmsd covalent geometry : bond 0.00580 (41232) covalent geometry : angle 0.56877 (55832) hydrogen bonds : bond 0.03567 ( 2057) hydrogen bonds : angle 3.64592 ( 5931) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 88 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASN cc_start: 0.9310 (m-40) cc_final: 0.9054 (p0) REVERT: B 337 ASN cc_start: 0.9363 (m-40) cc_final: 0.9044 (p0) REVERT: B 672 MET cc_start: 0.7087 (ptt) cc_final: 0.6802 (ptt) REVERT: C 337 ASN cc_start: 0.9311 (m-40) cc_final: 0.9056 (p0) REVERT: D 337 ASN cc_start: 0.9349 (m-40) cc_final: 0.9039 (p0) REVERT: D 672 MET cc_start: 0.7097 (ptt) cc_final: 0.6812 (ptt) REVERT: E 337 ASN cc_start: 0.9335 (m-40) cc_final: 0.9065 (p0) REVERT: F 337 ASN cc_start: 0.9359 (m-40) cc_final: 0.9043 (p0) REVERT: G 337 ASN cc_start: 0.9325 (m-40) cc_final: 0.9060 (p0) REVERT: H 337 ASN cc_start: 0.9359 (m-40) cc_final: 0.9044 (p0) REVERT: H 672 MET cc_start: 0.7259 (ptt) cc_final: 0.7024 (ptt) outliers start: 53 outliers final: 21 residues processed: 137 average time/residue: 0.7224 time to fit residues: 121.4574 Evaluate side-chains 99 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 667 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain G residue 303 LEU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 667 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 346 optimal weight: 9.9990 chunk 377 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 439 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 447 optimal weight: 6.9990 chunk 240 optimal weight: 5.9990 chunk 410 optimal weight: 20.0000 chunk 239 optimal weight: 4.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 616 ASN B 170 ASN B 616 ASN B 631 GLN C 81 GLN C 616 ASN D 616 ASN E 81 GLN E 616 ASN F 616 ASN F 631 GLN G 616 ASN H 170 ASN H 616 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.068038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.041636 restraints weight = 155597.395| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.39 r_work: 0.2705 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 41232 Z= 0.223 Angle : 0.547 10.729 55832 Z= 0.274 Chirality : 0.039 0.150 6368 Planarity : 0.003 0.043 7224 Dihedral : 8.517 83.483 6048 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.03 % Allowed : 16.96 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.12), residues: 5144 helix: 1.22 (0.09), residues: 3576 sheet: 0.44 (0.47), residues: 120 loop : 0.07 (0.18), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 86 TYR 0.006 0.001 TYR H 429 PHE 0.018 0.001 PHE A 308 TRP 0.008 0.001 TRP A 420 HIS 0.004 0.001 HIS H 640 Details of bonding type rmsd covalent geometry : bond 0.00514 (41232) covalent geometry : angle 0.54704 (55832) hydrogen bonds : bond 0.03414 ( 2057) hydrogen bonds : angle 3.58744 ( 5931) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 85 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.9747 (OUTLIER) cc_final: 0.9546 (mt) REVERT: A 337 ASN cc_start: 0.9308 (m-40) cc_final: 0.9071 (p0) REVERT: B 337 ASN cc_start: 0.9355 (m-40) cc_final: 0.9062 (p0) REVERT: C 72 LEU cc_start: 0.9746 (OUTLIER) cc_final: 0.9545 (mt) REVERT: C 337 ASN cc_start: 0.9317 (m-40) cc_final: 0.9077 (p0) REVERT: D 337 ASN cc_start: 0.9348 (m-40) cc_final: 0.9060 (p0) REVERT: E 72 LEU cc_start: 0.9746 (OUTLIER) cc_final: 0.9546 (mt) REVERT: E 337 ASN cc_start: 0.9336 (m-40) cc_final: 0.9092 (p0) REVERT: F 337 ASN cc_start: 0.9351 (m-40) cc_final: 0.9060 (p0) REVERT: G 337 ASN cc_start: 0.9331 (m-40) cc_final: 0.9089 (p0) REVERT: H 337 ASN cc_start: 0.9351 (m-40) cc_final: 0.9062 (p0) outliers start: 44 outliers final: 20 residues processed: 125 average time/residue: 0.6988 time to fit residues: 107.6623 Evaluate side-chains 98 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 667 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 667 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 410 optimal weight: 1.9990 chunk 447 optimal weight: 5.9990 chunk 365 optimal weight: 3.9990 chunk 309 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 376 optimal weight: 10.0000 chunk 266 optimal weight: 8.9990 chunk 178 optimal weight: 30.0000 chunk 59 optimal weight: 20.0000 chunk 148 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN B 616 ASN C 616 ASN D 616 ASN E 616 ASN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN H 616 ASN H 631 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.069067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.042712 restraints weight = 155639.426| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.44 r_work: 0.2743 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41232 Z= 0.130 Angle : 0.500 11.947 55832 Z= 0.250 Chirality : 0.037 0.145 6368 Planarity : 0.003 0.046 7224 Dihedral : 8.409 82.219 6048 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.79 % Allowed : 17.34 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.13), residues: 5144 helix: 1.48 (0.09), residues: 3576 sheet: 0.41 (0.47), residues: 120 loop : 0.28 (0.19), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D 307 TYR 0.004 0.001 TYR G 503 PHE 0.029 0.001 PHE F 308 TRP 0.007 0.001 TRP A 490 HIS 0.003 0.001 HIS D 640 Details of bonding type rmsd covalent geometry : bond 0.00309 (41232) covalent geometry : angle 0.50018 (55832) hydrogen bonds : bond 0.03031 ( 2057) hydrogen bonds : angle 3.42258 ( 5931) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASN cc_start: 0.9312 (m-40) cc_final: 0.9079 (p0) REVERT: A 672 MET cc_start: 0.7215 (ptt) cc_final: 0.7014 (ptt) REVERT: B 337 ASN cc_start: 0.9369 (m-40) cc_final: 0.9062 (p0) REVERT: B 622 SER cc_start: 0.7752 (OUTLIER) cc_final: 0.7265 (p) REVERT: C 72 LEU cc_start: 0.9741 (OUTLIER) cc_final: 0.9538 (mt) REVERT: C 337 ASN cc_start: 0.9316 (m-40) cc_final: 0.9075 (p0) REVERT: C 672 MET cc_start: 0.7234 (ptt) cc_final: 0.7029 (ptt) REVERT: D 337 ASN cc_start: 0.9356 (m-40) cc_final: 0.9059 (p0) REVERT: E 72 LEU cc_start: 0.9742 (OUTLIER) cc_final: 0.9540 (mt) REVERT: E 337 ASN cc_start: 0.9331 (m-40) cc_final: 0.9083 (p0) REVERT: E 672 MET cc_start: 0.7223 (ptt) cc_final: 0.7021 (ptt) REVERT: F 337 ASN cc_start: 0.9361 (m-40) cc_final: 0.9060 (p0) REVERT: G 337 ASN cc_start: 0.9324 (m-40) cc_final: 0.9077 (p0) REVERT: G 672 MET cc_start: 0.7230 (ptt) cc_final: 0.7026 (ptt) REVERT: H 337 ASN cc_start: 0.9357 (m-40) cc_final: 0.9058 (p0) outliers start: 34 outliers final: 22 residues processed: 126 average time/residue: 0.6530 time to fit residues: 102.9225 Evaluate side-chains 113 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 667 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 616 ASN Chi-restraints excluded: chain H residue 667 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 305 optimal weight: 0.1980 chunk 241 optimal weight: 40.0000 chunk 431 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 285 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 ASN C 616 ASN D 616 ASN E 616 ASN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.069120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.042760 restraints weight = 154381.090| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.45 r_work: 0.2744 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 41232 Z= 0.136 Angle : 0.675 59.196 55832 Z= 0.381 Chirality : 0.038 0.480 6368 Planarity : 0.003 0.046 7224 Dihedral : 8.414 82.213 6048 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.72 % Allowed : 17.36 % Favored : 81.92 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.13), residues: 5144 helix: 1.50 (0.09), residues: 3576 sheet: 0.36 (0.47), residues: 120 loop : 0.28 (0.19), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 307 TYR 0.005 0.001 TYR F 503 PHE 0.026 0.001 PHE F 308 TRP 0.007 0.001 TRP E 490 HIS 0.008 0.001 HIS F 640 Details of bonding type rmsd covalent geometry : bond 0.00309 (41232) covalent geometry : angle 0.67519 (55832) hydrogen bonds : bond 0.03029 ( 2057) hydrogen bonds : angle 3.42301 ( 5931) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10288 Ramachandran restraints generated. 5144 Oldfield, 0 Emsley, 5144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASN cc_start: 0.9307 (m-40) cc_final: 0.9077 (p0) REVERT: A 672 MET cc_start: 0.7201 (ptt) cc_final: 0.6988 (ptt) REVERT: B 337 ASN cc_start: 0.9363 (m-40) cc_final: 0.9059 (p0) REVERT: B 622 SER cc_start: 0.7750 (OUTLIER) cc_final: 0.7265 (p) REVERT: C 72 LEU cc_start: 0.9742 (OUTLIER) cc_final: 0.9539 (mt) REVERT: C 337 ASN cc_start: 0.9313 (m-40) cc_final: 0.9073 (p0) REVERT: C 672 MET cc_start: 0.7215 (ptt) cc_final: 0.7001 (ptt) REVERT: D 337 ASN cc_start: 0.9354 (m-40) cc_final: 0.9058 (p0) REVERT: E 72 LEU cc_start: 0.9743 (OUTLIER) cc_final: 0.9542 (mt) REVERT: E 337 ASN cc_start: 0.9326 (m-40) cc_final: 0.9079 (p0) REVERT: E 672 MET cc_start: 0.7206 (ptt) cc_final: 0.6995 (ptt) REVERT: F 337 ASN cc_start: 0.9357 (m-40) cc_final: 0.9058 (p0) REVERT: G 337 ASN cc_start: 0.9318 (m-40) cc_final: 0.9074 (p0) REVERT: G 672 MET cc_start: 0.7211 (ptt) cc_final: 0.6999 (ptt) REVERT: H 337 ASN cc_start: 0.9355 (m-40) cc_final: 0.9057 (p0) outliers start: 31 outliers final: 25 residues processed: 123 average time/residue: 0.6655 time to fit residues: 102.3371 Evaluate side-chains 120 residues out of total 4280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 667 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 667 VAL Chi-restraints excluded: chain G residue 364 VAL Chi-restraints excluded: chain G residue 616 ASN Chi-restraints excluded: chain G residue 667 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 667 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 413 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 422 optimal weight: 6.9990 chunk 254 optimal weight: 30.0000 chunk 314 optimal weight: 10.0000 chunk 401 optimal weight: 2.9990 chunk 440 optimal weight: 8.9990 chunk 414 optimal weight: 7.9990 chunk 360 optimal weight: 0.0270 chunk 40 optimal weight: 7.9990 chunk 237 optimal weight: 0.7980 overall best weight: 2.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 616 ASN ** 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 = 0.3725 r_free = 0.3725 target = 0.069120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.042736 restraints weight = 155287.741| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.46 r_work: 0.2743 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.385 41232 Z= 0.337 Angle : 0.904 59.200 55832 Z= 0.609 Chirality : 0.037 0.141 6368 Planarity : 0.006 0.189 7224 Dihedral : 8.416 82.215 6048 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.56 % Allowed : 17.36 % Favored : 82.08 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.13), residues: 5144 helix: 1.50 (0.09), residues: 3576 sheet: 0.31 (0.47), residues: 120 loop : 0.26 (0.19), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 307 TYR 0.005 0.001 TYR F 503 PHE 0.024 0.001 PHE F 308 TRP 0.007 0.001 TRP E 490 HIS 0.008 0.001 HIS H 640 Details of bonding type rmsd covalent geometry : bond 0.00613 (41232) covalent geometry : angle 0.90361 (55832) hydrogen bonds : bond 0.03036 ( 2057) hydrogen bonds : angle 3.42452 ( 5931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13270.77 seconds wall clock time: 226 minutes 35.87 seconds (13595.87 seconds total)