Starting phenix.real_space_refine on Sat Feb 17 19:00:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1u_0605/02_2024/6o1u_0605.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1u_0605/02_2024/6o1u_0605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1u_0605/02_2024/6o1u_0605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1u_0605/02_2024/6o1u_0605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1u_0605/02_2024/6o1u_0605.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1u_0605/02_2024/6o1u_0605.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 12652 2.51 5 N 3324 2.21 5 O 3496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 35": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C ARG 589": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C GLU 634": "OE1" <-> "OE2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D ARG 589": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D GLU 634": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19612 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4903 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 589} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4903 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 589} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4903 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 589} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4903 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 589} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 9.74, per 1000 atoms: 0.50 Number of scatterers: 19612 At special positions: 0 Unit cell: (130.257, 130.257, 120.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 3496 8.00 N 3324 7.00 C 12652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.99 Conformation dependent library (CDL) restraints added in 3.8 seconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 8 sheets defined 64.2% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.726A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 removed outlier: 4.078A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.802A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.193A pdb=" N VAL A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.578A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A 126 " --> pdb=" O HIS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.537A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.666A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.785A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.617A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.748A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.553A pdb=" N LEU A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.878A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.521A pdb=" N VAL A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 411 Proline residue: A 405 - end of helix removed outlier: 3.827A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.648A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 446 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.773A pdb=" N PHE A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 removed outlier: 3.600A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 499 through 512 removed outlier: 3.867A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.371A pdb=" N PHE A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 525 through 539 removed outlier: 3.559A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.721A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 584 removed outlier: 3.657A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 608 removed outlier: 3.536A pdb=" N ARG A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 47 removed outlier: 3.726A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 removed outlier: 4.079A pdb=" N ASN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 106 removed outlier: 3.803A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 112 through 116 removed outlier: 4.194A pdb=" N VAL B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.578A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET B 126 " --> pdb=" O HIS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.537A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 183 removed outlier: 3.666A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.784A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.618A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.748A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.553A pdb=" N LEU B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 310 removed outlier: 3.878A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.521A pdb=" N VAL B 331 " --> pdb=" O PRO B 327 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 411 Proline residue: B 405 - end of helix removed outlier: 3.827A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 removed outlier: 3.649A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 446 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.774A pdb=" N PHE B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 removed outlier: 3.600A pdb=" N THR B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'B' and resid 499 through 512 removed outlier: 3.867A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 4.371A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 524' Processing helix chain 'B' and resid 525 through 539 removed outlier: 3.559A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.721A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 584 removed outlier: 3.656A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 608 removed outlier: 3.537A pdb=" N ARG B 606 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.726A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 removed outlier: 4.078A pdb=" N ASN C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 106 removed outlier: 3.802A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.193A pdb=" N VAL C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.577A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET C 126 " --> pdb=" O HIS C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.537A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.666A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.785A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.617A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.748A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.553A pdb=" N LEU C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 310 removed outlier: 3.878A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.521A pdb=" N VAL C 331 " --> pdb=" O PRO C 327 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 411 Proline residue: C 405 - end of helix removed outlier: 3.826A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.649A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 446 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.773A pdb=" N PHE C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 removed outlier: 3.599A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 499 Processing helix chain 'C' and resid 499 through 512 removed outlier: 3.867A pdb=" N ALA C 505 " --> pdb=" O ILE C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 4.372A pdb=" N PHE C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 524' Processing helix chain 'C' and resid 525 through 539 removed outlier: 3.559A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.721A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 584 removed outlier: 3.657A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 608 removed outlier: 3.536A pdb=" N ARG C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 47 removed outlier: 3.726A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 removed outlier: 4.078A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 106 removed outlier: 3.802A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 112 through 116 removed outlier: 4.193A pdb=" N VAL D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.577A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET D 126 " --> pdb=" O HIS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.537A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 183 removed outlier: 3.666A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.784A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.618A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.748A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 249 " --> pdb=" O LYS D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 280 through 285 Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.553A pdb=" N LEU D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.878A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.521A pdb=" N VAL D 331 " --> pdb=" O PRO D 327 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 411 Proline residue: D 405 - end of helix removed outlier: 3.828A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 418 removed outlier: 3.649A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 446 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.773A pdb=" N PHE D 472 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 removed outlier: 3.600A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 499 Processing helix chain 'D' and resid 499 through 512 removed outlier: 3.867A pdb=" N ALA D 505 " --> pdb=" O ILE D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 4.371A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER D 524 " --> pdb=" O GLY D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 524' Processing helix chain 'D' and resid 525 through 539 removed outlier: 3.560A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.720A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 584 removed outlier: 3.657A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 608 removed outlier: 3.536A pdb=" N ARG D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.945A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.945A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.945A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.945A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 952 hydrogen bonds defined for protein. 2748 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: 6.20 Time building geometry restraints manager: 8.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3180 1.30 - 1.44: 5433 1.44 - 1.57: 11212 1.57 - 1.71: 7 1.71 - 1.84: 228 Bond restraints: 20060 Sorted by residual: bond pdb=" N TRP B 29 " pdb=" CA TRP B 29 " ideal model delta sigma weight residual 1.459 1.363 0.096 1.17e-02 7.31e+03 6.68e+01 bond pdb=" N TRP C 29 " pdb=" CA TRP C 29 " ideal model delta sigma weight residual 1.459 1.363 0.096 1.18e-02 7.18e+03 6.64e+01 bond pdb=" N TRP A 29 " pdb=" CA TRP A 29 " ideal model delta sigma weight residual 1.459 1.364 0.095 1.17e-02 7.31e+03 6.62e+01 bond pdb=" N TRP D 29 " pdb=" CA TRP D 29 " ideal model delta sigma weight residual 1.459 1.364 0.095 1.17e-02 7.31e+03 6.58e+01 bond pdb=" N MET A 474 " pdb=" CA MET A 474 " ideal model delta sigma weight residual 1.459 1.388 0.071 1.18e-02 7.18e+03 3.63e+01 ... (remaining 20055 not shown) Histogram of bond angle deviations from ideal: 98.98 - 106.02: 476 106.02 - 113.06: 10697 113.06 - 120.10: 7898 120.10 - 127.14: 7905 127.14 - 134.18: 260 Bond angle restraints: 27236 Sorted by residual: angle pdb=" CB MET C 440 " pdb=" CG MET C 440 " pdb=" SD MET C 440 " ideal model delta sigma weight residual 112.70 130.43 -17.73 3.00e+00 1.11e-01 3.49e+01 angle pdb=" CB MET D 440 " pdb=" CG MET D 440 " pdb=" SD MET D 440 " ideal model delta sigma weight residual 112.70 130.42 -17.72 3.00e+00 1.11e-01 3.49e+01 angle pdb=" CB MET A 440 " pdb=" CG MET A 440 " pdb=" SD MET A 440 " ideal model delta sigma weight residual 112.70 130.40 -17.70 3.00e+00 1.11e-01 3.48e+01 angle pdb=" CB MET B 440 " pdb=" CG MET B 440 " pdb=" SD MET B 440 " ideal model delta sigma weight residual 112.70 130.40 -17.70 3.00e+00 1.11e-01 3.48e+01 angle pdb=" N TRP A 29 " pdb=" CA TRP A 29 " pdb=" C TRP A 29 " ideal model delta sigma weight residual 110.97 117.21 -6.24 1.09e+00 8.42e-01 3.28e+01 ... (remaining 27231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 10579 17.20 - 34.40: 1066 34.40 - 51.60: 231 51.60 - 68.79: 56 68.79 - 85.99: 16 Dihedral angle restraints: 11948 sinusoidal: 4776 harmonic: 7172 Sorted by residual: dihedral pdb=" CA ASP C 364 " pdb=" C ASP C 364 " pdb=" N ILE C 365 " pdb=" CA ILE C 365 " ideal model delta harmonic sigma weight residual -180.00 -138.19 -41.81 0 5.00e+00 4.00e-02 6.99e+01 dihedral pdb=" CA ASP A 364 " pdb=" C ASP A 364 " pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta harmonic sigma weight residual -180.00 -138.19 -41.81 0 5.00e+00 4.00e-02 6.99e+01 dihedral pdb=" CA ASP D 364 " pdb=" C ASP D 364 " pdb=" N ILE D 365 " pdb=" CA ILE D 365 " ideal model delta harmonic sigma weight residual -180.00 -138.23 -41.77 0 5.00e+00 4.00e-02 6.98e+01 ... (remaining 11945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2697 0.083 - 0.167: 367 0.167 - 0.250: 28 0.250 - 0.333: 8 0.333 - 0.417: 4 Chirality restraints: 3104 Sorted by residual: chirality pdb=" CA TRP B 29 " pdb=" N TRP B 29 " pdb=" C TRP B 29 " pdb=" CB TRP B 29 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA TRP A 29 " pdb=" N TRP A 29 " pdb=" C TRP A 29 " pdb=" CB TRP A 29 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CA TRP C 29 " pdb=" N TRP C 29 " pdb=" C TRP C 29 " pdb=" CB TRP C 29 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 3101 not shown) Planarity restraints: 3464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 326 " -0.044 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO C 327 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 327 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 327 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 326 " 0.044 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO B 327 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 327 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 327 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 326 " 0.044 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO A 327 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " 0.037 5.00e-02 4.00e+02 ... (remaining 3461 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1657 2.72 - 3.27: 19207 3.27 - 3.81: 33319 3.81 - 4.36: 42029 4.36 - 4.90: 69678 Nonbonded interactions: 165890 Sorted by model distance: nonbonded pdb=" OG1 THR A 514 " pdb=" O GLN B 370 " model vdw 2.180 2.440 nonbonded pdb=" OD1 ASP B 34 " pdb=" NH1 ARG C 632 " model vdw 2.226 2.520 nonbonded pdb=" O GLN A 370 " pdb=" OG1 THR D 514 " model vdw 2.229 2.440 nonbonded pdb=" O LEU C 92 " pdb=" OG1 THR C 96 " model vdw 2.257 2.440 nonbonded pdb=" O LEU B 92 " pdb=" OG1 THR B 96 " model vdw 2.257 2.440 ... (remaining 165885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.710 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 52.540 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 0.100 20060 Z= 0.676 Angle : 1.084 17.727 27236 Z= 0.602 Chirality : 0.061 0.417 3104 Planarity : 0.007 0.065 3464 Dihedral : 14.745 85.992 7316 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.65 % Allowed : 8.08 % Favored : 89.27 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.22 (0.12), residues: 2448 helix: -3.92 (0.07), residues: 1392 sheet: -2.40 (0.46), residues: 84 loop : -2.54 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 593 HIS 0.007 0.002 HIS C 201 PHE 0.015 0.002 PHE B 537 TYR 0.023 0.003 TYR B 377 ARG 0.010 0.001 ARG C 589 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 336 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9215 (mtp) cc_final: 0.8953 (mtm) REVERT: A 213 CYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7903 (m) REVERT: A 306 GLN cc_start: 0.8573 (mt0) cc_final: 0.8340 (mm110) REVERT: A 406 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8171 (t0) REVERT: A 474 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8122 (mtt) REVERT: A 594 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7598 (ttp-110) REVERT: B 306 GLN cc_start: 0.8605 (mt0) cc_final: 0.8300 (mm110) REVERT: B 406 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8222 (t0) REVERT: B 474 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8158 (mtt) REVERT: B 481 MET cc_start: 0.6738 (mtm) cc_final: 0.6486 (mtt) REVERT: B 485 MET cc_start: 0.7677 (mtt) cc_final: 0.7281 (mpp) REVERT: B 569 LEU cc_start: 0.8387 (mp) cc_final: 0.8067 (tp) REVERT: C 29 TRP cc_start: 0.7451 (OUTLIER) cc_final: 0.6511 (t60) REVERT: C 306 GLN cc_start: 0.8620 (mt0) cc_final: 0.8405 (mm110) REVERT: C 324 TYR cc_start: 0.8542 (m-80) cc_final: 0.8208 (m-80) REVERT: C 406 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7907 (t0) REVERT: C 447 MET cc_start: 0.8216 (mtt) cc_final: 0.7963 (mtm) REVERT: C 474 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7373 (mtm) REVERT: C 554 MET cc_start: 0.8522 (tpt) cc_final: 0.8314 (tpt) REVERT: C 594 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7623 (ttp-110) REVERT: D 306 GLN cc_start: 0.8630 (mt0) cc_final: 0.8306 (mm110) REVERT: D 406 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8214 (t0) REVERT: D 447 MET cc_start: 0.8209 (mtt) cc_final: 0.7998 (mtm) REVERT: D 474 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7783 (mtm) outliers start: 56 outliers final: 9 residues processed: 372 average time/residue: 1.2114 time to fit residues: 511.4466 Evaluate side-chains 238 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 219 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 479 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 191 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 257 GLN A 265 HIS ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 ASN A 519 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 HIS B 74 GLN B 257 GLN B 265 HIS ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN B 519 ASN ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS C 74 GLN C 230 GLN C 257 GLN C 265 HIS ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS C 446 ASN C 519 ASN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS D 74 GLN D 257 GLN D 265 HIS D 370 GLN D 380 HIS D 446 ASN D 519 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20060 Z= 0.189 Angle : 0.617 7.428 27236 Z= 0.322 Chirality : 0.040 0.144 3104 Planarity : 0.005 0.055 3464 Dihedral : 6.125 47.046 2715 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.36 % Allowed : 15.26 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.14), residues: 2448 helix: -1.76 (0.11), residues: 1464 sheet: -1.64 (0.53), residues: 84 loop : -1.93 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 613 HIS 0.006 0.001 HIS B 380 PHE 0.010 0.001 PHE A 537 TYR 0.008 0.001 TYR B 623 ARG 0.008 0.001 ARG D 492 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 273 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8141 (pt0) cc_final: 0.7507 (pm20) REVERT: A 229 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7099 (tm) REVERT: A 302 ARG cc_start: 0.7896 (mtp-110) cc_final: 0.7668 (mtp85) REVERT: A 440 MET cc_start: 0.6440 (mmp) cc_final: 0.5930 (tpt) REVERT: A 474 MET cc_start: 0.7994 (mtp) cc_final: 0.7647 (mtm) REVERT: A 612 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7727 (mp) REVERT: B 31 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8215 (mt0) REVERT: B 229 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7127 (tm) REVERT: B 302 ARG cc_start: 0.7956 (mtp-110) cc_final: 0.7753 (mtp85) REVERT: B 338 LEU cc_start: 0.8833 (tt) cc_final: 0.8605 (mt) REVERT: B 474 MET cc_start: 0.7964 (mtp) cc_final: 0.7692 (mtm) REVERT: B 485 MET cc_start: 0.7503 (mtt) cc_final: 0.7190 (mpp) REVERT: B 608 MET cc_start: 0.8993 (ptm) cc_final: 0.8734 (ptm) REVERT: B 612 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7703 (mp) REVERT: C 229 LEU cc_start: 0.7435 (mm) cc_final: 0.6827 (tm) REVERT: C 302 ARG cc_start: 0.7916 (mtp-110) cc_final: 0.7684 (mtp85) REVERT: C 324 TYR cc_start: 0.8641 (m-80) cc_final: 0.8232 (m-80) REVERT: C 440 MET cc_start: 0.6371 (mmp) cc_final: 0.6034 (tpt) REVERT: C 474 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7492 (mtm) REVERT: C 492 ARG cc_start: 0.7188 (mtm110) cc_final: 0.6932 (mtm110) REVERT: C 554 MET cc_start: 0.8509 (tpt) cc_final: 0.8268 (tpt) REVERT: D 229 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.6985 (tm) REVERT: D 474 MET cc_start: 0.7928 (mtp) cc_final: 0.7655 (mtm) outliers start: 50 outliers final: 13 residues processed: 301 average time/residue: 1.1853 time to fit residues: 406.3938 Evaluate side-chains 217 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 197 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 380 HIS Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 239 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 261 GLN ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN C 261 GLN ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 306 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20060 Z= 0.338 Angle : 0.649 8.605 27236 Z= 0.334 Chirality : 0.043 0.146 3104 Planarity : 0.005 0.057 3464 Dihedral : 5.399 37.570 2687 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.88 % Allowed : 17.16 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.16), residues: 2448 helix: -0.65 (0.12), residues: 1472 sheet: -1.44 (0.51), residues: 84 loop : -1.92 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 29 HIS 0.005 0.001 HIS A 157 PHE 0.011 0.002 PHE C 537 TYR 0.012 0.002 TYR B 623 ARG 0.009 0.001 ARG D 594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 223 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 MET cc_start: 0.7964 (mtp) cc_final: 0.7710 (mtm) REVERT: A 612 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7894 (mp) REVERT: B 80 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: B 338 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8816 (mt) REVERT: B 474 MET cc_start: 0.8051 (mtp) cc_final: 0.7727 (mtm) REVERT: B 591 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: B 594 ARG cc_start: 0.7954 (ttp-110) cc_final: 0.7698 (ttp-110) REVERT: C 229 LEU cc_start: 0.7559 (mm) cc_final: 0.6884 (tm) REVERT: C 474 MET cc_start: 0.8049 (mtp) cc_final: 0.7737 (mtm) REVERT: D 80 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7662 (pm20) REVERT: D 474 MET cc_start: 0.7918 (mtp) cc_final: 0.7555 (mtm) outliers start: 82 outliers final: 30 residues processed: 280 average time/residue: 1.2073 time to fit residues: 385.1790 Evaluate side-chains 233 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 198 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 235 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20060 Z= 0.208 Angle : 0.585 8.781 27236 Z= 0.298 Chirality : 0.040 0.139 3104 Planarity : 0.004 0.057 3464 Dihedral : 4.878 32.410 2680 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.50 % Allowed : 18.76 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.16), residues: 2448 helix: 0.11 (0.13), residues: 1472 sheet: -1.11 (0.52), residues: 84 loop : -1.71 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 29 HIS 0.008 0.001 HIS C 380 PHE 0.010 0.001 PHE B 292 TYR 0.008 0.001 TYR C 555 ARG 0.011 0.000 ARG D 594 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 226 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7579 (pm20) REVERT: A 474 MET cc_start: 0.7897 (mtp) cc_final: 0.7550 (mtm) REVERT: A 485 MET cc_start: 0.7496 (mtt) cc_final: 0.7279 (mtp) REVERT: A 591 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6887 (tm-30) REVERT: B 31 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8301 (mt0) REVERT: B 80 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: B 474 MET cc_start: 0.7948 (mtp) cc_final: 0.7618 (mtm) REVERT: B 591 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: C 229 LEU cc_start: 0.7568 (mm) cc_final: 0.6979 (tm) REVERT: C 474 MET cc_start: 0.8005 (mtp) cc_final: 0.7714 (mtm) REVERT: C 594 ARG cc_start: 0.7907 (ttp-110) cc_final: 0.7620 (mtp180) REVERT: D 66 LEU cc_start: 0.8307 (tt) cc_final: 0.8093 (tp) REVERT: D 80 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7515 (pm20) REVERT: D 229 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7218 (tm) REVERT: D 302 ARG cc_start: 0.7979 (mtp85) cc_final: 0.7688 (ttm-80) REVERT: D 474 MET cc_start: 0.7830 (mtp) cc_final: 0.7527 (mtm) REVERT: D 594 ARG cc_start: 0.7974 (ttp-110) cc_final: 0.7492 (mtp180) outliers start: 74 outliers final: 17 residues processed: 279 average time/residue: 1.2411 time to fit residues: 393.6449 Evaluate side-chains 215 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN C 230 GLN ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20060 Z= 0.167 Angle : 0.564 8.994 27236 Z= 0.284 Chirality : 0.039 0.162 3104 Planarity : 0.004 0.059 3464 Dihedral : 4.560 31.636 2680 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.88 % Allowed : 19.28 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2448 helix: 0.65 (0.14), residues: 1472 sheet: -0.96 (0.53), residues: 84 loop : -1.56 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 29 HIS 0.007 0.001 HIS C 380 PHE 0.011 0.001 PHE B 292 TYR 0.007 0.001 TYR C 415 ARG 0.010 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 224 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: A 302 ARG cc_start: 0.7946 (mtp85) cc_final: 0.7722 (ttm-80) REVERT: A 474 MET cc_start: 0.7728 (mtp) cc_final: 0.7483 (mtm) REVERT: A 591 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6537 (tm-30) REVERT: A 594 ARG cc_start: 0.7969 (ttp-110) cc_final: 0.7711 (mtp180) REVERT: B 80 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: B 302 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7712 (ttm-80) REVERT: B 474 MET cc_start: 0.7819 (mtp) cc_final: 0.7595 (mtm) REVERT: B 591 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6756 (tm-30) REVERT: B 594 ARG cc_start: 0.7968 (ttp-110) cc_final: 0.7574 (mtp180) REVERT: C 31 GLN cc_start: 0.8449 (mt0) cc_final: 0.8207 (mt0) REVERT: C 229 LEU cc_start: 0.7630 (mm) cc_final: 0.7041 (tm) REVERT: C 474 MET cc_start: 0.7949 (mtp) cc_final: 0.7650 (mtm) REVERT: C 591 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6725 (tm-30) REVERT: C 594 ARG cc_start: 0.7885 (ttp-110) cc_final: 0.7666 (ttp-110) REVERT: D 80 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: D 302 ARG cc_start: 0.7976 (mtp85) cc_final: 0.7745 (ttm-80) REVERT: D 474 MET cc_start: 0.7713 (mtp) cc_final: 0.7476 (mtm) REVERT: D 569 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7885 (tt) outliers start: 61 outliers final: 19 residues processed: 262 average time/residue: 1.3423 time to fit residues: 397.1858 Evaluate side-chains 216 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 10.0000 chunk 212 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20060 Z= 0.272 Angle : 0.614 9.524 27236 Z= 0.308 Chirality : 0.042 0.170 3104 Planarity : 0.004 0.063 3464 Dihedral : 4.719 29.852 2680 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.84 % Allowed : 19.66 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2448 helix: 0.72 (0.14), residues: 1472 sheet: -0.99 (0.53), residues: 84 loop : -1.44 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 29 HIS 0.005 0.001 HIS C 380 PHE 0.013 0.001 PHE A 553 TYR 0.009 0.001 TYR C 555 ARG 0.012 0.000 ARG D 594 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 211 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7529 (pm20) REVERT: A 474 MET cc_start: 0.7804 (mtp) cc_final: 0.7528 (mtm) REVERT: A 591 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: A 594 ARG cc_start: 0.7996 (ttp-110) cc_final: 0.7614 (ttp-110) REVERT: B 80 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: B 440 MET cc_start: 0.6443 (OUTLIER) cc_final: 0.5432 (tpt) REVERT: B 474 MET cc_start: 0.7900 (mtp) cc_final: 0.7579 (mtm) REVERT: C 440 MET cc_start: 0.6282 (OUTLIER) cc_final: 0.5290 (tpt) REVERT: C 474 MET cc_start: 0.7874 (mtp) cc_final: 0.7588 (mtm) REVERT: C 591 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6974 (tm-30) REVERT: D 31 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8230 (mt0) REVERT: D 80 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: D 440 MET cc_start: 0.6421 (OUTLIER) cc_final: 0.5403 (tpt) REVERT: D 474 MET cc_start: 0.7743 (mtp) cc_final: 0.7478 (mtm) REVERT: D 594 ARG cc_start: 0.7994 (ttp-110) cc_final: 0.7444 (mtp180) outliers start: 60 outliers final: 31 residues processed: 251 average time/residue: 1.3194 time to fit residues: 373.4883 Evaluate side-chains 230 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 190 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 131 optimal weight: 0.0970 chunk 235 optimal weight: 0.2980 chunk 147 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20060 Z= 0.151 Angle : 0.554 8.971 27236 Z= 0.278 Chirality : 0.039 0.193 3104 Planarity : 0.004 0.063 3464 Dihedral : 4.416 30.532 2680 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.41 % Allowed : 20.27 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2448 helix: 1.10 (0.14), residues: 1476 sheet: -1.02 (0.52), residues: 92 loop : -1.27 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 29 HIS 0.005 0.001 HIS C 228 PHE 0.012 0.001 PHE B 292 TYR 0.007 0.001 TYR B 328 ARG 0.012 0.000 ARG C 594 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 218 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: A 485 MET cc_start: 0.7431 (mtt) cc_final: 0.7144 (mtm) REVERT: A 591 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6639 (tm-30) REVERT: B 80 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: B 474 MET cc_start: 0.7848 (mtp) cc_final: 0.7585 (mtm) REVERT: B 591 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6572 (tm-30) REVERT: B 594 ARG cc_start: 0.7935 (ttp-110) cc_final: 0.7428 (mtp180) REVERT: C 31 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8239 (mt0) REVERT: C 302 ARG cc_start: 0.7939 (mtp-110) cc_final: 0.7726 (ttm-80) REVERT: C 474 MET cc_start: 0.7770 (mtp) cc_final: 0.7545 (mtm) REVERT: C 591 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6503 (tm-30) REVERT: C 594 ARG cc_start: 0.7956 (ttp-110) cc_final: 0.7594 (mtp180) REVERT: D 80 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: D 485 MET cc_start: 0.7595 (mtp) cc_final: 0.6830 (mpp) outliers start: 51 outliers final: 14 residues processed: 252 average time/residue: 1.2692 time to fit residues: 364.4969 Evaluate side-chains 208 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 573 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 230 GLN ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20060 Z= 0.271 Angle : 0.628 9.680 27236 Z= 0.313 Chirality : 0.042 0.203 3104 Planarity : 0.004 0.068 3464 Dihedral : 4.617 29.182 2680 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.22 % Allowed : 20.51 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2448 helix: 1.09 (0.14), residues: 1464 sheet: -0.79 (0.55), residues: 84 loop : -1.26 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 29 HIS 0.005 0.001 HIS D 157 PHE 0.020 0.001 PHE D 611 TYR 0.011 0.001 TYR A 377 ARG 0.014 0.001 ARG D 594 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 191 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7549 (pm20) REVERT: A 591 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6645 (tm-30) REVERT: A 594 ARG cc_start: 0.7976 (ttp-110) cc_final: 0.7345 (mtp180) REVERT: B 80 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7531 (pm20) REVERT: B 440 MET cc_start: 0.6438 (OUTLIER) cc_final: 0.5439 (tpt) REVERT: B 474 MET cc_start: 0.7897 (mtp) cc_final: 0.7582 (mtm) REVERT: B 591 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6660 (tm-30) REVERT: B 594 ARG cc_start: 0.7972 (ttp-110) cc_final: 0.7354 (mtp180) REVERT: C 302 ARG cc_start: 0.7977 (mtp-110) cc_final: 0.7740 (ttm-80) REVERT: C 474 MET cc_start: 0.7897 (mtp) cc_final: 0.7599 (mtm) REVERT: C 591 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6900 (tm-30) REVERT: C 594 ARG cc_start: 0.7991 (ttp-110) cc_final: 0.7617 (ttp-110) REVERT: D 80 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7635 (pm20) outliers start: 47 outliers final: 25 residues processed: 224 average time/residue: 1.3145 time to fit residues: 332.5954 Evaluate side-chains 219 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 187 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20060 Z= 0.190 Angle : 0.591 9.609 27236 Z= 0.294 Chirality : 0.041 0.228 3104 Planarity : 0.004 0.068 3464 Dihedral : 4.482 29.878 2680 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.75 % Allowed : 21.17 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2448 helix: 1.25 (0.14), residues: 1468 sheet: -0.90 (0.54), residues: 92 loop : -1.14 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 29 HIS 0.004 0.001 HIS C 380 PHE 0.023 0.001 PHE D 611 TYR 0.012 0.001 TYR A 328 ARG 0.013 0.000 ARG D 594 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 189 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7501 (pm20) REVERT: A 302 ARG cc_start: 0.7925 (mtp-110) cc_final: 0.7643 (ttm-80) REVERT: A 591 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6916 (tm-30) REVERT: B 80 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: B 474 MET cc_start: 0.7841 (mtp) cc_final: 0.7575 (mtm) REVERT: B 569 LEU cc_start: 0.8305 (mp) cc_final: 0.7855 (tt) REVERT: B 591 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: C 474 MET cc_start: 0.7814 (mtp) cc_final: 0.7559 (mtm) REVERT: C 591 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: D 30 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7593 (mm-30) REVERT: D 80 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: D 594 ARG cc_start: 0.7954 (ttp-110) cc_final: 0.7426 (mtp180) outliers start: 37 outliers final: 22 residues processed: 218 average time/residue: 1.2780 time to fit residues: 315.9803 Evaluate side-chains 204 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 176 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.3980 chunk 231 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 chunk 243 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 149 optimal weight: 0.0000 chunk 118 optimal weight: 0.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20060 Z= 0.194 Angle : 0.599 11.311 27236 Z= 0.296 Chirality : 0.041 0.216 3104 Planarity : 0.004 0.066 3464 Dihedral : 4.451 29.977 2680 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.94 % Allowed : 21.22 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.17), residues: 2448 helix: 1.32 (0.14), residues: 1468 sheet: -0.88 (0.54), residues: 92 loop : -1.13 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 593 HIS 0.004 0.001 HIS C 380 PHE 0.022 0.001 PHE D 611 TYR 0.013 0.001 TYR B 328 ARG 0.014 0.001 ARG C 594 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 181 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: A 591 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6920 (tm-30) REVERT: B 80 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7453 (pm20) REVERT: B 474 MET cc_start: 0.7843 (mtp) cc_final: 0.7574 (mtm) REVERT: B 591 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6568 (tm-30) REVERT: B 594 ARG cc_start: 0.7956 (ttp-110) cc_final: 0.7457 (mtp180) REVERT: C 474 MET cc_start: 0.7828 (mtp) cc_final: 0.7577 (mtm) REVERT: C 591 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6615 (tm-30) REVERT: D 80 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7658 (pm20) REVERT: D 594 ARG cc_start: 0.7963 (ttp-110) cc_final: 0.7410 (mtp180) outliers start: 41 outliers final: 21 residues processed: 213 average time/residue: 1.3162 time to fit residues: 318.7502 Evaluate side-chains 204 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 177 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 608 MET Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 506 SER Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 554 MET Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.7980 chunk 206 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 193 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 572 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 = 0.3595 r_free = 0.3595 target = 0.114124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.091072 restraints weight = 34866.820| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.61 r_work: 0.3129 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20060 Z= 0.190 Angle : 0.596 11.274 27236 Z= 0.293 Chirality : 0.041 0.208 3104 Planarity : 0.004 0.063 3464 Dihedral : 4.400 28.862 2680 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.70 % Allowed : 21.41 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2448 helix: 1.37 (0.14), residues: 1468 sheet: -0.85 (0.54), residues: 92 loop : -1.11 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 593 HIS 0.004 0.001 HIS C 380 PHE 0.022 0.001 PHE D 611 TYR 0.014 0.001 TYR B 328 ARG 0.013 0.000 ARG C 594 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6370.44 seconds wall clock time: 114 minutes 43.21 seconds (6883.21 seconds total)