Starting phenix.real_space_refine on Sun Dec 17 00:20:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2023/7fd5_31535_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2023/7fd5_31535.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2023/7fd5_31535_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2023/7fd5_31535_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2023/7fd5_31535_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2023/7fd5_31535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2023/7fd5_31535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2023/7fd5_31535_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2023/7fd5_31535_updated.pdb" } resolution = 2.4 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= 0.004 sd= 0.144 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 S 135 5.16 5 B 6 2.79 5 C 23460 2.51 5 N 6514 2.21 5 O 7049 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 42": "NH1" <-> "NH2" Residue "F ARG 50": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 89": "NH1" <-> "NH2" Residue "F ARG 104": "NH1" <-> "NH2" Residue "F ARG 106": "NH1" <-> "NH2" Residue "F ARG 122": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F ARG 202": "NH1" <-> "NH2" Residue "F GLU 240": "OE1" <-> "OE2" Residue "F ARG 272": "NH1" <-> "NH2" Residue "F ARG 385": "NH1" <-> "NH2" Residue "F ARG 432": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "F ARG 536": "NH1" <-> "NH2" Residue "F ARG 584": "NH1" <-> "NH2" Residue "F ARG 693": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 709": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D ARG 536": "NH1" <-> "NH2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 227": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ARG 345": "NH1" <-> "NH2" Residue "C ARG 394": "NH1" <-> "NH2" Residue "C ARG 432": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C ARG 536": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E ARG 106": "NH1" <-> "NH2" Residue "E ARG 122": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ARG 198": "NH1" <-> "NH2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E ARG 432": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "E ARG 536": "NH1" <-> "NH2" Residue "E ARG 584": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 37179 Number of models: 1 Model: "" Number of chains: 13 Chain: "F" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "B" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "D" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "C" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 729} Chain: "E" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "A" Number of atoms: 6118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6118 Classifications: {'peptide': 779} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 730} Chain: "S" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 111 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'4KZ': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'4KZ': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'4KZ': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'4KZ': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.15, per 1000 atoms: 0.52 Number of scatterers: 37179 At special positions: 0 Unit cell: (191.06, 188.6, 199.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 135 16.00 P 15 15.00 O 7049 8.00 N 6514 7.00 C 23460 6.00 B 6 5.00 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.02 Conformation dependent library (CDL) restraints added in 6.0 seconds 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8732 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 169 helices and 34 sheets defined 40.2% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.01 Creating SS restraints... Processing helix chain 'F' and resid 31 through 37 Processing helix chain 'F' and resid 118 through 138 Processing helix chain 'F' and resid 146 through 148 No H-bonds generated for 'chain 'F' and resid 146 through 148' Processing helix chain 'F' and resid 152 through 154 No H-bonds generated for 'chain 'F' and resid 152 through 154' Processing helix chain 'F' and resid 158 through 168 removed outlier: 5.163A pdb=" N HIS F 168 " --> pdb=" O THR F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 181 Processing helix chain 'F' and resid 186 through 238 Processing helix chain 'F' and resid 244 through 253 removed outlier: 3.817A pdb=" N LYS F 251 " --> pdb=" O GLU F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 270 removed outlier: 4.107A pdb=" N LYS F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU F 269 " --> pdb=" O LYS F 265 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU F 270 " --> pdb=" O ALA F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 295 removed outlier: 4.289A pdb=" N GLU F 295 " --> pdb=" O ASP F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 318 Processing helix chain 'F' and resid 323 through 338 removed outlier: 3.740A pdb=" N TYR F 332 " --> pdb=" O ARG F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 371 removed outlier: 3.652A pdb=" N SER F 371 " --> pdb=" O SER F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 410 Processing helix chain 'F' and resid 440 through 443 No H-bonds generated for 'chain 'F' and resid 440 through 443' Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 479 through 484 removed outlier: 4.250A pdb=" N ARG F 484 " --> pdb=" O PRO F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 504 Processing helix chain 'F' and resid 507 through 514 removed outlier: 4.011A pdb=" N SER F 514 " --> pdb=" O GLN F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 541 through 560 Processing helix chain 'F' and resid 574 through 577 No H-bonds generated for 'chain 'F' and resid 574 through 577' Processing helix chain 'F' and resid 631 through 646 Processing helix chain 'F' and resid 680 through 692 removed outlier: 3.591A pdb=" N ALA F 686 " --> pdb=" O THR F 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 727 Processing helix chain 'F' and resid 737 through 745 removed outlier: 4.417A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU F 744 " --> pdb=" O ALA F 741 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU F 745 " --> pdb=" O GLN F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 751 No H-bonds generated for 'chain 'F' and resid 748 through 751' Processing helix chain 'F' and resid 762 through 769 Processing helix chain 'B' and resid 31 through 38 Processing helix chain 'B' and resid 118 through 138 removed outlier: 3.633A pdb=" N ALA B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASN B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.145A pdb=" N HIS B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 180 Processing helix chain 'B' and resid 185 through 236 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'B' and resid 260 through 275 removed outlier: 4.055A pdb=" N ARG B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 308 through 317 removed outlier: 3.560A pdb=" N GLU B 317 " --> pdb=" O GLN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 338 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 435 through 442 removed outlier: 4.033A pdb=" N LEU B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLU B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 476 No H-bonds generated for 'chain 'B' and resid 474 through 476' Processing helix chain 'B' and resid 479 through 484 removed outlier: 3.800A pdb=" N ASP B 483 " --> pdb=" O ARG B 479 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 479 through 484' Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 506 through 514 removed outlier: 3.758A pdb=" N SER B 514 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'B' and resid 541 through 560 removed outlier: 3.576A pdb=" N GLU B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 578 removed outlier: 3.723A pdb=" N ILE B 574 " --> pdb=" O ALA B 571 " (cutoff:3.500A) Proline residue: B 575 - end of helix removed outlier: 4.032A pdb=" N LEU B 578 " --> pdb=" O PRO B 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 571 through 578' Processing helix chain 'B' and resid 631 through 646 removed outlier: 3.658A pdb=" N ALA B 646 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 660 No H-bonds generated for 'chain 'B' and resid 657 through 660' Processing helix chain 'B' and resid 680 through 692 Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 741 through 745 removed outlier: 3.893A pdb=" N GLU B 744 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 745 " --> pdb=" O GLN B 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 741 through 745' Processing helix chain 'B' and resid 748 through 751 No H-bonds generated for 'chain 'B' and resid 748 through 751' Processing helix chain 'B' and resid 762 through 769 Processing helix chain 'D' and resid 28 through 39 removed outlier: 4.038A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 135 removed outlier: 3.563A pdb=" N LYS D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 158 through 167 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 185 through 236 Processing helix chain 'D' and resid 245 through 253 Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 283 through 293 removed outlier: 4.018A pdb=" N THR D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 317 Processing helix chain 'D' and resid 323 through 338 Processing helix chain 'D' and resid 362 through 371 removed outlier: 4.064A pdb=" N ARG D 366 " --> pdb=" O THR D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 424 through 426 No H-bonds generated for 'chain 'D' and resid 424 through 426' Processing helix chain 'D' and resid 439 through 442 No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 479 through 484 removed outlier: 4.320A pdb=" N ARG D 484 " --> pdb=" O PRO D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 506 through 514 removed outlier: 3.881A pdb=" N SER D 514 " --> pdb=" O GLN D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 541 through 560 removed outlier: 3.557A pdb=" N ARG D 545 " --> pdb=" O ARG D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 577 No H-bonds generated for 'chain 'D' and resid 574 through 577' Processing helix chain 'D' and resid 631 through 646 Processing helix chain 'D' and resid 680 through 691 Processing helix chain 'D' and resid 718 through 727 Processing helix chain 'D' and resid 737 through 739 No H-bonds generated for 'chain 'D' and resid 737 through 739' Processing helix chain 'D' and resid 742 through 744 No H-bonds generated for 'chain 'D' and resid 742 through 744' Processing helix chain 'D' and resid 748 through 753 Processing helix chain 'D' and resid 762 through 769 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.926A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 136 Processing helix chain 'C' and resid 158 through 168 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 186 through 238 Processing helix chain 'C' and resid 245 through 255 Processing helix chain 'C' and resid 260 through 275 removed outlier: 3.922A pdb=" N ARG C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 308 through 317 removed outlier: 3.851A pdb=" N GLN C 313 " --> pdb=" O ASN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 338 Processing helix chain 'C' and resid 361 through 371 removed outlier: 3.818A pdb=" N GLY C 365 " --> pdb=" O LYS C 361 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG C 366 " --> pdb=" O THR C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 404 through 412 Processing helix chain 'C' and resid 424 through 426 No H-bonds generated for 'chain 'C' and resid 424 through 426' Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 479 through 484 removed outlier: 3.903A pdb=" N ARG C 484 " --> pdb=" O PRO C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 504 removed outlier: 3.682A pdb=" N ALA C 500 " --> pdb=" O MET C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 514 removed outlier: 3.543A pdb=" N SER C 514 " --> pdb=" O GLN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 533 Processing helix chain 'C' and resid 541 through 559 Processing helix chain 'C' and resid 574 through 578 Processing helix chain 'C' and resid 631 through 646 Processing helix chain 'C' and resid 680 through 692 Processing helix chain 'C' and resid 718 through 726 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 741 through 745 removed outlier: 3.768A pdb=" N GLU C 744 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU C 745 " --> pdb=" O GLN C 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 741 through 745' Processing helix chain 'C' and resid 748 through 753 Processing helix chain 'C' and resid 762 through 769 Processing helix chain 'E' and resid 31 through 38 Processing helix chain 'E' and resid 118 through 138 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'E' and resid 185 through 236 Processing helix chain 'E' and resid 245 through 253 Processing helix chain 'E' and resid 261 through 275 removed outlier: 3.524A pdb=" N ARG E 275 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 291 Processing helix chain 'E' and resid 308 through 318 removed outlier: 3.625A pdb=" N GLU E 317 " --> pdb=" O GLN E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 338 Processing helix chain 'E' and resid 361 through 371 Processing helix chain 'E' and resid 404 through 411 Processing helix chain 'E' and resid 436 through 438 No H-bonds generated for 'chain 'E' and resid 436 through 438' Processing helix chain 'E' and resid 479 through 482 No H-bonds generated for 'chain 'E' and resid 479 through 482' Processing helix chain 'E' and resid 495 through 504 Processing helix chain 'E' and resid 506 through 513 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 541 through 559 removed outlier: 3.789A pdb=" N ARG E 545 " --> pdb=" O ARG E 541 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU E 546 " --> pdb=" O GLY E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 578 Processing helix chain 'E' and resid 631 through 646 removed outlier: 3.600A pdb=" N GLN E 638 " --> pdb=" O LYS E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 680 through 692 Processing helix chain 'E' and resid 718 through 726 Processing helix chain 'E' and resid 737 through 745 removed outlier: 4.433A pdb=" N ALA E 741 " --> pdb=" O ASP E 738 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN E 742 " --> pdb=" O ASN E 739 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU E 744 " --> pdb=" O ALA E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 753 Processing helix chain 'E' and resid 762 through 769 Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 119 through 141 removed outlier: 4.029A pdb=" N ALA A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 150 No H-bonds generated for 'chain 'A' and resid 147 through 150' Processing helix chain 'A' and resid 158 through 168 removed outlier: 3.869A pdb=" N HIS A 168 " --> pdb=" O THR A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 186 through 238 Processing helix chain 'A' and resid 244 through 255 removed outlier: 3.657A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 275 removed outlier: 4.137A pdb=" N ARG A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.608A pdb=" N GLN A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 removed outlier: 3.914A pdb=" N ARG A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 404 through 411 Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 506 through 512 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 541 through 560 removed outlier: 3.961A pdb=" N ARG A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 546 " --> pdb=" O GLY A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 Processing helix chain 'A' and resid 631 through 646 Processing helix chain 'A' and resid 680 through 692 Processing helix chain 'A' and resid 718 through 727 Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 741 through 745 removed outlier: 3.925A pdb=" N GLU A 744 " --> pdb=" O ALA A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 769 Processing sheet with id= A, first strand: chain 'F' and resid 7 through 10 removed outlier: 8.589A pdb=" N ILE F 8 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE F 45 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU F 10 " --> pdb=" O PHE F 45 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL F 47 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE F 44 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU F 87 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N MET F 85 " --> pdb=" O LYS F 72 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 485 through 490 removed outlier: 6.246A pdb=" N ILE F 350 " --> pdb=" O GLU F 486 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE F 488 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL F 352 " --> pdb=" O ILE F 488 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE F 490 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL F 354 " --> pdb=" O ILE F 490 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU F 351 " --> pdb=" O PHE F 467 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY F 355 " --> pdb=" O ALA F 471 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE F 419 " --> pdb=" O PHE F 466 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE F 468 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.650A pdb=" N ARG F 567 " --> pdb=" O GLU F 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'F' and resid 596 through 603 removed outlier: 3.575A pdb=" N GLY F 606 " --> pdb=" O THR F 603 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LYS F 622 " --> pdb=" O LEU F 663 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL F 665 " --> pdb=" O LYS F 622 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER F 624 " --> pdb=" O VAL F 665 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 700 through 702 removed outlier: 6.451A pdb=" N LYS F 732 " --> pdb=" O ALA F 701 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 7 through 9 removed outlier: 8.109A pdb=" N ILE B 8 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE B 45 " --> pdb=" O ILE B 8 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 21 through 25 removed outlier: 3.769A pdb=" N THR B 21 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 86 " --> pdb=" O THR B 21 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 486 through 490 removed outlier: 6.766A pdb=" N PHE B 467 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU B 353 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR B 469 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N GLY B 355 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 471 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.170A pdb=" N ARG B 567 " --> pdb=" O GLU B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 596 through 603 removed outlier: 5.006A pdb=" N THR B 611 " --> pdb=" O PRO B 668 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 667 " --> pdb=" O THR B 626 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 700 through 702 removed outlier: 6.458A pdb=" N LYS B 732 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU B 755 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU B 735 " --> pdb=" O GLU B 755 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LYS B 757 " --> pdb=" O LEU B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 43 through 45 Processing sheet with id= M, first strand: chain 'D' and resid 73 through 76 removed outlier: 3.542A pdb=" N GLN D 73 " --> pdb=" O MET D 85 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET D 75 " --> pdb=" O GLN D 83 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 351 through 354 removed outlier: 6.259A pdb=" N GLU D 486 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL D 354 " --> pdb=" O GLU D 486 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE D 488 " --> pdb=" O VAL D 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 376 through 380 removed outlier: 6.186A pdb=" N VAL D 418 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE D 379 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU D 420 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE D 466 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU D 421 " --> pdb=" O PHE D 466 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE D 468 " --> pdb=" O LEU D 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 520 through 522 removed outlier: 6.347A pdb=" N ARG D 567 " --> pdb=" O GLU D 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 596 through 603 removed outlier: 5.950A pdb=" N LYS D 622 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL D 665 " --> pdb=" O LYS D 622 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N VAL D 667 " --> pdb=" O SER D 624 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR D 626 " --> pdb=" O VAL D 667 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 732 through 736 removed outlier: 6.371A pdb=" N GLU D 755 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU D 735 " --> pdb=" O GLU D 755 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LYS D 757 " --> pdb=" O LEU D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 21 through 23 removed outlier: 3.959A pdb=" N THR C 21 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 486 through 490 removed outlier: 6.742A pdb=" N PHE C 467 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU C 353 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR C 469 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N GLY C 355 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA C 471 " --> pdb=" O GLY C 355 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 596 through 602 removed outlier: 5.852A pdb=" N LYS C 622 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL C 665 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 733 through 736 Processing sheet with id= W, first strand: chain 'E' and resid 65 through 67 Processing sheet with id= X, first strand: chain 'E' and resid 73 through 76 removed outlier: 3.921A pdb=" N GLN E 73 " --> pdb=" O MET E 85 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN E 83 " --> pdb=" O MET E 75 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 468 through 471 removed outlier: 6.553A pdb=" N LEU E 351 " --> pdb=" O THR E 469 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ALA E 471 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU E 353 " --> pdb=" O ALA E 471 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLU E 486 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL E 354 " --> pdb=" O GLU E 486 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE E 488 " --> pdb=" O VAL E 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'E' and resid 377 through 380 Processing sheet with id= AA, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.329A pdb=" N ARG E 567 " --> pdb=" O GLU E 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'E' and resid 596 through 602 removed outlier: 5.932A pdb=" N LYS E 622 " --> pdb=" O LEU E 663 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL E 665 " --> pdb=" O LYS E 622 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER E 624 " --> pdb=" O VAL E 665 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 733 through 736 Processing sheet with id= AD, first strand: chain 'A' and resid 43 through 46 removed outlier: 3.634A pdb=" N LEU A 46 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 67 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 486 through 490 removed outlier: 3.775A pdb=" N LEU A 351 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 355 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 470 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.385A pdb=" N ARG A 567 " --> pdb=" O GLU A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'A' and resid 596 through 603 removed outlier: 3.544A pdb=" N GLY A 606 " --> pdb=" O THR A 603 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LYS A 622 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL A 665 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A' and resid 732 through 736 removed outlier: 6.152A pdb=" N GLU A 755 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU A 735 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS A 757 " --> pdb=" O LEU A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH 1324 hydrogen bonds defined for protein. 3930 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: 12.80 Time building geometry restraints manager: 16.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.32: 7826 1.32 - 1.48: 14193 1.48 - 1.64: 15582 1.64 - 1.80: 211 1.80 - 1.95: 56 Bond restraints: 37868 Sorted by residual: bond pdb=" C18 4KZ A 802 " pdb=" N20 4KZ A 802 " ideal model delta sigma weight residual 1.457 1.292 0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" C18 4KZ F 802 " pdb=" N20 4KZ F 802 " ideal model delta sigma weight residual 1.457 1.302 0.155 2.00e-02 2.50e+03 5.99e+01 bond pdb=" C18 4KZ D 802 " pdb=" N20 4KZ D 802 " ideal model delta sigma weight residual 1.457 1.308 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" C7 4KZ D 802 " pdb=" N9 4KZ D 802 " ideal model delta sigma weight residual 1.455 1.306 0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" C18 4KZ C 802 " pdb=" N20 4KZ C 802 " ideal model delta sigma weight residual 1.457 1.310 0.147 2.00e-02 2.50e+03 5.41e+01 ... (remaining 37863 not shown) Histogram of bond angle deviations from ideal: 94.36 - 102.71: 281 102.71 - 111.06: 14495 111.06 - 119.41: 18544 119.41 - 127.76: 17673 127.76 - 136.11: 373 Bond angle restraints: 51366 Sorted by residual: angle pdb=" O ALA A 679 " pdb=" C ALA A 679 " pdb=" N GLY A 680 " ideal model delta sigma weight residual 122.06 106.66 15.40 1.34e+00 5.57e-01 1.32e+02 angle pdb=" O ALA B 679 " pdb=" C ALA B 679 " pdb=" N GLY B 680 " ideal model delta sigma weight residual 121.97 106.53 15.44 1.35e+00 5.49e-01 1.31e+02 angle pdb=" N LYS F 404 " pdb=" CA LYS F 404 " pdb=" C LYS F 404 " ideal model delta sigma weight residual 111.28 100.15 11.13 1.09e+00 8.42e-01 1.04e+02 angle pdb=" CA ALA B 679 " pdb=" C ALA B 679 " pdb=" N GLY B 680 " ideal model delta sigma weight residual 116.73 131.58 -14.85 1.64e+00 3.72e-01 8.20e+01 angle pdb=" N HIS F 407 " pdb=" CA HIS F 407 " pdb=" C HIS F 407 " ideal model delta sigma weight residual 111.07 103.04 8.03 1.07e+00 8.73e-01 5.63e+01 ... (remaining 51361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 23075 35.17 - 70.33: 202 70.33 - 105.50: 34 105.50 - 140.67: 4 140.67 - 175.83: 3 Dihedral angle restraints: 23318 sinusoidal: 9759 harmonic: 13559 Sorted by residual: dihedral pdb=" CA ASP A 51 " pdb=" C ASP A 51 " pdb=" N PRO A 52 " pdb=" CA PRO A 52 " ideal model delta harmonic sigma weight residual 180.00 -107.06 -72.94 0 5.00e+00 4.00e-02 2.13e+02 dihedral pdb=" CA ASP D 51 " pdb=" C ASP D 51 " pdb=" N PRO D 52 " pdb=" CA PRO D 52 " ideal model delta harmonic sigma weight residual -180.00 -108.60 -71.40 0 5.00e+00 4.00e-02 2.04e+02 dihedral pdb=" CA ASP C 51 " pdb=" C ASP C 51 " pdb=" N PRO C 52 " pdb=" CA PRO C 52 " ideal model delta harmonic sigma weight residual 180.00 -111.37 -68.63 0 5.00e+00 4.00e-02 1.88e+02 ... (remaining 23315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4954 0.099 - 0.198: 830 0.198 - 0.297: 49 0.297 - 0.396: 7 0.396 - 0.495: 2 Chirality restraints: 5842 Sorted by residual: chirality pdb=" CG LEU A 547 " pdb=" CB LEU A 547 " pdb=" CD1 LEU A 547 " pdb=" CD2 LEU A 547 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CB VAL B 540 " pdb=" CA VAL B 540 " pdb=" CG1 VAL B 540 " pdb=" CG2 VAL B 540 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA HIS F 407 " pdb=" N HIS F 407 " pdb=" C HIS F 407 " pdb=" CB HIS F 407 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 5839 not shown) Planarity restraints: 6658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 4KZ C 802 " -0.206 2.00e-02 2.50e+03 2.22e-01 6.17e+02 pdb=" C18 4KZ C 802 " 0.138 2.00e-02 2.50e+03 pdb=" C21 4KZ C 802 " -0.263 2.00e-02 2.50e+03 pdb=" N20 4KZ C 802 " 0.341 2.00e-02 2.50e+03 pdb=" O19 4KZ C 802 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 4KZ A 802 " 0.200 2.00e-02 2.50e+03 2.15e-01 5.78e+02 pdb=" C18 4KZ A 802 " -0.126 2.00e-02 2.50e+03 pdb=" C21 4KZ A 802 " 0.257 2.00e-02 2.50e+03 pdb=" N20 4KZ A 802 " -0.330 2.00e-02 2.50e+03 pdb=" O19 4KZ A 802 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 4KZ F 802 " -0.155 2.00e-02 2.50e+03 1.66e-01 3.43e+02 pdb=" C18 4KZ F 802 " 0.102 2.00e-02 2.50e+03 pdb=" C21 4KZ F 802 " -0.196 2.00e-02 2.50e+03 pdb=" N20 4KZ F 802 " 0.254 2.00e-02 2.50e+03 pdb=" O19 4KZ F 802 " -0.004 2.00e-02 2.50e+03 ... (remaining 6655 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4691 2.74 - 3.28: 33894 3.28 - 3.82: 58683 3.82 - 4.36: 70141 4.36 - 4.90: 120015 Nonbonded interactions: 287424 Sorted by model distance: nonbonded pdb=" O VAL C 359 " pdb=" O2B AGS C 801 " model vdw 2.203 2.440 nonbonded pdb=" O VAL A 359 " pdb=" O2B AGS A 801 " model vdw 2.210 2.440 nonbonded pdb=" O ASN A 138 " pdb=" OG SER A 141 " model vdw 2.265 2.440 nonbonded pdb=" OG1 THR E 95 " pdb=" O GLY E 107 " model vdw 2.270 2.440 nonbonded pdb=" O ASP E 291 " pdb=" OG1 THR E 294 " model vdw 2.271 2.440 ... (remaining 287419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 780 or resid 802)) selection = (chain 'B' and (resid 2 through 780 or resid 802)) selection = (chain 'C' and (resid 2 through 780 or resid 802)) selection = (chain 'D' and (resid 2 through 780 or resid 802)) selection = (chain 'E' and (resid 2 through 780 or resid 802)) selection = (chain 'F' and (resid 2 through 780 or resid 802)) } 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=0.00 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: 1.730 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: 0.030 Extract box with map and model: 9.920 Check model and map are aligned: 0.580 Set scattering table: 0.360 Process input model: 92.900 Find NCS groups from input model: 2.750 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 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 : 0.015 0.165 37868 Z= 0.953 Angle : 1.232 15.439 51366 Z= 0.671 Chirality : 0.072 0.495 5842 Planarity : 0.010 0.222 6658 Dihedral : 11.587 175.834 14586 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 0.51 % Allowed : 3.31 % Favored : 96.18 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 2.54 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.10), residues: 4662 helix: -2.39 (0.09), residues: 2001 sheet: -1.27 (0.20), residues: 632 loop : -2.95 (0.11), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP A 171 HIS 0.017 0.003 HIS A 454 PHE 0.039 0.004 PHE A 110 TYR 0.041 0.004 TYR B 505 ARG 0.025 0.002 ARG B 552 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 321 time to evaluate : 3.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 5 residues processed: 339 average time/residue: 2.1548 time to fit residues: 840.0035 Evaluate side-chains 202 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 197 time to evaluate : 4.089 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 5.7605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 391 optimal weight: 7.9990 chunk 351 optimal weight: 0.0970 chunk 195 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 237 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 chunk 363 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 221 optimal weight: 7.9990 chunk 270 optimal weight: 0.9980 chunk 421 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 GLN F 319 HIS F 377 HIS ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 ASN F 739 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN B 319 HIS B 664 HIS B 739 ASN D 18 HIS D 83 GLN D 475 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 GLN D 664 HIS D 739 ASN D 742 GLN C 234 GLN C 309 ASN C 666 HIS E 12 ASN ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN E 510 GLN E 598 GLN E 666 HIS E 739 ASN ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 177 GLN A 216 GLN A 319 HIS A 346 ASN ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 664 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 37868 Z= 0.162 Angle : 0.620 8.775 51366 Z= 0.313 Chirality : 0.044 0.208 5842 Planarity : 0.005 0.078 6658 Dihedral : 9.857 179.064 5310 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.35 % Favored : 95.58 % Rotamer: Outliers : 1.70 % Allowed : 6.95 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 2.17 % Twisted General : 0.09 % 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: -2.08 (0.11), residues: 4662 helix: -0.60 (0.11), residues: 2019 sheet: -0.58 (0.21), residues: 619 loop : -2.44 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 298 HIS 0.005 0.001 HIS F 407 PHE 0.014 0.001 PHE E 466 TYR 0.034 0.001 TYR B 224 ARG 0.009 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 236 time to evaluate : 4.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 11 residues processed: 284 average time/residue: 1.7109 time to fit residues: 582.0536 Evaluate side-chains 209 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 198 time to evaluate : 4.133 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 1 average time/residue: 0.3833 time to fit residues: 6.5081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 234 optimal weight: 50.0000 chunk 130 optimal weight: 1.9990 chunk 350 optimal weight: 30.0000 chunk 286 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 422 optimal weight: 7.9990 chunk 456 optimal weight: 0.6980 chunk 375 optimal weight: 0.6980 chunk 418 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 338 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN F 666 HIS B 277 GLN D 475 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN E 168 HIS E 177 GLN E 220 ASN ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37868 Z= 0.169 Angle : 0.573 11.552 51366 Z= 0.285 Chirality : 0.043 0.201 5842 Planarity : 0.005 0.070 6658 Dihedral : 9.200 178.718 5310 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 1.45 % Allowed : 8.40 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 2.17 % Twisted General : 0.07 % 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: -1.19 (0.12), residues: 4662 helix: 0.34 (0.12), residues: 2011 sheet: -0.46 (0.21), residues: 622 loop : -2.09 (0.12), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 298 HIS 0.009 0.001 HIS A 18 PHE 0.011 0.001 PHE A 110 TYR 0.029 0.001 TYR B 224 ARG 0.007 0.000 ARG D 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 208 time to evaluate : 4.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 23 residues processed: 246 average time/residue: 1.6755 time to fit residues: 496.0434 Evaluate side-chains 211 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 188 time to evaluate : 3.127 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 6 average time/residue: 0.9043 time to fit residues: 12.0162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 417 optimal weight: 3.9990 chunk 317 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 283 optimal weight: 7.9990 chunk 423 optimal weight: 6.9990 chunk 448 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 401 optimal weight: 40.0000 chunk 120 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37868 Z= 0.269 Angle : 0.596 8.697 51366 Z= 0.295 Chirality : 0.045 0.194 5842 Planarity : 0.005 0.069 6658 Dihedral : 9.067 178.684 5310 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 1.91 % Allowed : 8.73 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 1.45 % Twisted General : 0.05 % 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: -0.81 (0.12), residues: 4662 helix: 0.73 (0.12), residues: 2017 sheet: -0.33 (0.21), residues: 652 loop : -1.98 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 298 HIS 0.007 0.001 HIS A 454 PHE 0.019 0.001 PHE D 132 TYR 0.026 0.002 TYR B 224 ARG 0.005 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9324 Ramachandran restraints generated. 4662 Oldfield, 0 Emsley, 4662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 195 time to evaluate : 4.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 34 residues processed: 249 average time/residue: 1.5818 time to fit residues: 476.4056 Evaluate side-chains 221 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 3.910 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 31 residues processed: 5 average time/residue: 0.9504 time to fit residues: 11.8577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 373 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 333 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 382 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 229 optimal weight: 5.9990 chunk 402 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 138 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2385 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: