Starting phenix.real_space_refine (version: dev) on Tue Dec 20 01:35:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2022/7fd5_31535_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2022/7fd5_31535.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2022/7fd5_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_2022/7fd5_31535_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2022/7fd5_31535_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2022/7fd5_31535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2022/7fd5_31535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2022/7fd5_31535_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd5_31535/12_2022/7fd5_31535_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-dev-4807/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: 20.36, per 1000 atoms: 0.55 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: 15.66 Conformation dependent library (CDL) restraints added in 5.9 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: 5.04 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: 13.25 Time building geometry restraints manager: 16.60 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 1.452 1.292 0.160 2.00e-02 2.50e+03 6.36e+01 bond pdb=" C18 4KZ F 802 " pdb=" N20 4KZ F 802 " ideal model delta sigma weight residual 1.452 1.302 0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C7 4KZ D 802 " pdb=" N9 4KZ D 802 " ideal model delta sigma weight residual 1.451 1.306 0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" C18 4KZ D 802 " pdb=" N20 4KZ D 802 " ideal model delta sigma weight residual 1.452 1.308 0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" C18 4KZ C 802 " pdb=" N20 4KZ C 802 " ideal model delta sigma weight residual 1.452 1.310 0.142 2.00e-02 2.50e+03 5.05e+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: 23026 35.17 - 70.33: 186 70.33 - 105.50: 30 105.50 - 140.67: 4 140.67 - 175.83: 3 Dihedral angle restraints: 23249 sinusoidal: 9690 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 23246 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 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. 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: 2.570 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: 0.040 Extract box with map and model: 11.850 Check model and map are aligned: 0.600 Convert atoms to be neutral: 0.370 Process input model: 93.260 Find NCS groups from input model: 3.440 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 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 0.160 37868 Z= 0.952 Angle : 1.231 15.439 51366 Z= 0.670 Chirality : 0.072 0.495 5842 Planarity : 0.010 0.222 6658 Dihedral : 11.377 175.834 14517 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer Outliers : 0.51 % 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 *********************** 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 : 4.605 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: 1.9828 time to fit residues: 780.0749 Evaluate side-chains 202 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 197 time to evaluate : 4.548 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 6.1270 ------------------------------------------------------------------------------- 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 393 HIS ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 ASN F 666 HIS 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: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 37868 Z= 0.164 Angle : 0.628 8.694 51366 Z= 0.315 Chirality : 0.044 0.207 5842 Planarity : 0.005 0.079 6658 Dihedral : 9.231 179.021 5241 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.67 % Rotamer Outliers : 1.70 % 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: -2.11 (0.11), residues: 4662 helix: -0.65 (0.11), residues: 2021 sheet: -0.58 (0.21), residues: 611 loop : -2.43 (0.12), residues: 2030 *********************** 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 304 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 237 time to evaluate : 4.474 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: 67 outliers final: 11 residues processed: 285 average time/residue: 1.6207 time to fit residues: 557.4106 Evaluate side-chains 208 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 197 time to evaluate : 4.388 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 1 average time/residue: 0.3662 time to fit residues: 6.6357 ------------------------------------------------------------------------------- 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: 0.0570 chunk 130 optimal weight: 1.9990 chunk 350 optimal weight: 30.0000 chunk 286 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 422 optimal weight: 7.9990 chunk 456 optimal weight: 5.9990 chunk 375 optimal weight: 0.7980 chunk 418 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 338 optimal weight: 30.0000 overall best weight: 1.1702 ------------------------------------------------------------------------------- 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 B 277 GLN D 220 ASN D 475 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 ASN E 177 GLN ** E 220 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 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 37868 Z= 0.162 Angle : 0.577 11.528 51366 Z= 0.285 Chirality : 0.043 0.222 5842 Planarity : 0.005 0.076 6658 Dihedral : 8.646 179.013 5241 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.68 % Favored : 95.26 % Rotamer Outliers : 1.37 % 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: -1.27 (0.12), residues: 4662 helix: 0.25 (0.12), residues: 2012 sheet: -0.52 (0.21), residues: 627 loop : -2.10 (0.12), residues: 2023 *********************** 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: 54 poor density : 211 time to evaluate : 4.008 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: 54 outliers final: 22 residues processed: 249 average time/residue: 1.6217 time to fit residues: 489.5074 Evaluate side-chains 212 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 190 time to evaluate : 4.593 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 5 average time/residue: 1.1319 time to fit residues: 13.8269 ------------------------------------------------------------------------------- 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: 1.9990 chunk 317 optimal weight: 5.9990 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: 2.9990 chunk 448 optimal weight: 4.9990 chunk 221 optimal weight: 0.0870 chunk 401 optimal weight: 50.0000 chunk 120 optimal weight: 0.0030 overall best weight: 1.6174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 138 ASN B 277 GLN D 475 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 HIS E 220 ASN A 73 GLN A 83 GLN A 139 HIS ** 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: 0.7171 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 37868 Z= 0.180 Angle : 0.559 9.012 51366 Z= 0.275 Chirality : 0.043 0.196 5842 Planarity : 0.004 0.069 6658 Dihedral : 8.331 178.079 5241 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.40 % Favored : 95.54 % Rotamer Outliers : 1.42 % 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: -0.76 (0.12), residues: 4662 helix: 0.77 (0.12), residues: 2014 sheet: -0.23 (0.21), residues: 617 loop : -1.95 (0.13), residues: 2031 *********************** 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 255 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 199 time to evaluate : 4.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 27 residues processed: 236 average time/residue: 1.6092 time to fit residues: 461.5479 Evaluate side-chains 216 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 189 time to evaluate : 4.419 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 23 residues processed: 5 average time/residue: 0.7985 time to fit residues: 11.2966 ------------------------------------------------------------------------------- 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: 4.9990 chunk 254 optimal weight: 8.9990 chunk 6 optimal weight: 30.0000 chunk 333 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 382 optimal weight: 1.9990 chunk 310 optimal weight: 0.7980 chunk 0 optimal weight: 50.0000 chunk 229 optimal weight: 0.7980 chunk 402 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 472 ASN D 83 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7211 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 37868 Z= 0.279 Angle : 0.603 8.564 51366 Z= 0.297 Chirality : 0.045 0.199 5842 Planarity : 0.005 0.067 6658 Dihedral : 8.217 178.508 5241 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.91 % Favored : 95.02 % Rotamer Outliers : 2.14 % 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: -0.54 (0.12), residues: 4662 helix: 0.98 (0.12), residues: 2020 sheet: -0.15 (0.21), residues: 642 loop : -1.88 (0.13), residues: 2000 *********************** REFINEMENT MACRO_CYCLE 5 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 286 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 202 time to evaluate : 4.339 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: 84 outliers final: 41 residues processed: 262 average time/residue: 1.4605 time to fit residues: 470.7107 Evaluate side-chains 227 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 186 time to evaluate : 4.341 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 35 residues processed: 7 average time/residue: 1.2115 time to fit residues: 16.8879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 150 optimal weight: 0.9980 chunk 403 optimal weight: 30.0000 chunk 88 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 448 optimal weight: 1.9990 chunk 372 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 148 optimal weight: 0.8980 chunk 235 optimal weight: 30.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 GLN ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7185 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 37868 Z= 0.171 Angle : 0.553 11.565 51366 Z= 0.271 Chirality : 0.043 0.205 5842 Planarity : 0.004 0.066 6658 Dihedral : 8.049 177.872 5241 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.38 % Favored : 95.58 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 1.45 % 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: -0.23 (0.12), residues: 4662 helix: 1.30 (0.12), residues: 2007 sheet: 0.07 (0.21), residues: 611 loop : -1.77 (0.13), residues: 2044 *********************** REFINEMENT MACRO_CYCLE 6 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: 76 poor density : 194 time to evaluate : 4.576 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: 76 outliers final: 46 residues processed: 248 average time/residue: 1.5231 time to fit residues: 468.7370 Evaluate side-chains 231 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 185 time to evaluate : 4.830 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 42 residues processed: 7 average time/residue: 0.9240 time to fit residues: 15.7189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 327 optimal weight: 30.0000 chunk 254 optimal weight: 6.9990 chunk 377 optimal weight: 0.0070 chunk 250 optimal weight: 6.9990 chunk 447 optimal weight: 2.9990 chunk 279 optimal weight: 7.9990 chunk 272 optimal weight: 0.0770 chunk 206 optimal weight: 9.9990 overall best weight: 3.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN D 83 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 GLN A 83 GLN ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 37868 Z= 0.274 Angle : 0.598 11.574 51366 Z= 0.292 Chirality : 0.044 0.232 5842 Planarity : 0.005 0.065 6658 Dihedral : 8.019 178.108 5241 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.96 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 1.45 % 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 (0.12), residues: 4662 helix: 1.26 (0.12), residues: 2030 sheet: 0.16 (0.21), residues: 636 loop : -1.77 (0.13), residues: 1996 *********************** REFINEMENT MACRO_CYCLE 7 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 267 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 193 time to evaluate : 4.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 45 residues processed: 244 average time/residue: 1.5765 time to fit residues: 474.1425 Evaluate side-chains 231 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 186 time to evaluate : 4.587 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 40 residues processed: 7 average time/residue: 1.0751 time to fit residues: 16.2422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 276 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 267 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 284 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 221 optimal weight: 0.1980 chunk 41 optimal weight: 9.9990 chunk 351 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN ** 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: 0.7193 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 37868 Z= 0.183 Angle : 0.561 11.910 51366 Z= 0.272 Chirality : 0.043 0.183 5842 Planarity : 0.004 0.062 6658 Dihedral : 7.904 177.485 5241 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.62 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 1.45 % 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: 0.01 (0.12), residues: 4662 helix: 1.48 (0.12), residues: 2017 sheet: 0.27 (0.21), residues: 618 loop : -1.67 (0.13), residues: 2027 *********************** REFINEMENT MACRO_CYCLE 8 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 251 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 190 time to evaluate : 4.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 47 residues processed: 243 average time/residue: 1.5055 time to fit residues: 455.3684 Evaluate side-chains 233 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 186 time to evaluate : 3.990 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 44 residues processed: 5 average time/residue: 1.0279 time to fit residues: 12.6322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 406 optimal weight: 5.9990 chunk 428 optimal weight: 10.0000 chunk 390 optimal weight: 0.4980 chunk 416 optimal weight: 2.9990 chunk 250 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 327 optimal weight: 30.0000 chunk 127 optimal weight: 3.9990 chunk 376 optimal weight: 8.9990 chunk 394 optimal weight: 0.4980 chunk 415 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 649 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 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: 0.7200 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 37868 Z= 0.213 Angle : 0.571 11.718 51366 Z= 0.276 Chirality : 0.043 0.184 5842 Planarity : 0.004 0.061 6658 Dihedral : 7.841 176.843 5241 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.37 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 1.45 % 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: 0.06 (0.12), residues: 4662 helix: 1.51 (0.12), residues: 2024 sheet: 0.34 (0.21), residues: 626 loop : -1.67 (0.13), residues: 2012 *********************** REFINEMENT MACRO_CYCLE 9 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 244 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 187 time to evaluate : 4.850 Fit side-chains 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: 47 residues processed: 234 average time/residue: 1.5448 time to fit residues: 444.0596 Evaluate side-chains 232 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 185 time to evaluate : 4.685 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 45 residues processed: 4 average time/residue: 1.0564 time to fit residues: 11.9828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 273 optimal weight: 9.9990 chunk 440 optimal weight: 5.9990 chunk 268 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 306 optimal weight: 0.9990 chunk 462 optimal weight: 40.0000 chunk 425 optimal weight: 0.9980 chunk 368 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 284 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 37868 Z= 0.240 Angle : 0.590 13.712 51366 Z= 0.285 Chirality : 0.044 0.251 5842 Planarity : 0.004 0.061 6658 Dihedral : 7.820 176.357 5241 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.57 % Favored : 95.39 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 1.45 % 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: 0.08 (0.12), residues: 4662 helix: 1.53 (0.12), residues: 2024 sheet: 0.40 (0.21), residues: 622 loop : -1.67 (0.13), residues: 2016 ********************** REFINEMENT MACRO_CYCLE 10 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 242 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 187 time to evaluate : 4.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 49 residues processed: 234 average time/residue: 1.5487 time to fit residues: 449.3497 Evaluate side-chains 233 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 184 time to evaluate : 4.574 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 46 residues processed: 5 average time/residue: 1.3559 time to fit residues: 14.9715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 292 optimal weight: 2.9990 chunk 392 optimal weight: 30.0000 chunk 112 optimal weight: 3.9990 chunk 339 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 368 optimal weight: 8.9990 chunk 154 optimal weight: 30.0000 chunk 378 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 211 GLN D 220 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN ** A 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.179358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.105518 restraints weight = 65487.448| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.90 r_work: 0.2961 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 37868 Z= 0.262 Angle : 0.593 13.611 51366 Z= 0.287 Chirality : 0.044 0.214 5842 Planarity : 0.004 0.060 6658 Dihedral : 7.817 175.911 5241 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.63 % Favored : 95.32 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.43 % Twisted Proline : 1.45 % 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: 0.10 (0.13), residues: 4662 helix: 1.52 (0.12), residues: 2032 sheet: 0.50 (0.21), residues: 621 loop : -1.67 (0.13), residues: 2009 =============================================================================== Job complete usr+sys time: 12201.30 seconds wall clock time: 216 minutes 25.67 seconds (12985.67 seconds total)