Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 16:10:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fie_31590/05_2023/7fie_31590_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fie_31590/05_2023/7fie_31590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fie_31590/05_2023/7fie_31590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fie_31590/05_2023/7fie_31590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fie_31590/05_2023/7fie_31590_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fie_31590/05_2023/7fie_31590_updated.pdb" } resolution = 2.36 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= 0.000 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 136 5.16 5 C 23328 2.51 5 N 6490 2.21 5 O 7027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 91": "NH1" <-> "NH2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "E ARG 208": "NH1" <-> "NH2" Residue "A GLU 236": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 36997 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" 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: "C" 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: "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: "E" 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: "F" 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: "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: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.63, per 1000 atoms: 0.50 Number of scatterers: 36997 At special positions: 0 Unit cell: (182.04, 200.08, 218.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 P 16 15.00 O 7027 8.00 N 6490 7.00 C 23328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.63 Conformation dependent library (CDL) restraints added in 5.6 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: 170 helices and 35 sheets defined 40.1% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 809.38 Creating SS restraints... Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 118 through 138 removed outlier: 3.910A pdb=" N LYS B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASN B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.341A pdb=" N HIS B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 185 through 237 removed outlier: 3.614A pdb=" N LEU B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.720A pdb=" N GLU B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 281 through 295 removed outlier: 4.097A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 removed outlier: 3.834A pdb=" N ASP B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 338 Processing helix chain 'B' and resid 363 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 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 479 through 482 No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 506 through 513 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 541 through 560 removed outlier: 3.538A pdb=" N LEU B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 578 removed outlier: 3.700A pdb=" N ILE B 574 " --> pdb=" O ALA B 571 " (cutoff:3.500A) Proline residue: B 575 - end of helix removed outlier: 3.981A 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: 3.621A pdb=" N ALA B 646 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 692 Processing helix chain 'B' and resid 718 through 728 Processing helix chain 'B' and resid 737 through 745 removed outlier: 4.548A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU B 744 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 745 " --> pdb=" O GLN B 742 " (cutoff:3.500A) 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 'C' and resid 31 through 38 Processing helix chain 'C' and resid 118 through 135 removed outlier: 3.591A pdb=" N TYR C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 168 removed outlier: 3.534A pdb=" N ALA C 166 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR C 167 " --> pdb=" O ASP C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 187 through 235 Processing helix chain 'C' and resid 244 through 255 removed outlier: 3.893A pdb=" N GLU C 254 " --> pdb=" O ARG C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 removed outlier: 3.995A pdb=" N LYS C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 295 Processing helix chain 'C' and resid 308 through 317 removed outlier: 3.758A pdb=" N GLN C 313 " --> pdb=" O ASN C 309 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU C 317 " --> pdb=" O GLN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 338 Processing helix chain 'C' and resid 363 through 371 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 411 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 479 through 484 removed outlier: 4.007A pdb=" N ARG C 484 " --> pdb=" O PRO C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 506 through 514 removed outlier: 3.732A 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 560 removed outlier: 3.575A pdb=" N LEU C 559 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 560 " --> pdb=" O LYS C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 577 No H-bonds generated for 'chain 'C' and resid 574 through 577' Processing helix chain 'C' and resid 631 through 646 removed outlier: 3.703A pdb=" N ALA C 646 " --> pdb=" O THR C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 651 No H-bonds generated for 'chain 'C' and resid 648 through 651' Processing helix chain 'C' and resid 680 through 692 Processing helix chain 'C' and resid 718 through 727 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: 4.133A pdb=" N GLU C 744 " --> pdb=" O ALA C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 753 removed outlier: 3.603A pdb=" N GLU C 752 " --> pdb=" O LYS C 748 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY C 753 " --> pdb=" O GLU C 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 748 through 753' Processing helix chain 'C' and resid 762 through 769 Processing helix chain 'D' and resid 28 through 38 removed outlier: 3.924A pdb=" N MET D 38 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 118 through 137 Processing helix chain 'D' and resid 158 through 168 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 186 through 236 removed outlier: 4.500A pdb=" N GLU D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 255 removed outlier: 3.529A pdb=" N GLU D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 275 Processing helix chain 'D' and resid 281 through 293 removed outlier: 3.770A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP D 292 " --> pdb=" O THR D 288 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 317 removed outlier: 3.697A pdb=" N ASP D 316 " --> pdb=" O ARG D 312 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU D 317 " --> pdb=" O GLN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 338 Processing helix chain 'D' and resid 361 through 371 removed outlier: 3.870A pdb=" N GLY D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG D 366 " --> pdb=" O THR D 362 " (cutoff:3.500A) 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 435 through 442 removed outlier: 3.816A pdb=" N LEU D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU D 441 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 450 No H-bonds generated for 'chain 'D' and resid 448 through 450' Processing helix chain 'D' and resid 479 through 484 removed outlier: 3.800A 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 Processing helix chain 'D' and resid 524 through 533 Processing helix chain 'D' and resid 541 through 560 Processing helix chain 'D' and resid 571 through 578 removed outlier: 3.681A pdb=" N ILE D 574 " --> pdb=" O ALA D 571 " (cutoff:3.500A) Proline residue: D 575 - end of helix removed outlier: 3.999A pdb=" N LEU D 578 " --> pdb=" O PRO D 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 571 through 578' Processing helix chain 'D' and resid 631 through 646 removed outlier: 3.571A pdb=" N ALA D 646 " --> pdb=" O THR D 642 " (cutoff:3.500A) 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 741 through 745 removed outlier: 4.075A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU D 745 " --> pdb=" O GLN D 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 741 through 745' Processing helix chain 'D' and resid 750 through 753 No H-bonds generated for 'chain 'D' and resid 750 through 753' Processing helix chain 'D' and resid 762 through 769 Processing helix chain 'E' and resid 28 through 38 removed outlier: 4.038A pdb=" N ALA E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 136 Processing helix chain 'E' and resid 148 through 151 removed outlier: 3.683A pdb=" N ALA E 151 " --> pdb=" O GLN E 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 148 through 151' 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 removed outlier: 4.298A pdb=" N LYS E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU E 236 " --> pdb=" O ALA E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 255 Processing helix chain 'E' and resid 260 through 274 Processing helix chain 'E' and resid 281 through 294 removed outlier: 3.824A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 318 removed outlier: 3.716A pdb=" N ASP E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 338 Processing helix chain 'E' and resid 361 through 372 Processing helix chain 'E' and resid 404 through 411 removed outlier: 3.537A pdb=" N GLN E 411 " --> pdb=" O HIS E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 426 No H-bonds generated for 'chain 'E' and resid 424 through 426' Processing helix chain 'E' and resid 435 through 441 removed outlier: 3.558A pdb=" N ALA E 438 " --> pdb=" O PRO E 435 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N MET E 439 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU E 440 " --> pdb=" O SER E 437 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU E 441 " --> pdb=" O ALA E 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 435 through 441' Processing helix chain 'E' and resid 479 through 484 removed outlier: 3.561A pdb=" N ASP E 483 " --> pdb=" O ARG E 479 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ARG E 484 " --> pdb=" O PRO E 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 479 through 484' Processing helix chain 'E' and resid 495 through 504 Processing helix chain 'E' and resid 506 through 512 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 541 through 560 removed outlier: 3.601A pdb=" N LEU E 559 " --> pdb=" O ALA E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 578 Processing helix chain 'E' and resid 631 through 646 Processing helix chain 'E' and resid 680 through 692 Processing helix chain 'E' and resid 718 through 727 Processing helix chain 'E' and resid 737 through 739 No H-bonds generated for 'chain 'E' and resid 737 through 739' Processing helix chain 'E' and resid 742 through 745 Processing helix chain 'E' and resid 750 through 753 No H-bonds generated for 'chain 'E' and resid 750 through 753' Processing helix chain 'E' and resid 762 through 769 Processing helix chain 'F' and resid 31 through 38 removed outlier: 3.758A pdb=" N MET F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 136 Processing helix chain 'F' and resid 147 through 149 No H-bonds generated for 'chain 'F' and resid 147 through 149' Processing helix chain 'F' and resid 158 through 168 Processing helix chain 'F' and resid 173 through 181 Processing helix chain 'F' and resid 185 through 234 Processing helix chain 'F' and resid 249 through 252 No H-bonds generated for 'chain 'F' and resid 249 through 252' Processing helix chain 'F' and resid 260 through 270 Processing helix chain 'F' and resid 281 through 292 Processing helix chain 'F' and resid 308 through 317 removed outlier: 3.594A pdb=" N ASP F 316 " --> pdb=" O ARG F 312 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU F 317 " --> pdb=" O GLN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 338 removed outlier: 4.094A pdb=" N TYR F 332 " --> pdb=" O ARG F 328 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU F 338 " --> pdb=" O ALA F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 370 Processing helix chain 'F' and resid 406 through 409 No H-bonds generated for 'chain 'F' and resid 406 through 409' Processing helix chain 'F' and resid 435 through 443 Processing helix chain 'F' and resid 479 through 483 removed outlier: 3.877A pdb=" N ASP F 483 " --> pdb=" O ARG F 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 479 through 483' Processing helix chain 'F' and resid 495 through 504 Processing helix chain 'F' and resid 506 through 514 removed outlier: 3.842A 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 571 through 578 removed outlier: 3.746A pdb=" N ILE F 574 " --> pdb=" O ALA F 571 " (cutoff:3.500A) Proline residue: F 575 - end of helix removed outlier: 3.858A pdb=" N LEU F 578 " --> pdb=" O PRO F 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 571 through 578' Processing helix chain 'F' and resid 631 through 646 removed outlier: 3.536A pdb=" N ALA F 646 " --> pdb=" O THR F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 651 No H-bonds generated for 'chain 'F' and resid 648 through 651' Processing helix chain 'F' and resid 680 through 692 Processing helix chain 'F' and resid 718 through 726 Processing helix chain 'F' and resid 737 through 745 removed outlier: 3.580A pdb=" N GLU F 740 " --> pdb=" O LYS F 737 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU F 743 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU F 744 " --> pdb=" O ALA F 741 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU F 745 " --> pdb=" O GLN F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 750 through 753 No H-bonds generated for 'chain 'F' and resid 750 through 753' Processing helix chain 'F' and resid 762 through 769 Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 119 through 137 Processing helix chain 'A' and resid 147 through 150 removed outlier: 3.803A pdb=" N GLU A 150 " --> pdb=" O TYR A 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 150' Processing helix chain 'A' and resid 158 through 165 Processing helix chain 'A' and resid 176 through 179 No H-bonds generated for 'chain 'A' and resid 176 through 179' Processing helix chain 'A' and resid 187 through 236 removed outlier: 3.727A pdb=" N GLU A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 249 through 256 removed outlier: 4.176A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 275 removed outlier: 5.648A pdb=" N ARG A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.687A pdb=" N GLU A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 361 through 371 removed outlier: 3.911A pdb=" N GLY A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG A 366 " --> pdb=" O THR A 362 " (cutoff:3.500A) 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 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 435 through 442 removed outlier: 3.843A pdb=" N GLU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) 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 484 removed outlier: 4.575A pdb=" N ARG A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) 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 559 removed outlier: 3.711A pdb=" N LEU A 559 " --> pdb=" O ALA A 555 " (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 743 through 745 No H-bonds generated for 'chain 'A' and resid 743 through 745' Processing helix chain 'A' and resid 748 through 753 removed outlier: 3.667A pdb=" N GLY A 753 " --> pdb=" O GLU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 769 Processing sheet with id= A, first strand: chain 'B' and resid 4 through 6 Processing sheet with id= B, first strand: chain 'B' and resid 43 through 45 removed outlier: 3.506A pdb=" N GLY B 66 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA B 90 " --> pdb=" O GLN B 68 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 70 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA B 88 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 486 through 490 removed outlier: 6.832A pdb=" N PHE B 467 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU B 353 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR B 469 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N GLY B 355 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 471 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS B 375 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU B 420 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N HIS B 377 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.326A pdb=" N ARG B 567 " --> pdb=" O GLU B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 596 through 603 removed outlier: 5.893A pdb=" N LYS B 622 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL B 665 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 732 through 736 removed outlier: 6.520A pdb=" N GLU B 755 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU B 735 " --> pdb=" O GLU B 755 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS B 757 " --> pdb=" O LEU B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 43 through 47 Processing sheet with id= H, first strand: chain 'C' and resid 486 through 490 removed outlier: 6.739A pdb=" N PHE C 467 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N LEU C 353 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR C 469 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY C 355 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA C 471 " --> pdb=" O GLY C 355 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 520 through 522 removed outlier: 6.384A pdb=" N ARG C 567 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 596 through 602 removed outlier: 6.114A pdb=" N LYS C 622 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL C 665 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N VAL C 667 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR C 626 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 733 through 736 Processing sheet with id= L, first strand: chain 'D' and resid 20 through 22 removed outlier: 3.880A pdb=" N THR D 21 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D 86 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN D 68 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG D 91 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY D 66 " --> pdb=" O ARG D 91 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 486 through 490 removed outlier: 6.690A pdb=" N PHE D 467 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LEU D 353 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR D 469 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N GLY D 355 " --> pdb=" O THR D 469 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA D 471 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 470 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 520 through 522 removed outlier: 6.212A pdb=" N ARG D 567 " --> pdb=" O GLU D 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 596 through 603 Processing sheet with id= P, first strand: chain 'D' and resid 732 through 736 removed outlier: 6.281A pdb=" N GLU D 755 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU D 735 " --> pdb=" O GLU D 755 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LYS D 757 " --> pdb=" O LEU D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 19 through 24 removed outlier: 3.701A pdb=" N THR E 19 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA E 88 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU E 87 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA E 69 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE E 44 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.881A pdb=" N GLY E 66 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 74 through 77 removed outlier: 3.709A pdb=" N GLN E 83 " --> pdb=" O MET E 75 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU E 77 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 350 through 355 Processing sheet with id= U, first strand: chain 'E' and resid 375 through 380 removed outlier: 6.336A pdb=" N PHE E 466 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU E 421 " --> pdb=" O PHE E 466 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE E 468 " --> pdb=" O LEU E 421 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 520 through 522 removed outlier: 5.915A pdb=" N ARG E 567 " --> pdb=" O GLU E 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'E' and resid 596 through 603 removed outlier: 6.024A pdb=" N LYS E 622 " --> pdb=" O LEU E 663 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL E 665 " --> pdb=" O LYS E 622 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER E 624 " --> pdb=" O VAL E 665 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 732 through 736 removed outlier: 6.533A pdb=" N GLU E 755 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU E 735 " --> pdb=" O GLU E 755 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LYS E 757 " --> pdb=" O LEU E 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.916A pdb=" N LEU F 5 " --> pdb=" O ALA F 105 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA F 105 " --> pdb=" O LEU F 5 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 20 through 25 removed outlier: 3.566A pdb=" N VAL F 84 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL F 25 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU F 77 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET F 85 " --> pdb=" O GLN F 73 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 44 through 46 removed outlier: 4.213A pdb=" N ILE F 44 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA F 69 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY F 66 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA F 90 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL F 70 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ALA F 88 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 485 through 490 removed outlier: 6.225A pdb=" N ILE F 350 " --> pdb=" O GLU F 486 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE F 488 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL F 352 " --> pdb=" O ILE F 488 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE F 490 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL F 354 " --> pdb=" O ILE F 490 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU F 351 " --> pdb=" O PHE F 467 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY F 355 " --> pdb=" O ALA F 471 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.426A pdb=" N ARG F 567 " --> pdb=" O GLU F 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'F' and resid 596 through 603 removed outlier: 4.933A pdb=" N THR F 611 " --> pdb=" O PRO F 668 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS F 622 " --> pdb=" O LEU F 663 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL F 665 " --> pdb=" O LYS F 622 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER F 624 " --> pdb=" O VAL F 665 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL F 667 " --> pdb=" O SER F 624 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR F 626 " --> pdb=" O VAL F 667 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 732 through 736 removed outlier: 6.358A pdb=" N GLU F 755 " --> pdb=" O ILE F 733 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU F 735 " --> pdb=" O GLU F 755 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LYS F 757 " --> pdb=" O LEU F 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'A' and resid 486 through 490 removed outlier: 3.840A pdb=" N LEU A 351 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 355 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 470 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.488A pdb=" N ARG A 567 " --> pdb=" O GLU A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'A' and resid 596 through 603 removed outlier: 5.994A pdb=" N LYS A 622 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL A 665 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'A' and resid 732 through 736 removed outlier: 6.431A pdb=" N GLU A 755 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 735 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LYS A 757 " --> pdb=" O LEU A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI 1306 hydrogen bonds defined for protein. 3870 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: 12.60 Time building geometry restraints manager: 13.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.29: 6398 1.29 - 1.45: 9573 1.45 - 1.62: 21435 1.62 - 1.78: 44 1.78 - 1.95: 224 Bond restraints: 37674 Sorted by residual: bond pdb=" C ASP D 675 " pdb=" O ASP D 675 " ideal model delta sigma weight residual 1.234 1.122 0.112 1.20e-02 6.94e+03 8.65e+01 bond pdb=" C ASP E 675 " pdb=" O ASP E 675 " ideal model delta sigma weight residual 1.233 1.127 0.106 1.17e-02 7.31e+03 8.23e+01 bond pdb=" C ASP F 675 " pdb=" O ASP F 675 " ideal model delta sigma weight residual 1.233 1.128 0.105 1.17e-02 7.31e+03 8.05e+01 bond pdb=" C ASP A 675 " pdb=" O ASP A 675 " ideal model delta sigma weight residual 1.233 1.129 0.105 1.17e-02 7.31e+03 7.98e+01 bond pdb=" C ASP C 675 " pdb=" O ASP C 675 " ideal model delta sigma weight residual 1.234 1.127 0.107 1.20e-02 6.94e+03 7.94e+01 ... (remaining 37669 not shown) Histogram of bond angle deviations from ideal: 97.36 - 104.81: 951 104.81 - 112.27: 18482 112.27 - 119.73: 14603 119.73 - 127.19: 16650 127.19 - 134.65: 429 Bond angle restraints: 51115 Sorted by residual: angle pdb=" O ASP D 675 " pdb=" C ASP D 675 " pdb=" N GLY D 676 " ideal model delta sigma weight residual 123.42 106.19 17.23 1.07e+00 8.73e-01 2.59e+02 angle pdb=" O ASP A 675 " pdb=" C ASP A 675 " pdb=" N GLY A 676 " ideal model delta sigma weight residual 123.26 107.51 15.75 1.05e+00 9.07e-01 2.25e+02 angle pdb=" O ASP E 675 " pdb=" C ASP E 675 " pdb=" N GLY E 676 " ideal model delta sigma weight residual 123.26 107.67 15.59 1.05e+00 9.07e-01 2.21e+02 angle pdb=" O ASP F 675 " pdb=" C ASP F 675 " pdb=" N GLY F 676 " ideal model delta sigma weight residual 123.26 107.75 15.51 1.05e+00 9.07e-01 2.18e+02 angle pdb=" O ASP C 675 " pdb=" C ASP C 675 " pdb=" N GLY C 676 " ideal model delta sigma weight residual 123.42 107.67 15.75 1.07e+00 8.73e-01 2.17e+02 ... (remaining 51110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 22991 35.62 - 71.25: 206 71.25 - 106.87: 24 106.87 - 142.49: 5 142.49 - 178.11: 3 Dihedral angle restraints: 23229 sinusoidal: 9670 harmonic: 13559 Sorted by residual: dihedral pdb=" CA GLN B 278 " pdb=" C GLN B 278 " pdb=" N GLY B 279 " pdb=" CA GLY B 279 " ideal model delta harmonic sigma weight residual -180.00 -132.21 -47.79 0 5.00e+00 4.00e-02 9.14e+01 dihedral pdb=" CA ASN F 416 " pdb=" C ASN F 416 " pdb=" N PRO F 417 " pdb=" CA PRO F 417 " ideal model delta harmonic sigma weight residual -180.00 -145.26 -34.74 0 5.00e+00 4.00e-02 4.83e+01 dihedral pdb=" C2' ADP F 901 " pdb=" C1' ADP F 901 " pdb=" N9 ADP F 901 " pdb=" C4 ADP F 901 " ideal model delta sinusoidal sigma weight residual 91.55 -86.57 178.11 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 23226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 5212 0.097 - 0.193: 572 0.193 - 0.290: 42 0.290 - 0.387: 5 0.387 - 0.484: 1 Chirality restraints: 5832 Sorted by residual: chirality pdb=" CA GLU D 423 " pdb=" N GLU D 423 " pdb=" C GLU D 423 " pdb=" CB GLU D 423 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" CA LEU B 237 " pdb=" N LEU B 237 " pdb=" C LEU B 237 " pdb=" CB LEU B 237 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C3' ADP E 901 " pdb=" C2' ADP E 901 " pdb=" C4' ADP E 901 " pdb=" O3' ADP E 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.83 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 5829 not shown) Planarity restraints: 6628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 675 " -0.089 2.00e-02 2.50e+03 1.76e-01 3.10e+02 pdb=" C ASP C 675 " 0.303 2.00e-02 2.50e+03 pdb=" O ASP C 675 " -0.136 2.00e-02 2.50e+03 pdb=" N GLY C 676 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 675 " -0.089 2.00e-02 2.50e+03 1.76e-01 3.10e+02 pdb=" C ASP E 675 " 0.303 2.00e-02 2.50e+03 pdb=" O ASP E 675 " -0.136 2.00e-02 2.50e+03 pdb=" N GLY E 676 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 675 " 0.089 2.00e-02 2.50e+03 1.75e-01 3.08e+02 pdb=" C ASP B 675 " -0.302 2.00e-02 2.50e+03 pdb=" O ASP B 675 " 0.136 2.00e-02 2.50e+03 pdb=" N GLY B 676 " 0.077 2.00e-02 2.50e+03 ... (remaining 6625 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6870 2.77 - 3.31: 32247 3.31 - 3.84: 58786 3.84 - 4.37: 67235 4.37 - 4.90: 116442 Nonbonded interactions: 281580 Sorted by model distance: nonbonded pdb=" N GLY B 279 " pdb=" N SER B 280 " model vdw 2.243 2.560 nonbonded pdb=" O VAL B 359 " pdb=" O2B AGS B 901 " model vdw 2.266 2.440 nonbonded pdb=" O LYS A 268 " pdb=" NH1 ARG A 272 " model vdw 2.270 2.520 nonbonded pdb=" N ASP C 245 " pdb=" OD1 ASP C 245 " model vdw 2.276 2.520 nonbonded pdb=" OG1 THR A 603 " pdb=" O GLY A 606 " model vdw 2.281 2.440 ... (remaining 281575 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) selection = (chain 'B' and resid 2 through 780) selection = (chain 'C' and resid 2 through 780) selection = (chain 'D' and resid 2 through 780) selection = (chain 'E' and resid 2 through 780) selection = (chain 'F' and resid 2 through 780) } 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 11.050 Check model and map are aligned: 0.440 Set scattering table: 0.290 Process input model: 84.280 Find NCS groups from input model: 3.020 Set up NCS constraints: 0.260 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:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 : 0.008 0.113 37674 Z= 0.510 Angle : 1.107 17.230 51115 Z= 0.659 Chirality : 0.062 0.484 5832 Planarity : 0.009 0.176 6628 Dihedral : 11.566 178.114 14497 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.18 % Favored : 95.67 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.34 % Twisted Proline : 0.36 % 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: -3.44 (0.10), residues: 4662 helix: -2.33 (0.09), residues: 1909 sheet: -0.51 (0.21), residues: 541 loop : -2.68 (0.10), residues: 2212 *********************** 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 456 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 421 time to evaluate : 4.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 5 residues processed: 452 average time/residue: 1.7289 time to fit residues: 908.4755 Evaluate side-chains 248 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 243 time to evaluate : 3.228 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 4.5431 ------------------------------------------------------------------------------- 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: 50.0000 chunk 351 optimal weight: 8.9990 chunk 195 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 237 optimal weight: 40.0000 chunk 187 optimal weight: 4.9990 chunk 363 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 421 optimal weight: 0.8980 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: