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/7fid_31589/05_2023/7fid_31589_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fid_31589/05_2023/7fid_31589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fid_31589/05_2023/7fid_31589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fid_31589/05_2023/7fid_31589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fid_31589/05_2023/7fid_31589_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fid_31589/05_2023/7fid_31589_updated.pdb" } resolution = 2.44 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 15 5.49 5 S 135 5.16 5 C 23328 2.51 5 N 6490 2.21 5 O 7024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 202": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" 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: 36992 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': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} 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: "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': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} 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': 4, 'PCIS': 1, 'PTRANS': 45, 'TRANS': 728} Chain: "S" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 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: 16.48, per 1000 atoms: 0.45 Number of scatterers: 36992 At special positions: 0 Unit cell: (197.62, 200.08, 194.34, 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 135 16.00 P 15 15.00 O 7024 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: 10.44 Conformation dependent library (CDL) restraints added in 4.3 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: 172 helices and 35 sheets defined 40.8% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 818.57 Creating SS restraints... Processing helix chain 'B' and resid 28 through 38 removed outlier: 3.734A pdb=" N LYS B 31 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ARG B 32 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 36 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 138 Processing helix chain 'B' and resid 149 through 152 No H-bonds generated for 'chain 'B' and resid 149 through 152' Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 173 through 180 Processing helix chain 'B' and resid 186 through 235 Processing helix chain 'B' and resid 243 through 253 removed outlier: 3.901A pdb=" N GLU B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.984A pdb=" N ARG B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'B' and resid 308 through 317 removed outlier: 3.651A 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 363 through 371 removed outlier: 3.971A pdb=" N SER B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) 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 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 479 through 484 removed outlier: 3.824A pdb=" N ARG B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 506 through 514 removed outlier: 3.801A 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 Processing helix chain 'B' and resid 574 through 578 Processing helix chain 'B' and resid 631 through 646 removed outlier: 3.742A pdb=" N ALA B 646 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 651 No H-bonds generated for 'chain 'B' and resid 648 through 651' 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: 4.365A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU B 744 " --> pdb=" O ALA B 741 " (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 28 through 36 removed outlier: 3.997A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 134 Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 158 through 167 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 185 through 236 Processing helix chain 'C' and resid 244 through 255 Processing helix chain 'C' and resid 260 through 275 removed outlier: 3.884A pdb=" N ARG C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.937A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 317 removed outlier: 3.709A pdb=" N ASP C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU C 317 " --> pdb=" O GLN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 339 Processing helix chain 'C' and resid 362 through 371 removed outlier: 4.361A pdb=" N ARG C 366 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 367 " --> pdb=" O SER C 363 " (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 411 Processing helix chain 'C' and resid 435 through 442 removed outlier: 4.237A pdb=" N LEU C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU C 441 " --> pdb=" O SER C 437 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 479 through 484 removed outlier: 4.065A 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: 3.624A 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 543 through 560 Processing helix chain 'C' and resid 574 through 578 Processing helix chain 'C' and resid 631 through 646 removed outlier: 3.633A pdb=" N ALA C 646 " --> pdb=" O THR C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 660 No H-bonds generated for 'chain 'C' and resid 657 through 660' Processing helix chain 'C' and resid 680 through 691 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: 3.749A pdb=" N GLU C 744 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 3.603A 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 'D' and resid 28 through 39 removed outlier: 3.925A pdb=" N ARG D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 138 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 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 159 through 168 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 185 through 237 Processing helix chain 'D' and resid 246 through 255 Processing helix chain 'D' and resid 260 through 275 Processing helix chain 'D' and resid 281 through 294 removed outlier: 3.874A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 317 removed outlier: 3.906A 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 362 through 371 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 435 through 441 removed outlier: 4.477A pdb=" N GLU D 441 " --> pdb=" O SER D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 484 removed outlier: 4.167A 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 513 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 541 through 560 Processing helix chain 'D' and resid 574 through 578 Processing helix chain 'D' and resid 631 through 646 removed outlier: 3.587A pdb=" N ALA D 646 " --> pdb=" O THR D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 651 No H-bonds generated for 'chain 'D' and resid 648 through 651' Processing helix chain 'D' and resid 657 through 660 No H-bonds generated for 'chain 'D' and resid 657 through 660' Processing helix chain 'D' and resid 680 through 692 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 744 removed outlier: 3.791A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 741 through 744' Processing helix chain 'D' and resid 748 through 753 removed outlier: 3.913A pdb=" N GLY D 753 " --> pdb=" O GLU D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 769 Processing helix chain 'E' and resid 31 through 38 Processing helix chain 'E' and resid 118 through 141 removed outlier: 3.565A pdb=" N ASN E 138 " --> pdb=" O LYS E 134 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LYS E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N SER E 141 " --> pdb=" O ALA E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 168 removed outlier: 4.328A pdb=" N HIS E 168 " --> pdb=" O THR E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'E' and resid 186 through 237 Processing helix chain 'E' and resid 247 through 250 removed outlier: 3.878A pdb=" N ARG E 250 " --> pdb=" O GLU E 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 247 through 250' Processing helix chain 'E' and resid 260 through 270 Processing helix chain 'E' and resid 283 through 294 Processing helix chain 'E' and resid 308 through 318 removed outlier: 3.702A 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 362 through 371 Processing helix chain 'E' and resid 404 through 411 Processing helix chain 'E' and resid 436 through 443 removed outlier: 3.793A pdb=" N VAL E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) 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 507 through 513 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 541 through 560 Processing helix chain 'E' and resid 574 through 578 Processing helix chain 'E' and resid 631 through 651 removed outlier: 3.504A pdb=" N HIS E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR E 648 " --> pdb=" O LEU E 644 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLN E 649 " --> pdb=" O ARG E 645 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASP E 650 " --> pdb=" O ALA E 646 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR E 651 " --> pdb=" O HIS E 647 " (cutoff:3.500A) 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 745 removed outlier: 3.526A pdb=" N GLU E 740 " --> pdb=" O LYS E 737 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ALA E 741 " --> pdb=" O ASP E 738 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 743 " --> pdb=" O GLU E 740 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU E 744 " --> pdb=" O ALA E 741 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU E 745 " --> pdb=" O GLN E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 753 Processing helix chain 'E' and resid 762 through 769 Processing helix chain 'F' and resid 28 through 37 removed outlier: 3.843A pdb=" N ALA F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 135 Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 158 through 166 Processing helix chain 'F' and resid 173 through 180 Processing helix chain 'F' and resid 186 through 236 Processing helix chain 'F' and resid 247 through 253 Processing helix chain 'F' and resid 260 through 266 Processing helix chain 'F' and resid 285 through 293 Processing helix chain 'F' and resid 308 through 318 removed outlier: 4.337A pdb=" N GLU F 317 " --> pdb=" O GLN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 338 Processing helix chain 'F' and resid 362 through 371 Processing helix chain 'F' and resid 387 through 389 No H-bonds generated for 'chain 'F' and resid 387 through 389' Processing helix chain 'F' and resid 404 through 411 Processing helix chain 'F' and resid 424 through 426 No H-bonds generated for 'chain 'F' and resid 424 through 426' Processing helix chain 'F' and resid 436 through 443 Processing helix chain 'F' and resid 479 through 482 No H-bonds generated for 'chain 'F' and resid 479 through 482' Processing helix chain 'F' and resid 495 through 514 Proline residue: F 508 - end of helix removed outlier: 3.835A pdb=" N SER F 514 " --> pdb=" O GLN F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 534 removed outlier: 3.558A pdb=" N LEU F 528 " --> pdb=" O ASP F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 558 removed outlier: 3.531A pdb=" N ILE F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) 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 677 through 692 removed outlier: 3.541A pdb=" N GLY F 680 " --> pdb=" O PRO F 677 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE F 681 " --> pdb=" O SER F 678 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR F 682 " --> pdb=" O ALA F 679 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE F 687 " --> pdb=" O ALA F 684 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU F 691 " --> pdb=" O ALA F 688 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER F 692 " --> pdb=" O SER F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 726 Processing helix chain 'F' and resid 737 through 743 removed outlier: 4.640A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU F 743 " --> pdb=" O GLU F 740 " (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 'A' and resid 31 through 39 removed outlier: 3.701A pdb=" N MET A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 118 through 135 Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 185 through 237 Processing helix chain 'A' and resid 244 through 255 Processing helix chain 'A' and resid 260 through 272 removed outlier: 3.584A pdb=" N ASP A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 293 removed outlier: 4.268A pdb=" N THR A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.808A pdb=" N ARG A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 removed outlier: 4.066A pdb=" N ARG A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 4.177A pdb=" N SER A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) 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: 3.850A pdb=" N GLU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.514A 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: 3.722A pdb=" N ASP A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 484' Processing helix chain 'A' and resid 495 through 514 removed outlier: 5.041A pdb=" N TRP A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Proline residue: A 508 - end of helix removed outlier: 3.751A pdb=" N SER A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 541 through 560 Processing helix chain 'A' and resid 574 through 578 Processing helix chain 'A' and resid 631 through 646 Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' 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 742 removed outlier: 3.565A pdb=" N GLU A 740 " --> pdb=" O LYS A 737 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ALA A 741 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 769 Processing sheet with id= A, first strand: chain 'B' and resid 20 through 25 removed outlier: 3.892A pdb=" N THR B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 43 through 46 Processing sheet with id= C, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.858A pdb=" N ASP B 96 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 486 through 490 removed outlier: 6.689A pdb=" N PHE B 467 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU B 353 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR B 469 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N GLY B 355 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA B 471 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.277A pdb=" N ARG B 567 " --> pdb=" O GLU B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 596 through 602 removed outlier: 5.902A pdb=" N LYS B 622 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL B 665 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 733 through 736 Processing sheet with id= H, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.591A pdb=" N GLU C 87 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 70 " --> pdb=" O GLU C 87 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLN C 68 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG C 91 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY C 66 " --> pdb=" O ARG C 91 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 486 through 490 removed outlier: 6.590A pdb=" N PHE C 467 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU C 353 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR C 469 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLY C 355 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 471 " --> pdb=" O GLY C 355 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 596 through 603 removed outlier: 5.965A pdb=" N LYS C 622 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL C 665 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL C 667 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR C 626 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 700 through 702 removed outlier: 6.739A pdb=" N LYS C 732 " --> pdb=" O ALA C 701 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 7 through 9 removed outlier: 7.319A pdb=" N ILE D 8 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE D 45 " --> pdb=" O ILE D 8 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 21 through 23 removed outlier: 4.304A pdb=" N THR D 21 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D 86 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU D 87 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL D 71 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 351 through 355 removed outlier: 6.245A 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: 6.423A 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: 6.503A pdb=" N VAL D 418 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE D 379 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU D 420 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE D 466 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU D 421 " --> pdb=" O PHE D 466 " (cutoff:3.500A) removed outlier: 6.914A 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 596 through 603 removed outlier: 6.345A pdb=" N LYS D 622 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL D 665 " --> pdb=" O LYS D 622 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 732 through 736 removed outlier: 6.311A pdb=" N GLU D 755 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU D 735 " --> pdb=" O GLU D 755 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYS D 757 " --> pdb=" O LEU D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 7 through 9 removed outlier: 7.916A pdb=" N ILE E 8 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N PHE E 45 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET E 85 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ALA E 74 " --> pdb=" O GLN E 83 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLN E 83 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 486 through 489 removed outlier: 4.651A pdb=" N LEU E 351 " --> pdb=" O PHE E 467 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE E 419 " --> pdb=" O PHE E 466 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.183A pdb=" N ARG E 567 " --> pdb=" O GLU E 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 596 through 603 Processing sheet with id= V, first strand: chain 'E' and resid 700 through 702 removed outlier: 6.504A pdb=" N LYS E 732 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU E 755 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU E 735 " --> pdb=" O GLU E 755 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS E 757 " --> pdb=" O LEU E 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 8 through 10 removed outlier: 3.903A pdb=" N ILE F 8 " --> pdb=" O PHE F 45 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL F 47 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU F 10 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA F 90 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL F 70 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ALA F 88 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 21 through 25 Processing sheet with id= Y, first strand: chain 'F' and resid 485 through 490 removed outlier: 5.680A pdb=" N ILE F 350 " --> pdb=" O GLU F 486 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE F 488 " --> pdb=" O ILE F 350 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL F 352 " --> pdb=" O ILE F 488 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE F 490 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL F 354 " --> pdb=" O ILE F 490 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU F 351 " --> pdb=" O PHE F 467 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.641A pdb=" N ARG F 567 " --> pdb=" O GLU F 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'F' and resid 596 through 603 removed outlier: 4.993A pdb=" N THR F 611 " --> pdb=" O PRO F 668 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 733 through 736 Processing sheet with id= AC, first strand: chain 'A' and resid 4 through 6 removed outlier: 4.137A pdb=" N ARG A 104 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 106 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP A 96 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 7 through 9 removed outlier: 8.410A pdb=" N ILE A 8 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE A 45 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 22 through 25 removed outlier: 3.637A pdb=" N GLN A 73 " --> pdb=" O MET A 85 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 486 through 490 Processing sheet with id= AG, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.323A 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: 5.979A pdb=" N LYS A 622 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL A 665 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL A 667 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR A 626 " --> pdb=" O VAL A 667 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'A' and resid 733 through 736 1384 hydrogen bonds defined for protein. 4041 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: 11.20 Time building geometry restraints manager: 11.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 12595 1.35 - 1.50: 10662 1.50 - 1.65: 14145 1.65 - 1.80: 211 1.80 - 1.95: 56 Bond restraints: 37669 Sorted by residual: bond pdb=" C ILE F 113 " pdb=" N PHE F 114 " ideal model delta sigma weight residual 1.329 1.390 -0.061 1.35e-02 5.49e+03 2.05e+01 bond pdb=" C ASP A 51 " pdb=" N PRO A 52 " ideal model delta sigma weight residual 1.331 1.382 -0.051 1.21e-02 6.83e+03 1.75e+01 bond pdb=" CA GLU A 247 " pdb=" C GLU A 247 " ideal model delta sigma weight residual 1.522 1.469 0.053 1.40e-02 5.10e+03 1.45e+01 bond pdb=" N SER E 380 " pdb=" CA SER E 380 " ideal model delta sigma weight residual 1.461 1.510 -0.049 1.41e-02 5.03e+03 1.22e+01 bond pdb=" C ASP B 51 " pdb=" N PRO B 52 " ideal model delta sigma weight residual 1.334 1.404 -0.071 2.34e-02 1.83e+03 9.10e+00 ... (remaining 37664 not shown) Histogram of bond angle deviations from ideal: 96.42 - 106.37: 1399 106.37 - 116.33: 24448 116.33 - 126.29: 24629 126.29 - 136.25: 628 136.25 - 146.21: 2 Bond angle restraints: 51106 Sorted by residual: angle pdb=" CA LEU D 161 " pdb=" CB LEU D 161 " pdb=" CG LEU D 161 " ideal model delta sigma weight residual 116.30 146.21 -29.91 3.50e+00 8.16e-02 7.30e+01 angle pdb=" CB ARG D 328 " pdb=" CG ARG D 328 " pdb=" CD ARG D 328 " ideal model delta sigma weight residual 111.30 126.45 -15.15 2.30e+00 1.89e-01 4.34e+01 angle pdb=" N GLY D 242 " pdb=" CA GLY D 242 " pdb=" C GLY D 242 " ideal model delta sigma weight residual 115.32 108.02 7.30 1.31e+00 5.83e-01 3.10e+01 angle pdb=" N PRO F 52 " pdb=" CA PRO F 52 " pdb=" C PRO F 52 " ideal model delta sigma weight residual 111.15 119.44 -8.29 1.58e+00 4.01e-01 2.75e+01 angle pdb=" CA ARG B 395 " pdb=" CB ARG B 395 " pdb=" CG ARG B 395 " ideal model delta sigma weight residual 114.10 124.57 -10.47 2.00e+00 2.50e-01 2.74e+01 ... (remaining 51101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.32: 22959 33.32 - 66.64: 233 66.64 - 99.96: 30 99.96 - 133.28: 7 133.28 - 166.60: 2 Dihedral angle restraints: 23231 sinusoidal: 9672 harmonic: 13559 Sorted by residual: 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 -117.34 -62.66 0 5.00e+00 4.00e-02 1.57e+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 -119.70 -60.30 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA GLU D 304 " pdb=" C GLU D 304 " pdb=" N VAL D 305 " pdb=" CA VAL D 305 " ideal model delta harmonic sigma weight residual -180.00 -126.73 -53.27 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 23228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4959 0.088 - 0.176: 810 0.176 - 0.263: 56 0.263 - 0.351: 3 0.351 - 0.439: 2 Chirality restraints: 5830 Sorted by residual: chirality pdb=" CG LEU D 161 " pdb=" CB LEU D 161 " pdb=" CD1 LEU D 161 " pdb=" CD2 LEU D 161 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CG LEU E 270 " pdb=" CB LEU E 270 " pdb=" CD1 LEU E 270 " pdb=" CD2 LEU E 270 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CB ILE B 398 " pdb=" CA ILE B 398 " pdb=" CG1 ILE B 398 " pdb=" CG2 ILE B 398 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 5827 not shown) Planarity restraints: 6627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 404 " 0.031 2.00e-02 2.50e+03 6.00e-02 3.60e+01 pdb=" C LYS E 404 " -0.104 2.00e-02 2.50e+03 pdb=" O LYS E 404 " 0.039 2.00e-02 2.50e+03 pdb=" N LEU E 405 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 379 " 0.027 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C ILE E 379 " -0.091 2.00e-02 2.50e+03 pdb=" O ILE E 379 " 0.034 2.00e-02 2.50e+03 pdb=" N SER E 380 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 247 " 0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C GLU A 247 " -0.076 2.00e-02 2.50e+03 pdb=" O GLU A 247 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA A 248 " 0.026 2.00e-02 2.50e+03 ... (remaining 6624 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1734 2.71 - 3.26: 33778 3.26 - 3.81: 57385 3.81 - 4.35: 70288 4.35 - 4.90: 119510 Nonbonded interactions: 282695 Sorted by model distance: nonbonded pdb=" O ASP A 422 " pdb=" OG1 THR A 470 " model vdw 2.165 2.440 nonbonded pdb=" O VAL A 359 " pdb=" O2B AGS A 901 " model vdw 2.191 2.440 nonbonded pdb=" O1B AGS A 901 " pdb=" O3G AGS A 901 " model vdw 2.220 2.440 nonbonded pdb=" O1B AGS C 901 " pdb=" O2G AGS C 901 " model vdw 2.235 2.440 nonbonded pdb=" O VAL C 359 " pdb=" O2B AGS C 901 " model vdw 2.239 2.440 ... (remaining 282690 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.600 Check model and map are aligned: 0.520 Set scattering table: 0.280 Process input model: 75.850 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.126 37669 Z= 0.620 Angle : 1.103 29.913 51106 Z= 0.592 Chirality : 0.063 0.439 5830 Planarity : 0.008 0.086 6627 Dihedral : 11.254 166.601 14499 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.71 % Favored : 94.12 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.48 % Twisted Proline : 2.17 % 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: -3.56 (0.10), residues: 4662 helix: -2.36 (0.09), residues: 1984 sheet: -0.54 (0.21), residues: 582 loop : -2.87 (0.11), residues: 2096 *********************** 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 362 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 348 time to evaluate : 4.184 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: 14 outliers final: 4 residues processed: 361 average time/residue: 1.8057 time to fit residues: 758.7221 Evaluate side-chains 230 residues out of total 3930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 226 time to evaluate : 3.054 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 4.4516 ------------------------------------------------------------------------------- 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: 20.0000 chunk 195 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 237 optimal weight: 50.0000 chunk 187 optimal weight: 1.9990 chunk 363 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 221 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 421 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: