Starting phenix.real_space_refine on Sat Aug 10 13:39:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/08_2024/8hir_34827.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/08_2024/8hir_34827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/08_2024/8hir_34827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/08_2024/8hir_34827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/08_2024/8hir_34827.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hir_34827/08_2024/8hir_34827.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.133 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 Zn 4 6.06 5 S 208 5.16 5 Na 4 4.78 5 C 18908 2.51 5 N 4848 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A ASP 413": "OD1" <-> "OD2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A ASP 504": "OD1" <-> "OD2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A ASP 843": "OD1" <-> "OD2" Residue "A PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1014": "OE1" <-> "OE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B ASP 401": "OD1" <-> "OD2" Residue "B GLU 411": "OE1" <-> "OE2" Residue "B ASP 413": "OD1" <-> "OD2" Residue "B GLU 461": "OE1" <-> "OE2" Residue "B ASP 504": "OD1" <-> "OD2" Residue "B TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 631": "OE1" <-> "OE2" Residue "B TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 860": "OE1" <-> "OE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C ASP 384": "OD1" <-> "OD2" Residue "C ASP 401": "OD1" <-> "OD2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C ASP 413": "OD1" <-> "OD2" Residue "C GLU 461": "OE1" <-> "OE2" Residue "C ASP 504": "OD1" <-> "OD2" Residue "C TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "C TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 830": "OE1" <-> "OE2" Residue "C ASP 839": "OD1" <-> "OD2" Residue "C GLU 860": "OE1" <-> "OE2" Residue "C PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1148": "OE1" <-> "OE2" Residue "D PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 138": "OD1" <-> "OD2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 384": "OD1" <-> "OD2" Residue "D ASP 401": "OD1" <-> "OD2" Residue "D GLU 411": "OE1" <-> "OE2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D GLU 461": "OE1" <-> "OE2" Residue "D ASP 504": "OD1" <-> "OD2" Residue "D TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 839": "OD1" <-> "OD2" Residue "D TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1014": "OE1" <-> "OE2" Residue "D GLU 1148": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29168 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7278 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 41, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7278 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 41, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 125 Chain: "C" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7278 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 41, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 125 Chain: "D" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7278 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 41, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 125 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 17 Unusual residues: {' K': 4, ' NA': 1, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' NA': 1, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' NA': 1, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' NA': 1, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 8 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4558 SG CYS A 777 82.687 95.289 12.517 1.00113.91 S ATOM 4564 SG CYS A 778 85.660 98.570 12.340 1.00115.70 S ATOM 4618 SG CYS A 785 86.098 95.282 10.992 1.00138.43 S ATOM 11836 SG CYS B 777 95.308 67.082 12.496 1.00113.48 S ATOM 11842 SG CYS B 778 98.582 64.093 12.329 1.00117.04 S ATOM 11896 SG CYS B 785 95.296 63.676 10.963 1.00136.80 S ATOM 19114 SG CYS C 777 67.051 54.450 12.490 1.00112.86 S ATOM 19120 SG CYS C 778 64.079 51.170 12.324 1.00115.83 S ATOM 19174 SG CYS C 785 63.629 54.465 10.977 1.00137.33 S ATOM 26392 SG CYS D 777 54.468 82.685 12.517 1.00116.50 S ATOM 26398 SG CYS D 778 51.170 85.650 12.341 1.00118.42 S ATOM 26452 SG CYS D 785 54.472 86.094 10.989 1.00137.08 S Time building chain proxies: 15.47, per 1000 atoms: 0.53 Number of scatterers: 29168 At special positions: 0 Unit cell: (150.8, 150.8, 139.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 K 4 19.00 S 208 16.00 Na 4 11.00 O 5192 8.00 N 4848 7.00 C 18908 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: 12.34 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1307 " pdb="ZN ZN A1307 " - pdb=" ND1 HIS A 787 " pdb="ZN ZN A1307 " - pdb=" SG CYS A 777 " pdb="ZN ZN A1307 " - pdb=" SG CYS A 785 " pdb="ZN ZN A1307 " - pdb=" SG CYS A 778 " pdb=" ZN B1303 " pdb="ZN ZN B1303 " - pdb=" ND1 HIS B 787 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 785 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 778 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 777 " pdb=" ZN C1303 " pdb="ZN ZN C1303 " - pdb=" ND1 HIS C 787 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 785 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 778 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 777 " pdb=" ZN D1303 " pdb="ZN ZN D1303 " - pdb=" ND1 HIS D 787 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 785 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 778 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 777 " Number of angles added : 12 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7024 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 24 sheets defined 52.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.564A pdb=" N GLU A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 106 Processing helix chain 'A' and resid 108 through 136 removed outlier: 3.790A pdb=" N LEU A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.674A pdb=" N LEU A 168 " --> pdb=" O TRP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 198 Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 209 through 225 removed outlier: 3.600A pdb=" N GLU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 240 through 254 removed outlier: 4.033A pdb=" N LEU A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 293 removed outlier: 4.118A pdb=" N ILE A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 324 through 354 Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.682A pdb=" N GLN A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR A 370 " --> pdb=" O HIS A 366 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 394 removed outlier: 3.516A pdb=" N ASN A 391 " --> pdb=" O MET A 387 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.540A pdb=" N GLN A 400 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 removed outlier: 4.136A pdb=" N ARG A 418 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 removed outlier: 3.870A pdb=" N ARG A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.646A pdb=" N HIS A 469 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 removed outlier: 4.352A pdb=" N PHE A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 518 removed outlier: 3.590A pdb=" N ALA A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 534 removed outlier: 3.601A pdb=" N THR A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 557 removed outlier: 3.540A pdb=" N GLY A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 Processing helix chain 'A' and resid 629 through 633 Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.511A pdb=" N LEU A 779 " --> pdb=" O PRO A 775 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG A 780 " --> pdb=" O PHE A 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 775 through 780' Processing helix chain 'A' and resid 792 through 797 Processing helix chain 'A' and resid 811 through 823 removed outlier: 3.614A pdb=" N ASN A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 817 " --> pdb=" O GLY A 813 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 819 " --> pdb=" O TYR A 815 " (cutoff:3.500A) Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 843 through 851 removed outlier: 3.837A pdb=" N ALA A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 873 removed outlier: 4.225A pdb=" N LEU A 869 " --> pdb=" O ASN A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.106A pdb=" N SER A 890 " --> pdb=" O SER A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 898 removed outlier: 3.716A pdb=" N ALA A 897 " --> pdb=" O GLU A 893 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP A 898 " --> pdb=" O ASP A 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 893 through 898' Processing helix chain 'A' and resid 898 through 912 removed outlier: 3.657A pdb=" N VAL A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 930 removed outlier: 4.100A pdb=" N ARG A 928 " --> pdb=" O SER A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 953 removed outlier: 3.969A pdb=" N ALA A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 971 through 975 Processing helix chain 'A' and resid 976 through 985 removed outlier: 3.924A pdb=" N TYR A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 983 " --> pdb=" O LEU A 979 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A 984 " --> pdb=" O TYR A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 996 Processing helix chain 'A' and resid 1013 through 1017 Processing helix chain 'A' and resid 1021 through 1033 Processing helix chain 'A' and resid 1132 through 1142 removed outlier: 3.947A pdb=" N GLN A1136 " --> pdb=" O TRP A1132 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A1138 " --> pdb=" O SER A1134 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A1142 " --> pdb=" O LEU A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1161 Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.571A pdb=" N GLU B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 106 removed outlier: 3.541A pdb=" N LEU B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 136 removed outlier: 3.767A pdb=" N LEU B 113 " --> pdb=" O GLN B 109 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.643A pdb=" N LEU B 168 " --> pdb=" O TRP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 198 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 209 through 225 removed outlier: 3.616A pdb=" N GLU B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 240 through 254 removed outlier: 4.021A pdb=" N LEU B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 293 removed outlier: 4.040A pdb=" N ILE B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 324 through 354 Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.689A pdb=" N GLN B 369 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR B 370 " --> pdb=" O HIS B 366 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 394 removed outlier: 3.501A pdb=" N ASN B 391 " --> pdb=" O MET B 387 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU B 392 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.517A pdb=" N GLN B 400 " --> pdb=" O PRO B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 420 removed outlier: 4.121A pdb=" N ARG B 418 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 removed outlier: 3.896A pdb=" N ARG B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 482 removed outlier: 3.633A pdb=" N HIS B 469 " --> pdb=" O THR B 465 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 498 removed outlier: 3.500A pdb=" N ASN B 496 " --> pdb=" O LYS B 493 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 518 removed outlier: 3.591A pdb=" N ALA B 515 " --> pdb=" O GLU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 534 removed outlier: 3.601A pdb=" N THR B 531 " --> pdb=" O SER B 527 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 534 " --> pdb=" O ILE B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 557 removed outlier: 3.529A pdb=" N GLY B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 591 Processing helix chain 'B' and resid 629 through 633 Processing helix chain 'B' and resid 775 through 780 removed outlier: 3.512A pdb=" N LEU B 779 " --> pdb=" O PRO B 775 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG B 780 " --> pdb=" O PHE B 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 775 through 780' Processing helix chain 'B' and resid 792 through 797 Processing helix chain 'B' and resid 811 through 823 removed outlier: 3.635A pdb=" N ASN B 816 " --> pdb=" O ASN B 812 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 817 " --> pdb=" O GLY B 813 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 818 " --> pdb=" O LEU B 814 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 819 " --> pdb=" O TYR B 815 " (cutoff:3.500A) Proline residue: B 820 - end of helix Processing helix chain 'B' and resid 843 through 851 removed outlier: 3.830A pdb=" N ALA B 849 " --> pdb=" O HIS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 873 removed outlier: 4.236A pdb=" N LEU B 869 " --> pdb=" O ASN B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 891 removed outlier: 4.106A pdb=" N SER B 890 " --> pdb=" O SER B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 898 removed outlier: 3.722A pdb=" N ALA B 897 " --> pdb=" O GLU B 893 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 898 " --> pdb=" O ASP B 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 893 through 898' Processing helix chain 'B' and resid 898 through 912 removed outlier: 3.659A pdb=" N VAL B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 910 " --> pdb=" O GLN B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 930 removed outlier: 4.112A pdb=" N ARG B 928 " --> pdb=" O SER B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 953 removed outlier: 3.957A pdb=" N ALA B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 973 through 975 No H-bonds generated for 'chain 'B' and resid 973 through 975' Processing helix chain 'B' and resid 976 through 985 removed outlier: 3.930A pdb=" N TYR B 980 " --> pdb=" O ASP B 976 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 983 " --> pdb=" O LEU B 979 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL B 984 " --> pdb=" O TYR B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 996 Processing helix chain 'B' and resid 1013 through 1017 Processing helix chain 'B' and resid 1021 through 1033 Processing helix chain 'B' and resid 1132 through 1142 removed outlier: 3.949A pdb=" N GLN B1136 " --> pdb=" O TRP B1132 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B1138 " --> pdb=" O SER B1134 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B1142 " --> pdb=" O LEU B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1161 Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.585A pdb=" N GLU C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 106 Processing helix chain 'C' and resid 108 through 136 removed outlier: 3.783A pdb=" N LEU C 113 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 114 " --> pdb=" O ARG C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.637A pdb=" N LEU C 168 " --> pdb=" O TRP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 198 Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 209 through 225 removed outlier: 3.620A pdb=" N GLU C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Proline residue: C 221 - end of helix Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 240 through 256 removed outlier: 4.050A pdb=" N LEU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP C 255 " --> pdb=" O ASN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 293 removed outlier: 3.981A pdb=" N ILE C 273 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 324 through 354 Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.697A pdb=" N GLN C 369 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR C 370 " --> pdb=" O HIS C 366 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS C 372 " --> pdb=" O ALA C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 394 removed outlier: 3.591A pdb=" N ASN C 391 " --> pdb=" O MET C 387 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 400 removed outlier: 3.515A pdb=" N GLN C 400 " --> pdb=" O PRO C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 420 removed outlier: 4.104A pdb=" N ARG C 418 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 removed outlier: 3.888A pdb=" N ARG C 444 " --> pdb=" O GLN C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 482 removed outlier: 3.628A pdb=" N HIS C 469 " --> pdb=" O THR C 465 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 498 removed outlier: 3.511A pdb=" N ASN C 496 " --> pdb=" O LYS C 493 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 518 removed outlier: 3.591A pdb=" N ALA C 515 " --> pdb=" O GLU C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 534 removed outlier: 3.618A pdb=" N THR C 531 " --> pdb=" O SER C 527 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL C 534 " --> pdb=" O ILE C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 557 removed outlier: 3.535A pdb=" N GLY C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 591 Processing helix chain 'C' and resid 629 through 633 Processing helix chain 'C' and resid 775 through 780 removed outlier: 3.507A pdb=" N LEU C 779 " --> pdb=" O PRO C 775 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG C 780 " --> pdb=" O PHE C 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 775 through 780' Processing helix chain 'C' and resid 792 through 797 Processing helix chain 'C' and resid 811 through 823 removed outlier: 3.636A pdb=" N ASN C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE C 817 " --> pdb=" O GLY C 813 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 818 " --> pdb=" O LEU C 814 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 819 " --> pdb=" O TYR C 815 " (cutoff:3.500A) Proline residue: C 820 - end of helix Processing helix chain 'C' and resid 843 through 851 removed outlier: 3.832A pdb=" N ALA C 849 " --> pdb=" O HIS C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 873 removed outlier: 4.252A pdb=" N LEU C 869 " --> pdb=" O ASN C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.107A pdb=" N SER C 890 " --> pdb=" O SER C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 898 removed outlier: 3.731A pdb=" N ALA C 897 " --> pdb=" O GLU C 893 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASP C 898 " --> pdb=" O ASP C 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 893 through 898' Processing helix chain 'C' and resid 898 through 912 removed outlier: 3.664A pdb=" N VAL C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 910 " --> pdb=" O GLN C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 930 removed outlier: 4.094A pdb=" N ARG C 928 " --> pdb=" O SER C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 953 removed outlier: 3.969A pdb=" N ALA C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C 946 " --> pdb=" O LEU C 942 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 973 through 975 No H-bonds generated for 'chain 'C' and resid 973 through 975' Processing helix chain 'C' and resid 976 through 985 removed outlier: 3.926A pdb=" N TYR C 980 " --> pdb=" O ASP C 976 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 983 " --> pdb=" O LEU C 979 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL C 984 " --> pdb=" O TYR C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 996 Processing helix chain 'C' and resid 1013 through 1017 Processing helix chain 'C' and resid 1021 through 1033 Processing helix chain 'C' and resid 1132 through 1142 removed outlier: 3.946A pdb=" N GLN C1136 " --> pdb=" O TRP C1132 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C1138 " --> pdb=" O SER C1134 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG C1142 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing helix chain 'C' and resid 1144 through 1161 Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.578A pdb=" N GLU D 94 " --> pdb=" O PHE D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 106 removed outlier: 3.517A pdb=" N LEU D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 136 removed outlier: 3.760A pdb=" N LEU D 113 " --> pdb=" O GLN D 109 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 114 " --> pdb=" O ARG D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 142 Processing helix chain 'D' and resid 164 through 169 removed outlier: 3.670A pdb=" N LEU D 168 " --> pdb=" O TRP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 198 removed outlier: 3.531A pdb=" N ALA D 178 " --> pdb=" O MET D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 209 through 225 removed outlier: 3.598A pdb=" N GLU D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 240 through 254 removed outlier: 4.086A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 293 removed outlier: 4.119A pdb=" N ILE D 273 " --> pdb=" O ASN D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 324 through 354 Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 364 through 369 removed outlier: 3.709A pdb=" N GLN D 369 " --> pdb=" O ARG D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 394 removed outlier: 3.520A pdb=" N ASN D 391 " --> pdb=" O MET D 387 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 400 removed outlier: 3.541A pdb=" N GLN D 400 " --> pdb=" O PRO D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 420 removed outlier: 4.133A pdb=" N ARG D 418 " --> pdb=" O VAL D 414 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL D 419 " --> pdb=" O GLN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 removed outlier: 3.876A pdb=" N ARG D 444 " --> pdb=" O GLN D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 482 removed outlier: 3.636A pdb=" N HIS D 469 " --> pdb=" O THR D 465 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR D 471 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 498 removed outlier: 3.504A pdb=" N ASN D 496 " --> pdb=" O LYS D 493 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 518 removed outlier: 3.589A pdb=" N ALA D 515 " --> pdb=" O GLU D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 534 removed outlier: 3.602A pdb=" N THR D 531 " --> pdb=" O SER D 527 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 534 " --> pdb=" O ILE D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 557 removed outlier: 3.567A pdb=" N GLY D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 591 Processing helix chain 'D' and resid 629 through 633 Processing helix chain 'D' and resid 775 through 780 removed outlier: 3.510A pdb=" N LEU D 779 " --> pdb=" O PRO D 775 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG D 780 " --> pdb=" O PHE D 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 775 through 780' Processing helix chain 'D' and resid 792 through 797 Processing helix chain 'D' and resid 811 through 823 removed outlier: 3.612A pdb=" N ASN D 816 " --> pdb=" O ASN D 812 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE D 817 " --> pdb=" O GLY D 813 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 818 " --> pdb=" O LEU D 814 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL D 819 " --> pdb=" O TYR D 815 " (cutoff:3.500A) Proline residue: D 820 - end of helix Processing helix chain 'D' and resid 843 through 851 removed outlier: 3.838A pdb=" N ALA D 849 " --> pdb=" O HIS D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 873 removed outlier: 4.219A pdb=" N LEU D 869 " --> pdb=" O ASN D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 891 removed outlier: 4.102A pdb=" N SER D 890 " --> pdb=" O SER D 887 " (cutoff:3.500A) Processing helix chain 'D' and resid 893 through 898 removed outlier: 3.733A pdb=" N ALA D 897 " --> pdb=" O GLU D 893 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP D 898 " --> pdb=" O ASP D 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 893 through 898' Processing helix chain 'D' and resid 898 through 912 removed outlier: 3.686A pdb=" N VAL D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG D 910 " --> pdb=" O GLN D 906 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 930 removed outlier: 4.108A pdb=" N ARG D 928 " --> pdb=" O SER D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 953 removed outlier: 3.969A pdb=" N ALA D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS D 944 " --> pdb=" O LEU D 940 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 946 " --> pdb=" O LEU D 942 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 948 " --> pdb=" O LYS D 944 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU D 949 " --> pdb=" O LEU D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 966 Processing helix chain 'D' and resid 971 through 975 Processing helix chain 'D' and resid 976 through 985 removed outlier: 3.921A pdb=" N TYR D 980 " --> pdb=" O ASP D 976 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE D 983 " --> pdb=" O LEU D 979 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL D 984 " --> pdb=" O TYR D 980 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 996 Processing helix chain 'D' and resid 1013 through 1017 Processing helix chain 'D' and resid 1021 through 1033 Processing helix chain 'D' and resid 1132 through 1142 removed outlier: 3.941A pdb=" N GLN D1136 " --> pdb=" O TRP D1132 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D1138 " --> pdb=" O SER D1134 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG D1142 " --> pdb=" O LEU D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1144 through 1161 Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 433 removed outlier: 6.227A pdb=" N VAL A 404 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU A 432 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE A 406 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A 374 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU A 407 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU A 376 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 456 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 487 " --> pdb=" O HIS A 505 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL A 507 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 489 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 560 through 565 removed outlier: 6.832A pdb=" N ILE A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU A 595 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 750 through 752 Processing sheet with id=AA5, first strand: chain 'A' and resid 856 through 860 removed outlier: 6.297A pdb=" N ILE A 834 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N MET A 859 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU A 836 " --> pdb=" O MET A 859 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE A 803 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 837 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 805 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 802 " --> pdb=" O ASN A 879 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL A 881 " --> pdb=" O LEU A 802 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 804 " --> pdb=" O VAL A 881 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 916 " --> pdb=" O ASP A 878 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 4.094A pdb=" N ASP A1194 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A1039 " --> pdb=" O TYR A1197 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE A1199 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 143 through 144 Processing sheet with id=AA8, first strand: chain 'B' and resid 429 through 433 removed outlier: 6.234A pdb=" N VAL B 404 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 432 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE B 406 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL B 374 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU B 407 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 376 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 456 " --> pdb=" O CYS B 377 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 487 " --> pdb=" O HIS B 505 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N VAL B 507 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 489 " --> pdb=" O VAL B 507 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 560 through 565 removed outlier: 6.866A pdb=" N ILE B 625 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU B 595 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 750 through 752 Processing sheet with id=AB2, first strand: chain 'B' and resid 856 through 860 removed outlier: 6.275A pdb=" N ILE B 834 " --> pdb=" O TYR B 857 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N MET B 859 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU B 836 " --> pdb=" O MET B 859 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE B 803 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU B 837 " --> pdb=" O ILE B 803 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 805 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU B 802 " --> pdb=" O ALA B 877 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN B 879 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 916 " --> pdb=" O ASP B 878 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N PHE B 970 " --> pdb=" O ILE B 917 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR B 919 " --> pdb=" O PHE B 970 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 4.129A pdb=" N ASP B1194 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY B1039 " --> pdb=" O TYR B1197 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B1199 " --> pdb=" O PRO B1037 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AB5, first strand: chain 'C' and resid 429 through 433 removed outlier: 6.226A pdb=" N VAL C 404 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU C 432 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE C 406 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL C 374 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU C 407 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU C 376 " --> pdb=" O LEU C 407 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU C 487 " --> pdb=" O HIS C 505 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N VAL C 507 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 489 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 560 through 565 removed outlier: 6.861A pdb=" N ILE C 625 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU C 595 " --> pdb=" O ILE C 625 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 750 through 752 Processing sheet with id=AB8, first strand: chain 'C' and resid 856 through 860 removed outlier: 6.271A pdb=" N ILE C 834 " --> pdb=" O TYR C 857 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N MET C 859 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU C 836 " --> pdb=" O MET C 859 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE C 803 " --> pdb=" O VAL C 835 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU C 837 " --> pdb=" O ILE C 803 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 805 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU C 802 " --> pdb=" O ALA C 877 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN C 879 " --> pdb=" O LEU C 802 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 916 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE C 970 " --> pdb=" O ILE C 917 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR C 919 " --> pdb=" O PHE C 970 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 4.112A pdb=" N ASP C1194 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY C1039 " --> pdb=" O TYR C1197 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE C1199 " --> pdb=" O PRO C1037 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 143 through 144 Processing sheet with id=AC2, first strand: chain 'D' and resid 429 through 433 removed outlier: 6.216A pdb=" N VAL D 404 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU D 432 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE D 406 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL D 374 " --> pdb=" O VAL D 405 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU D 407 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU D 376 " --> pdb=" O LEU D 407 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU D 487 " --> pdb=" O HIS D 505 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N VAL D 507 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL D 489 " --> pdb=" O VAL D 507 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.840A pdb=" N ILE D 625 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU D 595 " --> pdb=" O ILE D 625 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 750 through 752 Processing sheet with id=AC5, first strand: chain 'D' and resid 856 through 860 removed outlier: 6.291A pdb=" N ILE D 834 " --> pdb=" O TYR D 857 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N MET D 859 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU D 836 " --> pdb=" O MET D 859 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE D 803 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU D 837 " --> pdb=" O ILE D 803 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL D 805 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU D 802 " --> pdb=" O ASN D 879 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N VAL D 881 " --> pdb=" O LEU D 802 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE D 804 " --> pdb=" O VAL D 881 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER D 916 " --> pdb=" O ASP D 878 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1006 through 1012 removed outlier: 4.104A pdb=" N ASP D1194 " --> pdb=" O ILE D1012 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY D1039 " --> pdb=" O TYR D1197 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE D1199 " --> pdb=" O PRO D1037 " (cutoff:3.500A) 1217 hydrogen bonds defined for protein. 3384 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: 10.92 Time building geometry restraints manager: 12.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9201 1.34 - 1.46: 6777 1.46 - 1.58: 13562 1.58 - 1.70: 0 1.70 - 1.81: 304 Bond restraints: 29844 Sorted by residual: bond pdb=" CB PRO C 230 " pdb=" CG PRO C 230 " ideal model delta sigma weight residual 1.492 1.390 0.102 5.00e-02 4.00e+02 4.14e+00 bond pdb=" CA PRO C 229 " pdb=" C PRO C 229 " ideal model delta sigma weight residual 1.517 1.536 -0.019 9.30e-03 1.16e+04 4.13e+00 bond pdb=" CA ILE C 203 " pdb=" CB ILE C 203 " ideal model delta sigma weight residual 1.540 1.563 -0.023 1.36e-02 5.41e+03 2.88e+00 bond pdb=" CA ILE B 203 " pdb=" CB ILE B 203 " ideal model delta sigma weight residual 1.540 1.562 -0.022 1.36e-02 5.41e+03 2.61e+00 bond pdb=" CA ILE D 203 " pdb=" CB ILE D 203 " ideal model delta sigma weight residual 1.540 1.562 -0.022 1.36e-02 5.41e+03 2.61e+00 ... (remaining 29839 not shown) Histogram of bond angle deviations from ideal: 82.95 - 93.59: 8 93.59 - 104.23: 457 104.23 - 114.87: 18106 114.87 - 125.51: 21448 125.51 - 136.15: 481 Bond angle restraints: 40500 Sorted by residual: angle pdb=" N ARG D 172 " pdb=" CA ARG D 172 " pdb=" C ARG D 172 " ideal model delta sigma weight residual 109.79 82.95 26.84 1.56e+00 4.11e-01 2.96e+02 angle pdb=" N ARG A 172 " pdb=" CA ARG A 172 " pdb=" C ARG A 172 " ideal model delta sigma weight residual 109.79 83.15 26.64 1.56e+00 4.11e-01 2.92e+02 angle pdb=" N ARG B 172 " pdb=" CA ARG B 172 " pdb=" C ARG B 172 " ideal model delta sigma weight residual 109.79 83.30 26.49 1.56e+00 4.11e-01 2.88e+02 angle pdb=" N ARG C 172 " pdb=" CA ARG C 172 " pdb=" C ARG C 172 " ideal model delta sigma weight residual 109.79 83.31 26.48 1.56e+00 4.11e-01 2.88e+02 angle pdb=" N LYS C 173 " pdb=" CA LYS C 173 " pdb=" CB LYS C 173 " ideal model delta sigma weight residual 110.39 91.56 18.83 1.59e+00 3.96e-01 1.40e+02 ... (remaining 40495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 15553 17.94 - 35.89: 1825 35.89 - 53.83: 393 53.83 - 71.77: 65 71.77 - 89.71: 16 Dihedral angle restraints: 17852 sinusoidal: 7008 harmonic: 10844 Sorted by residual: dihedral pdb=" C ARG A 172 " pdb=" N ARG A 172 " pdb=" CA ARG A 172 " pdb=" CB ARG A 172 " ideal model delta harmonic sigma weight residual -122.60 -106.79 -15.81 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" C ARG B 172 " pdb=" N ARG B 172 " pdb=" CA ARG B 172 " pdb=" CB ARG B 172 " ideal model delta harmonic sigma weight residual -122.60 -106.79 -15.81 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" C ARG C 172 " pdb=" N ARG C 172 " pdb=" CA ARG C 172 " pdb=" CB ARG C 172 " ideal model delta harmonic sigma weight residual -122.60 -106.87 -15.73 0 2.50e+00 1.60e-01 3.96e+01 ... (remaining 17849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 4522 0.115 - 0.229: 73 0.229 - 0.344: 5 0.344 - 0.458: 6 0.458 - 0.573: 6 Chirality restraints: 4612 Sorted by residual: chirality pdb=" CA ILE B 203 " pdb=" N ILE B 203 " pdb=" C ILE B 203 " pdb=" CB ILE B 203 " both_signs ideal model delta sigma weight residual False 2.43 3.01 -0.57 2.00e-01 2.50e+01 8.20e+00 chirality pdb=" CA ARG A 172 " pdb=" N ARG A 172 " pdb=" C ARG A 172 " pdb=" CB ARG A 172 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" CA ARG B 172 " pdb=" N ARG B 172 " pdb=" C ARG B 172 " pdb=" CB ARG B 172 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 4609 not shown) Planarity restraints: 5088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C 228 " 0.076 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO C 229 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO C 229 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 229 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B1191 " 0.035 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO B1192 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B1192 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B1192 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C1191 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO C1192 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C1192 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C1192 " -0.029 5.00e-02 4.00e+02 ... (remaining 5085 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.63: 385 2.63 - 3.26: 30062 3.26 - 3.88: 55919 3.88 - 4.51: 77382 4.51 - 5.14: 123735 Nonbonded interactions: 287483 Sorted by model distance: nonbonded pdb=" N ARG D 172 " pdb=" O ARG D 172 " model vdw 2.000 2.496 nonbonded pdb=" N ARG A 172 " pdb=" O ARG A 172 " model vdw 2.005 2.496 nonbonded pdb=" N ARG C 172 " pdb=" O ARG C 172 " model vdw 2.006 2.496 nonbonded pdb=" N ARG B 172 " pdb=" O ARG B 172 " model vdw 2.008 2.496 nonbonded pdb=" OD2 ASP C 468 " pdb=" ND2 ASN C 496 " model vdw 2.055 3.120 ... (remaining 287478 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 85 through 1205) selection = (chain 'B' and resid 85 through 1205) selection = (chain 'C' and resid 85 through 1205) selection = (chain 'D' and resid 85 through 1205) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 1.220 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 82.600 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.120 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.003 0.102 29844 Z= 0.186 Angle : 0.768 26.841 40500 Z= 0.427 Chirality : 0.049 0.573 4612 Planarity : 0.004 0.106 5088 Dihedral : 15.768 89.714 10828 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.09 % Allowed : 22.31 % Favored : 77.59 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.13), residues: 3632 helix: -1.67 (0.12), residues: 1636 sheet: -1.42 (0.26), residues: 396 loop : -0.45 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 177 HIS 0.004 0.001 HIS C 586 PHE 0.025 0.001 PHE D 932 TYR 0.025 0.001 TYR A 130 ARG 0.009 0.001 ARG A 828 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 560 time to evaluate : 3.325 Fit side-chains revert: symmetry clash REVERT: A 163 ASN cc_start: 0.8099 (m110) cc_final: 0.7328 (p0) REVERT: A 232 ARG cc_start: 0.6242 (mtt90) cc_final: 0.5994 (mmt90) REVERT: A 426 SER cc_start: 0.8059 (t) cc_final: 0.7592 (m) REVERT: A 576 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7714 (tp30) REVERT: A 876 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.5526 (p90) REVERT: A 909 PHE cc_start: 0.8291 (t80) cc_final: 0.7337 (m-80) REVERT: A 1020 ARG cc_start: 0.7803 (mtm110) cc_final: 0.7218 (ptp-170) REVERT: B 388 ASP cc_start: 0.7727 (m-30) cc_final: 0.7445 (m-30) REVERT: B 909 PHE cc_start: 0.8233 (t80) cc_final: 0.7294 (m-80) REVERT: B 1020 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7512 (mtm110) REVERT: C 163 ASN cc_start: 0.7807 (m-40) cc_final: 0.7182 (p0) REVERT: C 176 LEU cc_start: 0.8163 (mt) cc_final: 0.7960 (mm) REVERT: C 426 SER cc_start: 0.8031 (t) cc_final: 0.7560 (m) REVERT: C 576 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7730 (tp30) REVERT: C 792 ASP cc_start: 0.7633 (p0) cc_final: 0.7214 (p0) REVERT: C 909 PHE cc_start: 0.8238 (t80) cc_final: 0.7332 (m-10) REVERT: C 1020 ARG cc_start: 0.7806 (mtm110) cc_final: 0.7481 (mtm110) REVERT: D 174 MET cc_start: 0.7954 (pmm) cc_final: 0.6515 (mpp) REVERT: D 177 TRP cc_start: 0.8388 (t60) cc_final: 0.8081 (t60) REVERT: D 426 SER cc_start: 0.8076 (t) cc_final: 0.7610 (m) REVERT: D 794 LYS cc_start: 0.7652 (tptt) cc_final: 0.7450 (tptt) REVERT: D 909 PHE cc_start: 0.8040 (t80) cc_final: 0.7490 (m-80) REVERT: D 1020 ARG cc_start: 0.7807 (mtm110) cc_final: 0.7484 (mtm110) outliers start: 3 outliers final: 1 residues processed: 561 average time/residue: 0.4331 time to fit residues: 375.4001 Evaluate side-chains 525 residues out of total 3312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 523 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 1045 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.6126 > 50: distance: 4 - 30: 3.804 distance: 21 - 30: 5.366 distance: 22 - 55: 6.159 distance: 30 - 31: 7.390 distance: 31 - 32: 7.439 distance: 31 - 34: 5.037 distance: 32 - 33: 10.229 distance: 33 - 66: 19.918 distance: 35 - 36: 6.345 distance: 35 - 37: 5.869 distance: 38 - 39: 7.770 distance: 39 - 40: 6.821 distance: 39 - 42: 5.742 distance: 40 - 41: 15.654 distance: 40 - 46: 5.287 distance: 43 - 44: 3.683 distance: 43 - 45: 3.411 distance: 46 - 47: 16.450 distance: 47 - 48: 5.717 distance: 47 - 50: 4.817 distance: 48 - 49: 6.460 distance: 48 - 55: 5.187 distance: 50 - 51: 9.669 distance: 51 - 52: 11.248 distance: 52 - 53: 6.078 distance: 52 - 54: 4.188 distance: 55 - 56: 5.001 distance: 56 - 59: 7.301 distance: 57 - 58: 6.038 distance: 57 - 66: 4.958 distance: 59 - 60: 5.636 distance: 60 - 61: 4.992 distance: 60 - 62: 3.957 distance: 61 - 63: 4.241 distance: 62 - 64: 4.395 distance: 63 - 65: 4.928 distance: 64 - 65: 5.894 distance: 66 - 67: 9.672 distance: 67 - 68: 4.519 distance: 67 - 70: 5.672 distance: 68 - 69: 16.823 distance: 68 - 78: 13.783 distance: 70 - 71: 3.324 distance: 71 - 72: 7.504 distance: 71 - 73: 3.806 distance: 72 - 74: 3.363 distance: 74 - 76: 5.553 distance: 75 - 76: 6.753 distance: 78 - 79: 8.682 distance: 79 - 80: 6.872 distance: 79 - 82: 13.075 distance: 80 - 81: 6.094 distance: 80 - 83: 8.182 distance: 83 - 84: 6.656 distance: 84 - 85: 5.687 distance: 84 - 87: 6.447 distance: 85 - 86: 19.023 distance: 85 - 93: 7.146 distance: 86 - 111: 24.755 distance: 87 - 88: 8.292 distance: 88 - 89: 4.997 distance: 88 - 90: 13.150 distance: 89 - 91: 13.621 distance: 90 - 92: 8.316 distance: 91 - 92: 9.163 distance: 93 - 94: 11.480 distance: 93 - 99: 27.553 distance: 94 - 95: 20.579 distance: 94 - 97: 18.853 distance: 95 - 96: 9.730 distance: 95 - 100: 9.442 distance: 97 - 98: 23.760 distance: 98 - 99: 24.020 distance: 100 - 101: 11.830 distance: 101 - 102: 9.991 distance: 101 - 104: 5.619 distance: 102 - 103: 12.641 distance: 102 - 111: 9.381 distance: 104 - 105: 10.760 distance: 105 - 106: 24.548 distance: 106 - 107: 9.441 distance: 107 - 108: 14.777 distance: 108 - 109: 16.890 distance: 108 - 110: 15.701 distance: 111 - 112: 8.474 distance: 112 - 113: 11.644 distance: 112 - 115: 6.816 distance: 113 - 114: 4.630 distance: 113 - 119: 5.821 distance: 115 - 116: 14.103 distance: 116 - 117: 12.313 distance: 116 - 118: 11.598 distance: 200 - 208: 3.049