Starting phenix.real_space_refine on Wed Mar 20 02:23:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypa_33997/03_2024/7ypa_33997.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypa_33997/03_2024/7ypa_33997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypa_33997/03_2024/7ypa_33997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypa_33997/03_2024/7ypa_33997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypa_33997/03_2024/7ypa_33997.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypa_33997/03_2024/7ypa_33997.pdb" } resolution = 3.05 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= 0.000 sd= 0.006 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 Zn 2 6.06 5 P 83 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 16044 2.51 5 N 4596 2.21 5 O 5191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 15": "OD1" <-> "OD2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A ASP 118": "OD1" <-> "OD2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A ASP 197": "OD1" <-> "OD2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "B ASP 135": "OD1" <-> "OD2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ARG 218": "NH1" <-> "NH2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ASP 189": "OD1" <-> "OD2" Residue "C ASP 192": "OD1" <-> "OD2" Residue "C ASP 234": "OD1" <-> "OD2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 349": "OE1" <-> "OE2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C ASP 396": "OD1" <-> "OD2" Residue "C ASP 434": "OD1" <-> "OD2" Residue "C GLU 441": "OE1" <-> "OE2" Residue "C ASP 444": "OD1" <-> "OD2" Residue "C GLU 541": "OE1" <-> "OE2" Residue "C ARG 542": "NH1" <-> "NH2" Residue "C ASP 549": "OD1" <-> "OD2" Residue "C TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C ASP 601": "OD1" <-> "OD2" Residue "C TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 624": "OD1" <-> "OD2" Residue "C GLU 625": "OE1" <-> "OE2" Residue "C ASP 632": "OD1" <-> "OD2" Residue "C PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 675": "OD1" <-> "OD2" Residue "C ASP 696": "OD1" <-> "OD2" Residue "C GLU 745": "OE1" <-> "OE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 775": "OE1" <-> "OE2" Residue "C PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 814": "OD1" <-> "OD2" Residue "C ARG 821": "NH1" <-> "NH2" Residue "C GLU 849": "OE1" <-> "OE2" Residue "C ASP 853": "OD1" <-> "OD2" Residue "C ASP 881": "OD1" <-> "OD2" Residue "C ASP 930": "OD1" <-> "OD2" Residue "C ARG 936": "NH1" <-> "NH2" Residue "C GLU 950": "OE1" <-> "OE2" Residue "C GLU 962": "OE1" <-> "OE2" Residue "C PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1012": "OE1" <-> "OE2" Residue "C GLU 1024": "OE1" <-> "OE2" Residue "C GLU 1030": "OE1" <-> "OE2" Residue "C ARG 1034": "NH1" <-> "NH2" Residue "C ASP 1040": "OD1" <-> "OD2" Residue "C ASP 1095": "OD1" <-> "OD2" Residue "C GLU 1137": "OE1" <-> "OE2" Residue "C ASP 1150": "OD1" <-> "OD2" Residue "C ASP 1160": "OD1" <-> "OD2" Residue "C GLU 1174": "OE1" <-> "OE2" Residue "C GLU 1192": "OE1" <-> "OE2" Residue "C ASP 1203": "OD1" <-> "OD2" Residue "C ASP 1297": "OD1" <-> "OD2" Residue "C GLU 1316": "OE1" <-> "OE2" Residue "C GLU 1329": "OE1" <-> "OE2" Residue "C GLU 1338": "OE1" <-> "OE2" Residue "C ASP 1341": "OD1" <-> "OD2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "D PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 177": "OD1" <-> "OD2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 289": "OD1" <-> "OD2" Residue "D GLU 301": "OE1" <-> "OE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D GLU 663": "OE1" <-> "OE2" Residue "D GLU 666": "OE1" <-> "OE2" Residue "D ASP 684": "OD1" <-> "OD2" Residue "D ASP 691": "OD1" <-> "OD2" Residue "D ASP 699": "OD1" <-> "OD2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D ASP 751": "OD1" <-> "OD2" Residue "D ASP 802": "OD1" <-> "OD2" Residue "D ASP 806": "OD1" <-> "OD2" Residue "D ASP 812": "OD1" <-> "OD2" Residue "D ASP 830": "OD1" <-> "OD2" Residue "D GLU 833": "OE1" <-> "OE2" Residue "D ASP 837": "OD1" <-> "OD2" Residue "D ASP 878": "OD1" <-> "OD2" Residue "D ASP 889": "OD1" <-> "OD2" Residue "D ASP 891": "OD1" <-> "OD2" Residue "D ARG 978": "NH1" <-> "NH2" Residue "D GLU 981": "OE1" <-> "OE2" Residue "D ASP 986": "OD1" <-> "OD2" Residue "D GLU 993": "OE1" <-> "OE2" Residue "D ASP 1021": "OD1" <-> "OD2" Residue "D ASP 1039": "OD1" <-> "OD2" Residue "D ASP 1042": "OD1" <-> "OD2" Residue "D ASP 1073": "OD1" <-> "OD2" Residue "D ASP 1082": "OD1" <-> "OD2" Residue "D ASP 1094": "OD1" <-> "OD2" Residue "D PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1119": "OD1" <-> "OD2" Residue "D GLU 1158": "OE1" <-> "OE2" Residue "D PHE 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1168": "OE1" <-> "OE2" Residue "D GLU 1187": "OE1" <-> "OE2" Residue "D ASP 1212": "OD1" <-> "OD2" Residue "D ASP 1273": "OD1" <-> "OD2" Residue "D GLU 1293": "OE1" <-> "OE2" Residue "D TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1345": "NH1" <-> "NH2" Residue "E ASP 18": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26022 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1663 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1655 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 10060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10060 Classifications: {'peptide': 1285} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1231} Chain breaks: 3 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 64 Chain: "D" Number of atoms: 10269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 10269 Classifications: {'peptide': 1333} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1277} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "E" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 591 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "F" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 577 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "G" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 580 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 416 Classifications: {'RNA': 20} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 13} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "I" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 208 Classifications: {'RNA': 10} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13795 SG CYS D 72 112.384 48.935 61.085 1.00 68.58 S ATOM 13892 SG CYS D 85 115.189 49.139 63.467 1.00 72.91 S ATOM 13912 SG CYS D 88 112.079 51.998 63.043 1.00 76.43 S ATOM 19579 SG CYS D 814 87.667 67.919 125.063 1.00 37.98 S ATOM 20144 SG CYS D 888 86.105 68.261 121.576 1.00 29.67 S ATOM 20195 SG CYS D 895 84.867 65.130 123.142 1.00 23.03 S ATOM 20216 SG CYS D 898 83.072 68.255 123.998 1.00 21.40 S Time building chain proxies: 14.02, per 1000 atoms: 0.54 Number of scatterers: 26022 At special positions: 0 Unit cell: (135.928, 160.761, 164.682, 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 2 29.99 S 105 16.00 P 83 15.00 Mg 1 11.99 O 5191 8.00 N 4596 7.00 C 16044 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: 9.13 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " Number of angles added : 6 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5776 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 45 sheets defined 36.2% alpha, 17.4% beta 36 base pairs and 65 stacking pairs defined. Time for finding SS restraints: 8.52 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.865A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.889A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 234 removed outlier: 4.643A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.769A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.748A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 227 removed outlier: 3.773A pdb=" N GLN B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.744A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.952A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.560A pdb=" N GLN C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 removed outlier: 4.186A pdb=" N SER C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 167' Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.553A pdb=" N ASP C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 295 removed outlier: 3.624A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.654A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.537A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.660A pdb=" N LEU C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 removed outlier: 3.616A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.631A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.517A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.668A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.861A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.899A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.752A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 664 through 668' Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.530A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 942 through 980 removed outlier: 4.232A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1037 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.156A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.706A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 4.023A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.530A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.858A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.726A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.889A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.794A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.537A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.540A pdb=" N TYR D 165 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.726A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 207 removed outlier: 3.799A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.543A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.673A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.806A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 415 removed outlier: 3.984A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 573 through 581 removed outlier: 3.697A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 612 Processing helix chain 'D' and resid 614 through 632 removed outlier: 3.525A pdb=" N VAL D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.615A pdb=" N GLY D 671 " --> pdb=" O GLN D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.499A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.615A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 Processing helix chain 'D' and resid 865 through 874 removed outlier: 3.757A pdb=" N GLU D 874 " --> pdb=" O ASP D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.770A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 removed outlier: 3.615A pdb=" N LEU D 930 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1072 removed outlier: 3.699A pdb=" N GLY D1071 " --> pdb=" O THR D1068 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS D1072 " --> pdb=" O ALA D1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1068 through 1072' Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.839A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.659A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1310 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.619A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.697A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1370 removed outlier: 3.708A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.683A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 32 removed outlier: 3.930A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 75 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 8.998A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.153A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLY A 151 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.153A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 151 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.898A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 16 removed outlier: 3.524A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 105 removed outlier: 3.711A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 171 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.843A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 133 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.814A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.595A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.559A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 118 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.635A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.502A pdb=" N GLN C 148 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 159 removed outlier: 3.680A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 240 removed outlier: 3.687A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 257 removed outlier: 4.351A pdb=" N VAL C 263 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA C 257 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.426A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.375A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.915A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.676A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.145A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 841 removed outlier: 4.322A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.807A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD6, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.616A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 removed outlier: 3.622A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.711A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 707 through 708 removed outlier: 3.752A pdb=" N ILE D 707 " --> pdb=" O GLU D 714 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'D' and resid 848 through 849 removed outlier: 7.235A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 857 " --> pdb=" O VAL D 848 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 949 through 951 removed outlier: 4.663A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 991 through 996 removed outlier: 3.831A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1034 through 1038 removed outlier: 3.746A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1046 through 1048 removed outlier: 3.836A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1188 through 1190 removed outlier: 3.711A pdb=" N GLU D1188 " --> pdb=" O LEU D1175 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D1175 " --> pdb=" O GLU D1188 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.844A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 949 hydrogen bonds defined for protein. 2703 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 65 stacking parallelities Total time for adding SS restraints: 13.18 Time building geometry restraints manager: 9.88 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: 7678 1.34 - 1.45: 4121 1.45 - 1.57: 14441 1.57 - 1.69: 165 1.69 - 1.81: 182 Bond restraints: 26587 Sorted by residual: bond pdb=" C3' DC G -7 " pdb=" O3' DC G -7 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.83e+00 bond pdb=" C ALA D 426 " pdb=" N PRO D 427 " ideal model delta sigma weight residual 1.334 1.377 -0.044 2.34e-02 1.83e+03 3.47e+00 bond pdb=" C GLU A 29 " pdb=" N PRO A 30 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.36e+00 bond pdb=" CA LEU D1261 " pdb=" CB LEU D1261 " ideal model delta sigma weight residual 1.526 1.553 -0.026 1.53e-02 4.27e+03 2.99e+00 bond pdb=" C3' DA F 11 " pdb=" O3' DA F 11 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 2.95e+00 ... (remaining 26582 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.43: 1161 106.43 - 113.34: 14582 113.34 - 120.26: 9714 120.26 - 127.18: 10496 127.18 - 134.09: 371 Bond angle restraints: 36324 Sorted by residual: angle pdb=" C ASP D 902 " pdb=" N LEU D 903 " pdb=" CA LEU D 903 " ideal model delta sigma weight residual 121.54 129.08 -7.54 1.91e+00 2.74e-01 1.56e+01 angle pdb=" C THR D 703 " pdb=" N GLU D 704 " pdb=" CA GLU D 704 " ideal model delta sigma weight residual 122.08 127.24 -5.16 1.47e+00 4.63e-01 1.23e+01 angle pdb=" C GLY D 73 " pdb=" N LYS D 74 " pdb=" CA LYS D 74 " ideal model delta sigma weight residual 125.02 131.08 -6.06 1.76e+00 3.23e-01 1.19e+01 angle pdb=" C ARG A 191 " pdb=" N VAL A 192 " pdb=" CA VAL A 192 " ideal model delta sigma weight residual 121.54 127.00 -5.46 1.64e+00 3.72e-01 1.11e+01 angle pdb=" C3' DC G -7 " pdb=" O3' DC G -7 " pdb=" P DG G -6 " ideal model delta sigma weight residual 120.20 124.86 -4.66 1.50e+00 4.44e-01 9.67e+00 ... (remaining 36319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 15715 35.19 - 70.39: 477 70.39 - 105.58: 39 105.58 - 140.78: 1 140.78 - 175.97: 3 Dihedral angle restraints: 16235 sinusoidal: 7259 harmonic: 8976 Sorted by residual: dihedral pdb=" C4' DC G -7 " pdb=" C3' DC G -7 " pdb=" O3' DC G -7 " pdb=" P DG G -6 " ideal model delta sinusoidal sigma weight residual -140.00 35.97 -175.97 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA F -1 " pdb=" C3' DA F -1 " pdb=" O3' DA F -1 " pdb=" P DA F 0 " ideal model delta sinusoidal sigma weight residual 220.00 76.80 143.20 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" C4' DA F 11 " pdb=" C3' DA F 11 " pdb=" O3' DA F 11 " pdb=" P DC F 12 " ideal model delta sinusoidal sigma weight residual -140.00 3.12 -143.12 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 16232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3257 0.046 - 0.092: 673 0.092 - 0.138: 244 0.138 - 0.185: 28 0.185 - 0.231: 4 Chirality restraints: 4206 Sorted by residual: chirality pdb=" CB ILE E 13 " pdb=" CA ILE E 13 " pdb=" CG1 ILE E 13 " pdb=" CG2 ILE E 13 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" P DC F 12 " pdb=" OP1 DC F 12 " pdb=" OP2 DC F 12 " pdb=" O5' DC F 12 " both_signs ideal model delta sigma weight residual True 2.35 -2.56 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB ILE C 232 " pdb=" CA ILE C 232 " pdb=" CG1 ILE C 232 " pdb=" CG2 ILE C 232 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 4203 not shown) Planarity restraints: 4441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 189 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO C 190 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 212 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO B 213 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 245 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO D 246 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 246 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 246 " 0.028 5.00e-02 4.00e+02 ... (remaining 4438 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1432 2.73 - 3.27: 22578 3.27 - 3.82: 41563 3.82 - 4.36: 49680 4.36 - 4.90: 85978 Nonbonded interactions: 201231 Sorted by model distance: nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.191 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.226 2.170 nonbonded pdb=" O GLY D 613 " pdb=" OG1 THR D 617 " model vdw 2.298 2.440 nonbonded pdb=" O PHE C 804 " pdb=" OG SER D 638 " model vdw 2.307 2.440 nonbonded pdb=" O SER D1064 " pdb=" OG SER D1064 " model vdw 2.321 2.440 ... (remaining 201226 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 7 through 66 or (resid 67 and (name N or name CA or name C \ or name O or name CB )) or resid 68 through 117 or (resid 118 and (name N or na \ me CA or name C or name O or name CB )) or resid 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB )) or resid 121 through 157 or (resid 1 \ 70 and (name N or name CA or name C or name O or name CB )) or resid 171 through \ 192 or (resid 193 through 194 and (name N or name CA or name C or name O or nam \ e CB )) or resid 195 through 232)) selection = (chain 'B' and (resid 7 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 92 or (resid 93 and (name N or name \ CA or name C or name O or name CB )) or resid 94 through 157 or resid 170 throu \ gh 190 or (resid 191 and (name N or name CA or name C or name O or name CB )) or \ resid 192 through 232)) } 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: 1.130 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: 0.020 Extract box with map and model: 4.690 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 77.900 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 0.059 26587 Z= 0.174 Angle : 0.587 10.586 36324 Z= 0.337 Chirality : 0.044 0.231 4206 Planarity : 0.005 0.057 4441 Dihedral : 15.656 175.971 10459 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -3.59 (0.11), residues: 3105 helix: -2.51 (0.10), residues: 1032 sheet: -1.45 (0.25), residues: 391 loop : -2.57 (0.12), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 807 HIS 0.003 0.000 HIS D 777 PHE 0.010 0.001 PHE C 514 TYR 0.019 0.001 TYR B 68 ARG 0.002 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 500 time to evaluate : 2.737 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PRO C 847 " (corrupted residue). Skipping it. Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable