Starting phenix.real_space_refine on Fri Aug 9 22:30:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwe_26830/08_2024/7uwe_26830.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwe_26830/08_2024/7uwe_26830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwe_26830/08_2024/7uwe_26830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwe_26830/08_2024/7uwe_26830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwe_26830/08_2024/7uwe_26830.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwe_26830/08_2024/7uwe_26830.cif" } resolution = 2.9 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= 0.002 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 55 5.49 5 Mg 1 5.21 5 S 112 5.16 5 C 16965 2.51 5 N 4844 2.21 5 O 5348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G ASP 96": "OD1" <-> "OD2" Residue "G GLU 122": "OE1" <-> "OE2" Residue "G ASP 174": "OD1" <-> "OD2" Residue "G GLU 181": "OE1" <-> "OE2" Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H ASP 114": "OD1" <-> "OD2" Residue "H ASP 199": "OD1" <-> "OD2" Residue "H GLU 206": "OE1" <-> "OE2" Residue "I TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 7": "OE1" <-> "OE2" Residue "I TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 67": "OE1" <-> "OE2" Residue "I TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 189": "OD1" <-> "OD2" Residue "I ASP 192": "OD1" <-> "OD2" Residue "I PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 412": "OE1" <-> "OE2" Residue "I GLU 413": "OE1" <-> "OE2" Residue "I GLU 415": "OE1" <-> "OE2" Residue "I GLU 441": "OE1" <-> "OE2" Residue "I GLU 472": "OE1" <-> "OE2" Residue "I ASP 483": "OD1" <-> "OD2" Residue "I PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 546": "OE1" <-> "OE2" Residue "I TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 562": "OE1" <-> "OE2" Residue "I TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 641": "OE1" <-> "OE2" Residue "I ASP 674": "OD1" <-> "OD2" Residue "I ASP 675": "OD1" <-> "OD2" Residue "I GLU 738": "OE1" <-> "OE2" Residue "I TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 781": "OD1" <-> "OD2" Residue "I PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 876": "OE1" <-> "OE2" Residue "I ASP 930": "OD1" <-> "OD2" Residue "I GLU 1083": "OE1" <-> "OE2" Residue "I TYR 1087": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1088": "OD1" <-> "OD2" Residue "I ASP 1126": "OD1" <-> "OD2" Residue "I GLU 1143": "OE1" <-> "OE2" Residue "I PHE 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1166": "OD1" <-> "OD2" Residue "I ARG 1171": "NH1" <-> "NH2" Residue "I PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1188": "OD1" <-> "OD2" Residue "I GLU 1194": "OE1" <-> "OE2" Residue "I TYR 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1241": "OD1" <-> "OD2" Residue "I GLU 1274": "OE1" <-> "OE2" Residue "I GLU 1279": "OE1" <-> "OE2" Residue "I ASP 1297": "OD1" <-> "OD2" Residue "I GLU 1329": "OE1" <-> "OE2" Residue "I GLU 1340": "OE1" <-> "OE2" Residue "J PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 199": "OE1" <-> "OE2" Residue "J GLU 204": "OE1" <-> "OE2" Residue "J GLU 295": "OE1" <-> "OE2" Residue "J ASP 308": "OD1" <-> "OD2" Residue "J GLU 532": "OE1" <-> "OE2" Residue "J GLU 534": "OE1" <-> "OE2" Residue "J GLU 554": "OE1" <-> "OE2" Residue "J TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 562": "OE1" <-> "OE2" Residue "J TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 658": "OE1" <-> "OE2" Residue "J GLU 713": "OE1" <-> "OE2" Residue "J PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 756": "OE1" <-> "OE2" Residue "J PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 813": "OD1" <-> "OD2" Residue "J ASP 830": "OD1" <-> "OD2" Residue "J GLU 833": "OE1" <-> "OE2" Residue "J GLU 846": "OE1" <-> "OE2" Residue "J PHE 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 987": "OE1" <-> "OE2" Residue "J TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 1146": "OE1" <-> "OE2" Residue "J GLU 1152": "OE1" <-> "OE2" Residue "J GLU 1168": "OE1" <-> "OE2" Residue "J GLU 1187": "OE1" <-> "OE2" Residue "J ASP 1212": "OD1" <-> "OD2" Residue "J GLU 1236": "OE1" <-> "OE2" Residue "J GLU 1254": "OE1" <-> "OE2" Residue "J PHE 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 1305": "OD1" <-> "OD2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K GLU 71": "OE1" <-> "OE2" Residue "C TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27327 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "B" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 520 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "G" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1698 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "H" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Chain: "I" Number of atoms: 10407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10407 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 Chain: "J" Number of atoms: 10352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 10352 Classifications: {'peptide': 1330} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1274} Chain breaks: 3 Chain: "K" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "C" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1448 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 13, 'TRANS': 175} Chain: "J" 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 15391 SG CYS J 70 106.631 75.891 26.167 1.00 58.13 S ATOM 15405 SG CYS J 72 106.235 75.954 22.858 1.00 59.71 S ATOM 21225 SG CYS J 814 108.267 87.899 93.260 1.00 22.17 S ATOM 21790 SG CYS J 888 105.934 87.832 90.203 1.00 15.87 S ATOM 21841 SG CYS J 895 107.042 84.581 91.826 1.00 10.26 S ATOM 21862 SG CYS J 898 104.698 86.683 93.680 1.00 10.05 S Time building chain proxies: 14.36, per 1000 atoms: 0.53 Number of scatterers: 27327 At special positions: 0 Unit cell: (142.284, 165.288, 148.248, 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 112 16.00 P 55 15.00 Mg 1 11.99 O 5348 8.00 N 4844 7.00 C 16965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.88 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 6 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6186 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 50 sheets defined 38.2% alpha, 15.6% beta 11 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 9.70 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 159 removed outlier: 3.979A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 228 Processing helix chain 'G' and resid 229 through 231 No H-bonds generated for 'chain 'G' and resid 229 through 231' Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.787A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 226 removed outlier: 3.543A pdb=" N ALA H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.518A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.640A pdb=" N LEU I 213 " --> pdb=" O ILE I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 219 through 224 removed outlier: 4.268A pdb=" N LEU I 223 " --> pdb=" O GLN I 219 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE I 224 " --> pdb=" O ILE I 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 219 through 224' Processing helix chain 'I' and resid 242 through 247 removed outlier: 4.393A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 288 through 293 removed outlier: 4.230A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 293' Processing helix chain 'I' and resid 318 through 328 removed outlier: 3.952A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 removed outlier: 3.604A pdb=" N ALA I 362 " --> pdb=" O ASP I 358 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 387 Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 480 Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.630A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 544 through 549 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.864A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 607 through 614 removed outlier: 3.901A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 688 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 826 Processing helix chain 'I' and resid 858 through 863 Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 985 through 990 removed outlier: 4.194A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 4.145A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.311A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.936A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1138 through 1151 Processing helix chain 'I' and resid 1165 through 1176 removed outlier: 3.510A pdb=" N LEU I1172 " --> pdb=" O GLU I1168 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA I1173 " --> pdb=" O VAL I1169 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU I1174 " --> pdb=" O MET I1170 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN I1175 " --> pdb=" O ARG I1171 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU I1176 " --> pdb=" O LEU I1172 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.813A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 96 through 101 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 139 removed outlier: 3.508A pdb=" N ARG J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU J 139 " --> pdb=" O ILE J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 169 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 194 through 204 Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.704A pdb=" N LEU J 223 " --> pdb=" O LYS J 219 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 285 removed outlier: 4.497A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP J 284 " --> pdb=" O LYS J 280 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU J 285 " --> pdb=" O ARG J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 326 through 332 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 removed outlier: 3.893A pdb=" N ALA J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 417 removed outlier: 4.353A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 540 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 589 through 593 removed outlier: 3.557A pdb=" N VAL J 592 " --> pdb=" O TYR J 589 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 640 through 644 Processing helix chain 'J' and resid 649 through 671 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 737 through 742 removed outlier: 3.877A pdb=" N ALA J 741 " --> pdb=" O ILE J 737 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 773 Processing helix chain 'J' and resid 775 through 789 removed outlier: 3.788A pdb=" N ALA J 779 " --> pdb=" O SER J 775 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG J 780 " --> pdb=" O THR J 776 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA J 787 " --> pdb=" O LEU J 783 " (cutoff:3.500A) Processing helix chain 'J' and resid 789 through 802 Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.535A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 915 through 925 Processing helix chain 'J' and resid 1068 through 1074 removed outlier: 3.620A pdb=" N LYS J1072 " --> pdb=" O THR J1068 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU J1074 " --> pdb=" O GLY J1070 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 1068 through 1074' Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.370A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.561A pdb=" N GLU J1291 " --> pdb=" O ILE J1287 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1319 through 1325 Processing helix chain 'J' and resid 1328 through 1339 Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1362 through 1373 removed outlier: 3.562A pdb=" N HIS J1366 " --> pdb=" O GLY J1362 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 33 removed outlier: 4.150A pdb=" N GLY K 33 " --> pdb=" O GLN K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 60 through 74 Processing helix chain 'C' and resid 50 through 65 removed outlier: 3.805A pdb=" N GLU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 97 removed outlier: 7.062A pdb=" N ILE C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N LEU C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HIS C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 129 through 154 removed outlier: 3.543A pdb=" N VAL C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 158 through 163 removed outlier: 3.510A pdb=" N HIS C 162 " --> pdb=" O GLY C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 178 Processing helix chain 'C' and resid 187 through 194 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.720A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.655A pdb=" N VAL G 153 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 104 removed outlier: 6.352A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.587A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 12 through 18 removed outlier: 5.690A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR H 27 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 101 removed outlier: 4.012A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 91 removed outlier: 3.524A pdb=" N ARG H 91 " --> pdb=" O GLU H 122 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU H 122 " --> pdb=" O ARG H 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB1, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AB2, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.812A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 59 through 60 removed outlier: 4.683A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET I 124 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN I 120 " --> pdb=" O LEU I 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 137 removed outlier: 3.532A pdb=" N VAL I 144 " --> pdb=" O GLN I 513 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN I 513 " --> pdb=" O VAL I 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 451 through 453 removed outlier: 6.241A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.671A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 180 through 181 Processing sheet with id=AB9, first strand: chain 'I' and resid 284 through 285 removed outlier: 3.526A pdb=" N ILE I 285 " --> pdb=" O MET I 239 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 249 through 250 removed outlier: 4.317A pdb=" N GLU I 249 " --> pdb=" O ILE I 269 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.869A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.715A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 removed outlier: 6.928A pdb=" N LEU I 587 " --> pdb=" O LEU I 606 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU I 606 " --> pdb=" O LEU I 587 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR I 589 " --> pdb=" O HIS I 604 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N HIS I 604 " --> pdb=" O THR I 589 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR I 591 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU I 602 " --> pdb=" O TYR I 591 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS I 593 " --> pdb=" O THR I 600 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.610A pdb=" N ASP I 654 " --> pdb=" O ALA I 617 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 634 through 637 removed outlier: 3.593A pdb=" N VAL I 634 " --> pdb=" O PHE I 645 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 717 through 718 removed outlier: 3.800A pdb=" N ASP I 781 " --> pdb=" O ALA I 718 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.540A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AD1, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AD2, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AD3, first strand: chain 'I' and resid 1066 through 1067 removed outlier: 4.544A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 1066 through 1067 Processing sheet with id=AD5, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.830A pdb=" N GLY I 846 " --> pdb=" O THR I 843 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR I 843 " --> pdb=" O GLY I 846 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.135A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 887 through 888 Processing sheet with id=AD8, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.555A pdb=" N SER J 353 " --> pdb=" O MET J 466 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AE1, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AE2, first strand: chain 'I' and resid 1335 through 1338 Processing sheet with id=AE3, first strand: chain 'J' and resid 34 through 37 removed outlier: 5.011A pdb=" N SER J 34 " --> pdb=" O MET J 102 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N HIS J 104 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLY J 36 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N GLU J 106 " --> pdb=" O GLY J 36 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 526 through 527 removed outlier: 3.562A pdb=" N LEU J 527 " --> pdb=" O LYS J 549 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG J 551 " --> pdb=" O LEU J 527 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR J 572 " --> pdb=" O VAL J 548 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL J 550 " --> pdb=" O LYS J 570 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS J 570 " --> pdb=" O VAL J 550 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE J 552 " --> pdb=" O SER J 568 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER J 568 " --> pdb=" O ILE J 552 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE6, first strand: chain 'J' and resid 820 through 822 removed outlier: 3.541A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 949 through 950 removed outlier: 3.981A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 957 through 961 removed outlier: 4.356A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AF1, first strand: chain 'J' and resid 1098 through 1100 removed outlier: 3.501A pdb=" N GLY J1033 " --> pdb=" O ILE J1115 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 1046 through 1049 removed outlier: 3.900A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 1187 through 1190 removed outlier: 3.510A pdb=" N LEU J1175 " --> pdb=" O GLU J1188 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL J1204 " --> pdb=" O GLY J1161 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.871A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 67 through 73 removed outlier: 6.416A pdb=" N ALA C 13 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASP C 108 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL C 15 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL C 105 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL C 122 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE C 107 " --> pdb=" O VAL C 122 " (cutoff:3.500A) 1051 hydrogen bonds defined for protein. 2952 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 15.73 Time building geometry restraints manager: 11.66 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: 9033 1.34 - 1.46: 4380 1.46 - 1.58: 14140 1.58 - 1.70: 107 1.70 - 1.82: 195 Bond restraints: 27855 Sorted by residual: bond pdb=" C GLY C 21 " pdb=" N PRO C 22 " ideal model delta sigma weight residual 1.332 1.391 -0.059 1.33e-02 5.65e+03 2.00e+01 bond pdb=" O3' DC A 4 " pdb=" P DT A 5 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.15e+01 bond pdb=" CA THR I 635 " pdb=" C THR I 635 " ideal model delta sigma weight residual 1.524 1.566 -0.042 1.26e-02 6.30e+03 1.13e+01 bond pdb=" CA ARG J 731 " pdb=" C ARG J 731 " ideal model delta sigma weight residual 1.519 1.555 -0.036 1.14e-02 7.69e+03 9.77e+00 bond pdb=" C ILE I1109 " pdb=" N GLY I1110 " ideal model delta sigma weight residual 1.334 1.372 -0.038 1.27e-02 6.20e+03 8.74e+00 ... (remaining 27850 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.12: 938 106.12 - 113.22: 15290 113.22 - 120.32: 10305 120.32 - 127.42: 11067 127.42 - 134.52: 263 Bond angle restraints: 37863 Sorted by residual: angle pdb=" N ARG J 156 " pdb=" CA ARG J 156 " pdb=" C ARG J 156 " ideal model delta sigma weight residual 111.07 118.98 -7.91 1.07e+00 8.73e-01 5.46e+01 angle pdb=" N LYS J1170 " pdb=" CA LYS J1170 " pdb=" C LYS J1170 " ideal model delta sigma weight residual 111.24 102.74 8.50 1.29e+00 6.01e-01 4.34e+01 angle pdb=" C ALA J 328 " pdb=" N ASP J 329 " pdb=" CA ASP J 329 " ideal model delta sigma weight residual 120.38 128.72 -8.34 1.37e+00 5.33e-01 3.71e+01 angle pdb=" N THR J1169 " pdb=" CA THR J1169 " pdb=" C THR J1169 " ideal model delta sigma weight residual 112.58 119.64 -7.06 1.22e+00 6.72e-01 3.35e+01 angle pdb=" C ARG J 322 " pdb=" N PRO J 323 " pdb=" CA PRO J 323 " ideal model delta sigma weight residual 119.76 125.64 -5.88 1.03e+00 9.43e-01 3.26e+01 ... (remaining 37858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 15472 17.89 - 35.78: 1130 35.78 - 53.67: 327 53.67 - 71.56: 81 71.56 - 89.45: 15 Dihedral angle restraints: 17025 sinusoidal: 7412 harmonic: 9613 Sorted by residual: dihedral pdb=" CA GLU I1137 " pdb=" C GLU I1137 " pdb=" N VAL I1138 " pdb=" CA VAL I1138 " ideal model delta harmonic sigma weight residual -180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ALA C 26 " pdb=" C ALA C 26 " pdb=" N VAL C 27 " pdb=" CA VAL C 27 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA LEU C 81 " pdb=" C LEU C 81 " pdb=" N ASN C 82 " pdb=" CA ASN C 82 " ideal model delta harmonic sigma weight residual -180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 17022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3934 0.084 - 0.168: 368 0.168 - 0.252: 19 0.252 - 0.336: 4 0.336 - 0.420: 2 Chirality restraints: 4327 Sorted by residual: chirality pdb=" CA ILE J1248 " pdb=" N ILE J1248 " pdb=" C ILE J1248 " pdb=" CB ILE J1248 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CG LEU I 468 " pdb=" CB LEU I 468 " pdb=" CD1 LEU I 468 " pdb=" CD2 LEU I 468 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA ASN C 82 " pdb=" N ASN C 82 " pdb=" C ASN C 82 " pdb=" CB ASN C 82 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 4324 not shown) Planarity restraints: 4761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP J 751 " 0.026 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C ASP J 751 " -0.089 2.00e-02 2.50e+03 pdb=" O ASP J 751 " 0.033 2.00e-02 2.50e+03 pdb=" N GLY J 752 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 19 " -0.022 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C GLY C 19 " 0.081 2.00e-02 2.50e+03 pdb=" O GLY C 19 " -0.032 2.00e-02 2.50e+03 pdb=" N ARG C 20 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 45 " -0.015 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" CG ASP C 45 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASP C 45 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP C 45 " -0.019 2.00e-02 2.50e+03 ... (remaining 4758 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 365 2.66 - 3.22: 24302 3.22 - 3.78: 39745 3.78 - 4.34: 54244 4.34 - 4.90: 89628 Nonbonded interactions: 208284 Sorted by model distance: nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.097 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.097 2.170 nonbonded pdb=" OG SER J 119 " pdb=" O PRO J 121 " model vdw 2.201 3.040 nonbonded pdb=" OG SER J 977 " pdb=" OG1 THR J 980 " model vdw 2.208 3.040 nonbonded pdb=" OG SER I 318 " pdb=" OD1 ASP I 320 " model vdw 2.231 3.040 ... (remaining 208279 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 'G' and (resid 7 through 158 or resid 170 through 232)) selection = (chain 'H' and resid 7 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: 2.150 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: 1.070 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 86.280 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.110 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:18.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 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 : 0.004 0.059 27855 Z= 0.248 Angle : 0.746 9.832 37863 Z= 0.477 Chirality : 0.048 0.420 4327 Planarity : 0.005 0.092 4761 Dihedral : 14.004 89.445 10839 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.42 % Favored : 95.46 % Rotamer: Outliers : 0.67 % Allowed : 2.43 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: -0.75 (0.14), residues: 3325 helix: 0.96 (0.16), residues: 1156 sheet: -0.07 (0.25), residues: 414 loop : -1.67 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 68 HIS 0.011 0.001 HIS C 177 PHE 0.018 0.001 PHE J 35 TYR 0.024 0.001 TYR C 157 ARG 0.009 0.000 ARG K 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 538 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 208 THR cc_start: 0.5961 (m) cc_final: 0.5154 (t) REVERT: J 932 MET cc_start: 0.6556 (tpt) cc_final: 0.6342 (tpp) REVERT: C 159 PHE cc_start: 0.6096 (m-80) cc_final: 0.5299 (m-10) outliers start: 19 outliers final: 6 residues processed: 552 average time/residue: 1.5046 time to fit residues: 950.7957 Evaluate side-chains 302 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 296 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 849 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 744 ARG Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain C residue 183 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 0.9990 chunk 255 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 102 optimal weight: 0.4980 chunk 160 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 306 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 HIS I 834 GLN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 GLN J 320 ASN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27855 Z= 0.190 Angle : 0.622 9.312 37863 Z= 0.318 Chirality : 0.042 0.209 4327 Planarity : 0.005 0.089 4761 Dihedral : 11.703 73.278 4320 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.97 % Allowed : 12.00 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: -0.45 (0.14), residues: 3325 helix: 1.24 (0.15), residues: 1177 sheet: -0.07 (0.25), residues: 413 loop : -1.50 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J1193 HIS 0.009 0.001 HIS J 651 PHE 0.015 0.001 PHE C 154 TYR 0.012 0.001 TYR J1365 ARG 0.011 0.001 ARG I 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 337 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 228 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8580 (pp) REVERT: I 1232 MET cc_start: 0.7905 (mmm) cc_final: 0.7655 (mmm) outliers start: 56 outliers final: 26 residues processed: 368 average time/residue: 1.3780 time to fit residues: 590.5968 Evaluate side-chains 302 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 275 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1335 ILE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 153 ASN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain C residue 58 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 170 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 254 optimal weight: 0.0980 chunk 208 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 306 optimal weight: 4.9990 chunk 331 optimal weight: 0.7980 chunk 273 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS I 622 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 465 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 897 HIS J1218 HIS ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 27855 Z= 0.292 Angle : 0.672 11.317 37863 Z= 0.349 Chirality : 0.045 0.183 4327 Planarity : 0.005 0.066 4761 Dihedral : 11.688 75.989 4309 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.46 % Allowed : 14.26 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: -0.45 (0.14), residues: 3325 helix: 1.15 (0.15), residues: 1171 sheet: 0.06 (0.24), residues: 442 loop : -1.48 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 68 HIS 0.009 0.001 HIS J 545 PHE 0.025 0.002 PHE I 514 TYR 0.015 0.001 TYR J1365 ARG 0.012 0.001 ARG I 407 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 315 time to evaluate : 3.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.6084 (mmp80) cc_final: 0.5848 (mmm160) REVERT: I 1304 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7269 (tpt) REVERT: J 1040 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.5482 (ppp) REVERT: C 137 ILE cc_start: 0.7239 (pp) cc_final: 0.7022 (pp) outliers start: 70 outliers final: 32 residues processed: 360 average time/residue: 1.4258 time to fit residues: 596.3339 Evaluate side-chains 283 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 249 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 768 MET Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 1040 MET Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain C residue 58 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 302 optimal weight: 10.0000 chunk 230 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 146 optimal weight: 30.0000 chunk 205 optimal weight: 9.9990 chunk 307 optimal weight: 0.8980 chunk 325 optimal weight: 40.0000 chunk 160 optimal weight: 2.9990 chunk 291 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 622 ASN ** J 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 792 ASN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27855 Z= 0.261 Angle : 0.641 10.029 37863 Z= 0.331 Chirality : 0.044 0.189 4327 Planarity : 0.005 0.069 4761 Dihedral : 11.471 86.401 4309 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.60 % Allowed : 16.44 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: -0.38 (0.14), residues: 3325 helix: 1.22 (0.15), residues: 1169 sheet: 0.05 (0.25), residues: 453 loop : -1.44 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 997 HIS 0.008 0.001 HIS C 85 PHE 0.019 0.001 PHE I 972 TYR 0.013 0.001 TYR C 165 ARG 0.013 0.001 ARG J 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6650 Ramachandran restraints generated. 3325 Oldfield, 0 Emsley, 3325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 285 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 542 ARG cc_start: 0.5499 (OUTLIER) cc_final: 0.5275 (tmt170) REVERT: I 1304 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7235 (tpt) REVERT: C 137 ILE cc_start: 0.7059 (pp) cc_final: 0.6820 (pp) outliers start: 74 outliers final: 25 residues processed: 336 average time/residue: 1.2298 time to fit residues: 480.5678 Evaluate side-chains 263 residues out of total 2841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 236 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 542 ARG Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 111 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain C residue 58 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 271 optimal weight: 30.0000 chunk 184 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 242 optimal weight: 0.0010 chunk 134 optimal weight: 6.9990 chunk 277 optimal weight: 10.0000 chunk 225 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 292 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 overall best weight: 3.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: