Starting phenix.real_space_refine on Tue Mar 19 12:15:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mbv_3460/03_2024/5mbv_3460.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mbv_3460/03_2024/5mbv_3460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mbv_3460/03_2024/5mbv_3460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mbv_3460/03_2024/5mbv_3460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mbv_3460/03_2024/5mbv_3460.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mbv_3460/03_2024/5mbv_3460.pdb" } resolution = 3.8 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= -0.001 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 15225 2.51 5 N 4267 2.21 5 O 4516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 19": "NH1" <-> "NH2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 395": "NH1" <-> "NH2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 423": "NH1" <-> "NH2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 471": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B ASP 639": "OD1" <-> "OD2" Residue "B ARG 653": "NH1" <-> "NH2" Residue "B ARG 655": "NH1" <-> "NH2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B ARG 682": "NH1" <-> "NH2" Residue "B ARG 683": "NH1" <-> "NH2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 771": "NH1" <-> "NH2" Residue "B ASP 798": "OD1" <-> "OD2" Residue "B ARG 823": "NH1" <-> "NH2" Residue "B ARG 824": "NH1" <-> "NH2" Residue "B ARG 840": "NH1" <-> "NH2" Residue "B ASP 882": "OD1" <-> "OD2" Residue "B ARG 895": "NH1" <-> "NH2" Residue "B TYR 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1015": "NH1" <-> "NH2" Residue "B PHE 1023": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1037": "OD1" <-> "OD2" Residue "B PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1106": "NH1" <-> "NH2" Residue "B ARG 1120": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 9": "NH1" <-> "NH2" Residue "C ARG 23": "NH1" <-> "NH2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 348": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 433": "NH1" <-> "NH2" Residue "C TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 443": "NH1" <-> "NH2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 494": "NH1" <-> "NH2" Residue "C ARG 525": "NH1" <-> "NH2" Residue "C ARG 530": "NH1" <-> "NH2" Residue "C ARG 575": "NH1" <-> "NH2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C ARG 644": "NH1" <-> "NH2" Residue "C ASP 646": "OD1" <-> "OD2" Residue "C ARG 653": "NH1" <-> "NH2" Residue "C PHE 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 703": "NH1" <-> "NH2" Residue "C ARG 709": "NH1" <-> "NH2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C PHE 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 742": "NH1" <-> "NH2" Residue "C TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 799": "NH1" <-> "NH2" Residue "C ARG 839": "NH1" <-> "NH2" Residue "C ARG 858": "NH1" <-> "NH2" Residue "C GLU 860": "OE1" <-> "OE2" Residue "C ARG 877": "NH1" <-> "NH2" Residue "C ARG 896": "NH1" <-> "NH2" Residue "C ARG 900": "NH1" <-> "NH2" Residue "C ARG 902": "NH1" <-> "NH2" Residue "C ARG 966": "NH1" <-> "NH2" Residue "C ARG 1001": "NH1" <-> "NH2" Residue "C ARG 1007": "NH1" <-> "NH2" Residue "C GLU 1029": "OE1" <-> "OE2" Residue "C TYR 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1118": "NH1" <-> "NH2" Residue "D ASP 95": "OD1" <-> "OD2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 211": "NH1" <-> "NH2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D ARG 281": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 509": "NH1" <-> "NH2" Residue "D ARG 526": "NH1" <-> "NH2" Residue "D ARG 574": "NH1" <-> "NH2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "D TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A ASP 90": "OD1" <-> "OD2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A ASP 133": "OD1" <-> "OD2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E ASP 109": "OD1" <-> "OD2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E ASP 133": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24118 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 9037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1127, 9037 Classifications: {'peptide': 1127} Link IDs: {'PTRANS': 50, 'TRANS': 1076} Chain breaks: 2 Chain: "C" Number of atoms: 9078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9078 Classifications: {'peptide': 1121} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1053} Chain: "D" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4570 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 24, 'TRANS': 568} Chain breaks: 2 Chain: "A" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 817 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain: "E" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 616 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Time building chain proxies: 11.58, per 1000 atoms: 0.48 Number of scatterers: 24118 At special positions: 0 Unit cell: (152.76, 160.8, 116.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 4516 8.00 N 4267 7.00 C 15225 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: 8.82 Conformation dependent library (CDL) restraints added in 4.0 seconds 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5700 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 17 sheets defined 58.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.672A pdb=" N ALA B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 55 through 58 Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 106 through 120 Processing helix chain 'B' and resid 128 through 138 removed outlier: 3.627A pdb=" N GLN B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 4.055A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 171 Processing helix chain 'B' and resid 176 through 187 removed outlier: 3.904A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 5.037A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 240 removed outlier: 3.805A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 4.178A pdb=" N ASN B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 280 Processing helix chain 'B' and resid 281 through 289 Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.889A pdb=" N ASP B 314 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU B 319 " --> pdb=" O GLN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 3.673A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.525A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 removed outlier: 3.809A pdb=" N LEU B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.785A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 424 removed outlier: 4.400A pdb=" N PHE B 422 " --> pdb=" O ILE B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.670A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 510 through 534 Processing helix chain 'B' and resid 560 through 574 removed outlier: 3.702A pdb=" N LEU B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.623A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 597 " --> pdb=" O ALA B 593 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP B 598 " --> pdb=" O GLN B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 Processing helix chain 'B' and resid 624 through 634 Processing helix chain 'B' and resid 634 through 655 removed outlier: 3.632A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 669 removed outlier: 3.573A pdb=" N MET B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 Processing helix chain 'B' and resid 679 through 701 removed outlier: 3.779A pdb=" N ARG B 683 " --> pdb=" O GLY B 679 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 717 removed outlier: 3.520A pdb=" N GLU B 717 " --> pdb=" O GLN B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 731 through 735 Processing helix chain 'B' and resid 783 through 808 removed outlier: 3.788A pdb=" N VAL B 787 " --> pdb=" O ALA B 783 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 827 removed outlier: 4.158A pdb=" N LYS B 827 " --> pdb=" O ARG B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 835 removed outlier: 4.366A pdb=" N HIS B 834 " --> pdb=" O THR B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 843 removed outlier: 3.507A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.959A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 941 through 945 removed outlier: 3.534A pdb=" N PHE B 945 " --> pdb=" O PRO B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 962 removed outlier: 3.849A pdb=" N PHE B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 981 Processing helix chain 'B' and resid 986 through 999 removed outlier: 4.308A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 995 " --> pdb=" O THR B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 Processing helix chain 'B' and resid 1013 through 1015 No H-bonds generated for 'chain 'B' and resid 1013 through 1015' Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.625A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1048 Processing helix chain 'B' and resid 1094 through 1105 removed outlier: 3.635A pdb=" N ALA B1099 " --> pdb=" O GLN B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1106 through 1126 removed outlier: 4.123A pdb=" N GLN B1110 " --> pdb=" O ARG B1106 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1134 Processing helix chain 'B' and resid 1163 through 1174 removed outlier: 3.572A pdb=" N LEU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.948A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 55 removed outlier: 3.813A pdb=" N ALA C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 77 removed outlier: 3.577A pdb=" N ARG C 75 " --> pdb=" O ASP C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 102 removed outlier: 3.677A pdb=" N TRP C 93 " --> pdb=" O GLN C 89 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 116 removed outlier: 3.653A pdb=" N HIS C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.751A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 removed outlier: 3.890A pdb=" N GLN C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 166 " --> pdb=" O GLN C 162 " (cutoff:3.500A) Proline residue: C 167 - end of helix Processing helix chain 'C' and resid 185 through 199 removed outlier: 3.988A pdb=" N TYR C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 Processing helix chain 'C' and resid 255 through 262 removed outlier: 3.637A pdb=" N ALA C 258 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 261 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR C 262 " --> pdb=" O LYS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 removed outlier: 4.137A pdb=" N ASN C 282 " --> pdb=" O ARG C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 315 removed outlier: 4.065A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.988A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.555A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP C 400 " --> pdb=" O MET C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 414 through 428 removed outlier: 3.693A pdb=" N TYR C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Proline residue: C 420 - end of helix Processing helix chain 'C' and resid 447 through 458 removed outlier: 3.621A pdb=" N LEU C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 463 Processing helix chain 'C' and resid 466 through 474 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.805A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.787A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.646A pdb=" N VAL C 511 " --> pdb=" O ASP C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.646A pdb=" N GLY C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 586 Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.168A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 597 " --> pdb=" O ASP C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 626 removed outlier: 4.389A pdb=" N ALA C 608 " --> pdb=" O GLU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 647 removed outlier: 3.879A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C 647 " --> pdb=" O GLN C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 removed outlier: 3.690A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 768 through 780 Processing helix chain 'C' and resid 790 through 795 removed outlier: 3.513A pdb=" N GLN C 795 " --> pdb=" O GLN C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 806 through 812 Processing helix chain 'C' and resid 834 through 843 removed outlier: 4.112A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 851 removed outlier: 3.675A pdb=" N PHE C 849 " --> pdb=" O VAL C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 890 removed outlier: 3.581A pdb=" N ILE C 880 " --> pdb=" O SER C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 904 removed outlier: 4.007A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 935 removed outlier: 3.571A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN C 926 " --> pdb=" O GLN C 922 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 933 " --> pdb=" O ASP C 929 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N CYS C 934 " --> pdb=" O ARG C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 990 removed outlier: 4.004A pdb=" N SER C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 Processing helix chain 'C' and resid 1040 through 1049 Processing helix chain 'C' and resid 1060 through 1076 Processing helix chain 'C' and resid 1087 through 1094 removed outlier: 4.001A pdb=" N LEU C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP C1094 " --> pdb=" O TYR C1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1113 through 1120 removed outlier: 3.969A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.539A pdb=" N GLU D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU D 12 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 65 through 71 Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.688A pdb=" N CYS D 84 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 152 through 164 Processing helix chain 'D' and resid 176 through 192 removed outlier: 3.713A pdb=" N ALA D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 221 Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 240 through 245 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.759A pdb=" N ASP D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.602A pdb=" N VAL D 304 " --> pdb=" O GLN D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'D' and resid 315 through 319 removed outlier: 3.919A pdb=" N ASN D 318 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 334 removed outlier: 3.571A pdb=" N ARG D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 351 removed outlier: 3.586A pdb=" N SER D 351 " --> pdb=" O SER D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 375 removed outlier: 3.999A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.615A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 415 through 424 Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.696A pdb=" N ASN D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 removed outlier: 3.883A pdb=" N GLU D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.789A pdb=" N LEU D 527 " --> pdb=" O PRO D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 571 Processing helix chain 'D' and resid 582 through 592 Processing helix chain 'D' and resid 599 through 605 removed outlier: 3.547A pdb=" N SER D 605 " --> pdb=" O ALA D 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 77 removed outlier: 3.612A pdb=" N ALA A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 4.073A pdb=" N PHE A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.663A pdb=" N GLN A 113 " --> pdb=" O ASP A 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 79 removed outlier: 3.791A pdb=" N LYS E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY E 78 " --> pdb=" O ASP E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 93 removed outlier: 3.719A pdb=" N PHE E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN E 93 " --> pdb=" O ILE E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 107 Processing helix chain 'E' and resid 109 through 135 removed outlier: 3.621A pdb=" N GLN E 113 " --> pdb=" O ASP E 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.602A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 207 through 208 Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA4, first strand: chain 'B' and resid 487 through 490 Processing sheet with id=AA5, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.331A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS B 812 " --> pdb=" O PRO B 750 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS B 500 " --> pdb=" O LEU B 815 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL B 817 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N TRP B 502 " --> pdb=" O VAL B 817 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA B 870 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 503 " --> pdb=" O ALA B 870 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 904 through 905 removed outlier: 6.578A pdb=" N VAL B1058 " --> pdb=" O GLU B1029 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU B1029 " --> pdb=" O VAL B1058 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B1064 " --> pdb=" O PHE B1023 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B1023 " --> pdb=" O GLY B1064 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B1068 " --> pdb=" O VAL B1019 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B1019 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE B1070 " --> pdb=" O LYS B1017 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LYS B1017 " --> pdb=" O PHE B1070 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 904 through 905 removed outlier: 9.735A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B1070 " --> pdb=" O TYR B1077 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N TYR B1076 " --> pdb=" O GLY B1137 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ILE B1139 " --> pdb=" O TYR B1076 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU B1078 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU B1141 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASP B1080 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 61 removed outlier: 4.457A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N THR C 241 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL C 4 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ALA C 325 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N HIS C 6 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ARG C 265 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.282A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 437 through 439 removed outlier: 6.390A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR C 375 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N TYR C 731 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N HIS C 377 " --> pdb=" O TYR C 731 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 831 through 833 removed outlier: 3.689A pdb=" N THR C 953 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 831 through 833 removed outlier: 3.689A pdb=" N THR C 953 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 14.975A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 12.527A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1050 through 1051 removed outlier: 3.528A pdb=" N ALA C1056 " --> pdb=" O ASP C1051 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.126A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 237 through 239 removed outlier: 9.507A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU D 201 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY D 296 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 395 through 396 removed outlier: 6.078A pdb=" N ALA D 549 " --> pdb=" O SER D 578 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N TYR D 580 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU D 551 " --> pdb=" O TYR D 580 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN D 439 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE D 552 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU D 441 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 519 through 522 removed outlier: 5.299A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 480 " --> pdb=" O ALA D 501 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET D 483 " --> pdb=" O GLU D 531 " (cutoff:3.500A) 1178 hydrogen bonds defined for protein. 3396 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.70 Time building geometry restraints manager: 9.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8254 1.34 - 1.46: 5194 1.46 - 1.58: 11005 1.58 - 1.69: 0 1.69 - 1.81: 185 Bond restraints: 24638 Sorted by residual: bond pdb=" N ALA C 161 " pdb=" CA ALA C 161 " ideal model delta sigma weight residual 1.456 1.470 -0.014 1.23e-02 6.61e+03 1.35e+00 bond pdb=" C ARG C 968 " pdb=" N PRO C 969 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.32e+00 bond pdb=" CG PRO D 428 " pdb=" CD PRO D 428 " ideal model delta sigma weight residual 1.503 1.464 0.039 3.40e-02 8.65e+02 1.29e+00 bond pdb=" N GLY C 555 " pdb=" CA GLY C 555 " ideal model delta sigma weight residual 1.438 1.451 -0.013 1.41e-02 5.03e+03 8.17e-01 bond pdb=" C SER D 64 " pdb=" N HIS D 65 " ideal model delta sigma weight residual 1.331 1.349 -0.018 2.07e-02 2.33e+03 7.76e-01 ... (remaining 24633 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.37: 774 106.37 - 113.28: 13125 113.28 - 120.19: 8966 120.19 - 127.10: 10210 127.10 - 134.01: 336 Bond angle restraints: 33411 Sorted by residual: angle pdb=" C ASP B 882 " pdb=" CA ASP B 882 " pdb=" CB ASP B 882 " ideal model delta sigma weight residual 116.34 110.36 5.98 1.40e+00 5.10e-01 1.83e+01 angle pdb=" C ASP D 389 " pdb=" N PHE D 390 " pdb=" CA PHE D 390 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" N GLY C 555 " pdb=" CA GLY C 555 " pdb=" C GLY C 555 " ideal model delta sigma weight residual 112.79 116.64 -3.85 1.20e+00 6.94e-01 1.03e+01 angle pdb=" C GLY D 479 " pdb=" N ARG D 480 " pdb=" CA ARG D 480 " ideal model delta sigma weight residual 121.27 110.45 10.82 3.40e+00 8.65e-02 1.01e+01 angle pdb=" C PHE D 390 " pdb=" N THR D 391 " pdb=" CA THR D 391 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.47e+00 ... (remaining 33406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 14233 17.76 - 35.51: 566 35.51 - 53.27: 87 53.27 - 71.02: 18 71.02 - 88.78: 15 Dihedral angle restraints: 14919 sinusoidal: 6135 harmonic: 8784 Sorted by residual: dihedral pdb=" CA GLN C 545 " pdb=" C GLN C 545 " pdb=" N SER C 546 " pdb=" CA SER C 546 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ALA C 283 " pdb=" C ALA C 283 " pdb=" N GLY C 284 " pdb=" CA GLY C 284 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA GLY C 657 " pdb=" C GLY C 657 " pdb=" N PRO C 658 " pdb=" CA PRO C 658 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 14916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2452 0.028 - 0.055: 775 0.055 - 0.083: 232 0.083 - 0.111: 156 0.111 - 0.139: 42 Chirality restraints: 3657 Sorted by residual: chirality pdb=" CA ILE C 864 " pdb=" N ILE C 864 " pdb=" C ILE C 864 " pdb=" CB ILE C 864 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE C 661 " pdb=" N ILE C 661 " pdb=" C ILE C 661 " pdb=" CB ILE C 661 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA VAL B 126 " pdb=" N VAL B 126 " pdb=" C VAL B 126 " pdb=" CB VAL B 126 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 3654 not shown) Planarity restraints: 4403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO C 658 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 907 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO C 908 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 908 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 908 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 381 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO C 382 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 382 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 382 " -0.026 5.00e-02 4.00e+02 ... (remaining 4400 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 652 2.72 - 3.26: 24369 3.26 - 3.81: 36975 3.81 - 4.35: 47811 4.35 - 4.90: 79038 Nonbonded interactions: 188845 Sorted by model distance: nonbonded pdb=" O LEU D 67 " pdb=" OG1 THR D 70 " model vdw 2.172 2.440 nonbonded pdb=" OH TYR D 316 " pdb=" O ALA D 601 " model vdw 2.221 2.440 nonbonded pdb=" O TYR B 580 " pdb=" ND2 ASN B 583 " model vdw 2.221 2.520 nonbonded pdb=" O ARG B 255 " pdb=" OH TYR B 280 " model vdw 2.227 2.440 nonbonded pdb=" O GLU B 978 " pdb=" NE2 GLN C 617 " model vdw 2.256 2.520 ... (remaining 188840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 0.240 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: 0.040 Extract box with map and model: 2.690 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 60.370 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 : 0.002 0.039 24638 Z= 0.114 Angle : 0.506 10.823 33411 Z= 0.308 Chirality : 0.036 0.139 3657 Planarity : 0.003 0.069 4403 Dihedral : 10.209 88.779 9219 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.74 % Favored : 95.16 % Rotamer: Outliers : 0.74 % Allowed : 3.82 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -3.37 (0.12), residues: 2996 helix: -3.28 (0.08), residues: 1534 sheet: -0.33 (0.27), residues: 290 loop : -0.86 (0.16), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 248 HIS 0.003 0.001 HIS C 267 PHE 0.007 0.001 PHE C 694 TYR 0.010 0.001 TYR D 477 ARG 0.003 0.000 ARG D 572 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 278 time to evaluate : 2.805 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: B 259 ARG cc_start: 0.9414 (ttp80) cc_final: 0.9154 (ttt180) REVERT: B 311 GLU cc_start: 0.9335 (tt0) cc_final: 0.9018 (tp30) REVERT: B 314 ASP cc_start: 0.9055 (t0) cc_final: 0.8827 (t0) REVERT: B 660 MET cc_start: 0.8351 (ttp) cc_final: 0.7737 (tmm) REVERT: B 906 TYR cc_start: 0.7780 (p90) cc_final: 0.7559 (t80) REVERT: B 992 GLU cc_start: 0.9028 (pt0) cc_final: 0.8439 (mp0) REVERT: B 1015 ARG cc_start: 0.8365 (mmt90) cc_final: 0.8141 (tmm-80) REVERT: B 1050 CYS cc_start: 0.8658 (m) cc_final: 0.8423 (m) REVERT: B 1056 MET cc_start: 0.7680 (mtp) cc_final: 0.7431 (mpp) REVERT: B 1058 VAL cc_start: 0.7068 (t) cc_final: 0.6807 (m) REVERT: B 1069 VAL cc_start: 0.6350 (OUTLIER) cc_final: 0.5983 (p) REVERT: B 1077 TYR cc_start: 0.8194 (m-80) cc_final: 0.7053 (m-80) REVERT: B 1113 LEU cc_start: 0.7829 (mt) cc_final: 0.7348 (pp) REVERT: C 272 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.8013 (ttp80) REVERT: C 350 VAL cc_start: 0.8872 (t) cc_final: 0.8573 (m) REVERT: C 634 LEU cc_start: 0.8828 (tp) cc_final: 0.8608 (tp) REVERT: C 944 ASP cc_start: 0.7486 (t0) cc_final: 0.7260 (m-30) REVERT: C 1080 MET cc_start: 0.8743 (tpp) cc_final: 0.8535 (ptp) REVERT: D 226 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8112 (m) REVERT: D 242 ARG cc_start: 0.9235 (ttt-90) cc_final: 0.8992 (tpp-160) REVERT: D 273 MET cc_start: 0.8787 (mtm) cc_final: 0.7974 (mpp) REVERT: D 278 MET cc_start: 0.9023 (mmm) cc_final: 0.8750 (mmm) REVERT: D 295 LEU cc_start: 0.8514 (mt) cc_final: 0.7976 (tt) REVERT: D 547 ASP cc_start: 0.8848 (t0) cc_final: 0.8612 (t70) REVERT: A 100 LYS cc_start: 0.9556 (mtmt) cc_final: 0.9333 (tptt) REVERT: A 115 ARG cc_start: 0.9170 (mmm160) cc_final: 0.8823 (mmm160) REVERT: A 116 MET cc_start: 0.9254 (tpt) cc_final: 0.8956 (mmm) REVERT: E 111 GLU cc_start: 0.9639 (tt0) cc_final: 0.9192 (tp30) REVERT: E 122 TYR cc_start: 0.9162 (t80) cc_final: 0.8803 (t80) REVERT: E 123 MET cc_start: 0.9555 (mtp) cc_final: 0.9242 (mtp) REVERT: E 127 ILE cc_start: 0.9425 (mt) cc_final: 0.9146 (tp) outliers start: 19 outliers final: 1 residues processed: 293 average time/residue: 0.3996 time to fit residues: 176.4764 Evaluate side-chains 146 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 chunk 234 optimal weight: 10.0000 chunk 90 optimal weight: 40.0000 chunk 142 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 chunk 271 optimal weight: 0.4980 overall best weight: 5.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 120 GLN B 138 ASN B 140 ASN B 162 GLN B 222 HIS ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN B 458 ASN B 463 GLN B 484 ASN B 650 GLN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 GLN B 894 GLN ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 HIS C 126 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 233 HIS C 336 HIS C 390 HIS C 448 HIS C 510 ASN C 647 GLN C 660 ASN ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 HIS C 793 ASN C 817 HIS C 822 GLN C 881 ASN C 886 ASN C 920 GLN C 925 GLN C 926 GLN C 951 GLN C 979 GLN C1108 GLN D 44 HIS D 79 GLN D 115 ASN D 255 HIS D 256 HIS A 113 GLN A 131 GLN E 81 GLN E 113 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24638 Z= 0.290 Angle : 0.630 8.291 33411 Z= 0.323 Chirality : 0.041 0.159 3657 Planarity : 0.005 0.060 4403 Dihedral : 4.307 45.725 3317 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.27 % Favored : 97.70 % Rotamer: Outliers : 1.48 % Allowed : 7.61 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -0.84 (0.14), residues: 2996 helix: -0.38 (0.12), residues: 1557 sheet: -0.16 (0.26), residues: 300 loop : -0.68 (0.17), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 574 HIS 0.009 0.002 HIS E 119 PHE 0.019 0.002 PHE B 945 TYR 0.020 0.002 TYR B1111 ARG 0.008 0.001 ARG C 649 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 156 time to evaluate : 3.020 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: B 259 ARG cc_start: 0.9621 (ttp80) cc_final: 0.9108 (ttt180) REVERT: B 311 GLU cc_start: 0.9425 (tt0) cc_final: 0.9136 (tp30) REVERT: B 314 ASP cc_start: 0.9107 (t0) cc_final: 0.8837 (t0) REVERT: B 518 MET cc_start: 0.9174 (mmt) cc_final: 0.8889 (mmt) REVERT: B 604 MET cc_start: 0.4639 (mmm) cc_final: 0.4356 (ttm) REVERT: B 658 MET cc_start: 0.8887 (mmm) cc_final: 0.8395 (mmt) REVERT: B 660 MET cc_start: 0.8719 (ttp) cc_final: 0.8318 (tmm) REVERT: B 1021 MET cc_start: 0.5741 (tmm) cc_final: 0.4137 (tmm) REVERT: B 1056 MET cc_start: 0.7952 (mtp) cc_final: 0.7728 (mpp) REVERT: B 1061 MET cc_start: 0.7781 (mmm) cc_final: 0.7429 (mmm) REVERT: B 1077 TYR cc_start: 0.7975 (m-80) cc_final: 0.7502 (m-80) REVERT: C 34 MET cc_start: 0.8324 (mmm) cc_final: 0.8107 (tpp) REVERT: C 59 ASN cc_start: 0.8205 (m-40) cc_final: 0.7672 (t0) REVERT: C 1080 MET cc_start: 0.8781 (tpp) cc_final: 0.8080 (ptp) REVERT: D 226 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8099 (m) REVERT: D 242 ARG cc_start: 0.9272 (ttt-90) cc_final: 0.9063 (tpp-160) REVERT: D 273 MET cc_start: 0.8374 (mtm) cc_final: 0.8171 (mpp) REVERT: D 295 LEU cc_start: 0.8684 (mt) cc_final: 0.8208 (tt) REVERT: D 596 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8089 (mmp-170) REVERT: A 41 MET cc_start: 0.7716 (tpp) cc_final: 0.7398 (tpp) REVERT: A 100 LYS cc_start: 0.9558 (mtmt) cc_final: 0.9334 (tptt) REVERT: A 116 MET cc_start: 0.9193 (tpt) cc_final: 0.8938 (mmm) REVERT: E 116 MET cc_start: 0.9619 (tpp) cc_final: 0.8915 (mmm) REVERT: E 122 TYR cc_start: 0.9222 (t80) cc_final: 0.8793 (t80) outliers start: 38 outliers final: 14 residues processed: 185 average time/residue: 0.3635 time to fit residues: 106.2462 Evaluate side-chains 145 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 882 ASP Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 537 MET Chi-restraints excluded: chain C residue 1102 MET Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 67 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 272 optimal weight: 20.0000 chunk 293 optimal weight: 20.0000 chunk 242 optimal weight: 7.9990 chunk 269 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 181 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 HIS B1110 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN D 241 HIS D 388 GLN E 113 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24638 Z= 0.313 Angle : 0.615 9.564 33411 Z= 0.314 Chirality : 0.041 0.286 3657 Planarity : 0.004 0.051 4403 Dihedral : 4.377 45.434 3316 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.96 % Rotamer: Outliers : 1.76 % Allowed : 8.23 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.29 (0.15), residues: 2996 helix: 0.90 (0.13), residues: 1564 sheet: -0.06 (0.29), residues: 272 loop : -0.63 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 574 HIS 0.008 0.001 HIS E 119 PHE 0.016 0.002 PHE C 849 TYR 0.020 0.002 TYR B1111 ARG 0.006 0.001 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 129 time to evaluate : 2.380 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: B 259 ARG cc_start: 0.9658 (ttp80) cc_final: 0.9133 (ttt180) REVERT: B 518 MET cc_start: 0.9140 (mmt) cc_final: 0.8897 (mmp) REVERT: B 604 MET cc_start: 0.4740 (mmm) cc_final: 0.3950 (ttm) REVERT: B 658 MET cc_start: 0.8874 (mmm) cc_final: 0.8495 (mmt) REVERT: B 1015 ARG cc_start: 0.8351 (mmt90) cc_final: 0.8006 (tmm-80) REVERT: B 1021 MET cc_start: 0.5797 (tmm) cc_final: 0.4626 (tmm) REVERT: B 1061 MET cc_start: 0.7896 (mmm) cc_final: 0.7197 (mmm) REVERT: B 1098 MET cc_start: 0.4709 (OUTLIER) cc_final: 0.2416 (mtt) REVERT: C 752 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8645 (pt) REVERT: C 787 MET cc_start: 0.8502 (mpp) cc_final: 0.8196 (mpp) REVERT: C 1057 MET cc_start: 0.6392 (mtm) cc_final: 0.6026 (ttm) REVERT: C 1080 MET cc_start: 0.8875 (tpp) cc_final: 0.8564 (ptp) REVERT: D 184 LEU cc_start: 0.9660 (tp) cc_final: 0.9444 (mm) REVERT: D 226 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8211 (m) REVERT: D 273 MET cc_start: 0.8360 (mtm) cc_final: 0.7825 (mpp) REVERT: D 295 LEU cc_start: 0.8786 (mt) cc_final: 0.8447 (tp) REVERT: D 462 MET cc_start: 0.2969 (ppp) cc_final: 0.2567 (ppp) REVERT: D 483 MET cc_start: 0.5913 (ppp) cc_final: 0.5477 (ppp) REVERT: A 41 MET cc_start: 0.7708 (tpp) cc_final: 0.7376 (tpp) REVERT: A 100 LYS cc_start: 0.9608 (mtmt) cc_final: 0.9363 (tptt) REVERT: A 116 MET cc_start: 0.9219 (tpt) cc_final: 0.8912 (mmm) REVERT: E 116 MET cc_start: 0.9686 (tpp) cc_final: 0.9264 (tpp) REVERT: E 122 TYR cc_start: 0.9270 (t80) cc_final: 0.9012 (t80) outliers start: 45 outliers final: 21 residues processed: 168 average time/residue: 0.3796 time to fit residues: 100.5937 Evaluate side-chains 136 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 882 ASP Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 1102 MET Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 107 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 272 optimal weight: 7.9990 chunk 289 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 258 optimal weight: 30.0000 chunk 77 optimal weight: 5.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 GLN B 307 HIS ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 GLN B 911 GLN ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1110 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24638 Z= 0.236 Angle : 0.548 10.216 33411 Z= 0.275 Chirality : 0.040 0.198 3657 Planarity : 0.004 0.048 4403 Dihedral : 4.183 44.479 3316 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 1.95 % Allowed : 9.29 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.74 (0.15), residues: 2996 helix: 1.42 (0.13), residues: 1554 sheet: 0.02 (0.29), residues: 272 loop : -0.60 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 164 HIS 0.005 0.001 HIS E 91 PHE 0.011 0.001 PHE C 421 TYR 0.019 0.001 TYR B1111 ARG 0.011 0.000 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 125 time to evaluate : 2.766 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: B 259 ARG cc_start: 0.9588 (ttp80) cc_final: 0.9036 (ttt180) REVERT: B 658 MET cc_start: 0.8873 (mmm) cc_final: 0.8537 (mmt) REVERT: B 660 MET cc_start: 0.8541 (ttp) cc_final: 0.8061 (ttp) REVERT: B 1015 ARG cc_start: 0.8247 (mmt90) cc_final: 0.7853 (tmm-80) REVERT: B 1021 MET cc_start: 0.6003 (tmm) cc_final: 0.4717 (tmm) REVERT: B 1061 MET cc_start: 0.8144 (mmm) cc_final: 0.7386 (mmm) REVERT: B 1098 MET cc_start: 0.4595 (OUTLIER) cc_final: 0.2887 (mtm) REVERT: B 1135 PHE cc_start: 0.8714 (t80) cc_final: 0.8421 (t80) REVERT: C 667 MET cc_start: 0.9215 (mmt) cc_final: 0.8988 (mmp) REVERT: C 752 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8588 (mt) REVERT: C 787 MET cc_start: 0.8629 (mpp) cc_final: 0.8266 (mpp) REVERT: C 1057 MET cc_start: 0.6406 (mtm) cc_final: 0.6008 (ttm) REVERT: D 226 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8326 (m) REVERT: D 273 MET cc_start: 0.8312 (mtm) cc_final: 0.7829 (mpp) REVERT: D 279 MET cc_start: 0.9606 (mmm) cc_final: 0.8905 (tpp) REVERT: D 295 LEU cc_start: 0.8852 (mt) cc_final: 0.8570 (tp) REVERT: D 462 MET cc_start: 0.2928 (ppp) cc_final: 0.2615 (ppp) REVERT: D 483 MET cc_start: 0.5908 (ppp) cc_final: 0.5706 (ppp) REVERT: D 518 ASN cc_start: 0.8040 (m-40) cc_final: 0.7701 (t0) REVERT: A 41 MET cc_start: 0.7643 (tpp) cc_final: 0.7363 (tpp) REVERT: A 100 LYS cc_start: 0.9615 (mtmt) cc_final: 0.9367 (tptt) REVERT: A 116 MET cc_start: 0.9101 (tpt) cc_final: 0.8708 (mmm) REVERT: E 70 GLU cc_start: 0.8948 (pp20) cc_final: 0.8589 (tm-30) REVERT: E 116 MET cc_start: 0.9685 (tpp) cc_final: 0.9278 (tpp) REVERT: E 122 TYR cc_start: 0.9250 (t80) cc_final: 0.8922 (t80) outliers start: 50 outliers final: 20 residues processed: 166 average time/residue: 0.3638 time to fit residues: 97.3596 Evaluate side-chains 141 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 537 MET Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 1102 MET Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 107 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 20.0000 chunk 164 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 246 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 259 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 757 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24638 Z= 0.276 Angle : 0.590 14.000 33411 Z= 0.294 Chirality : 0.041 0.270 3657 Planarity : 0.004 0.049 4403 Dihedral : 4.236 43.759 3316 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.67 % Favored : 96.26 % Rotamer: Outliers : 1.95 % Allowed : 9.83 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.87 (0.15), residues: 2996 helix: 1.54 (0.13), residues: 1561 sheet: 0.08 (0.30), residues: 276 loop : -0.57 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 841 HIS 0.006 0.001 HIS E 119 PHE 0.014 0.001 PHE C 901 TYR 0.015 0.001 TYR B1111 ARG 0.004 0.000 ARG B 662 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 117 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 436 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8804 (tp30) REVERT: B 504 MET cc_start: 0.8034 (tpp) cc_final: 0.7714 (tpp) REVERT: B 518 MET cc_start: 0.8873 (mmp) cc_final: 0.8640 (mmm) REVERT: B 1015 ARG cc_start: 0.8303 (mmt90) cc_final: 0.7919 (tmm-80) REVERT: B 1021 MET cc_start: 0.6251 (tmm) cc_final: 0.4965 (tmm) REVERT: B 1061 MET cc_start: 0.8060 (mmm) cc_final: 0.7122 (mmm) REVERT: B 1098 MET cc_start: 0.4755 (OUTLIER) cc_final: 0.2145 (ttt) REVERT: B 1135 PHE cc_start: 0.8669 (t80) cc_final: 0.8418 (t80) REVERT: C 667 MET cc_start: 0.9242 (mmt) cc_final: 0.9037 (mmp) REVERT: C 752 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8642 (pt) REVERT: C 787 MET cc_start: 0.8610 (mpp) cc_final: 0.8172 (mpp) REVERT: C 978 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7520 (tmm) REVERT: D 273 MET cc_start: 0.8378 (mtm) cc_final: 0.7890 (mpp) REVERT: D 295 LEU cc_start: 0.8893 (mt) cc_final: 0.8599 (tp) REVERT: D 462 MET cc_start: 0.3084 (ppp) cc_final: 0.2802 (ppp) REVERT: D 483 MET cc_start: 0.6033 (ppp) cc_final: 0.5787 (ppp) REVERT: D 518 ASN cc_start: 0.8009 (m-40) cc_final: 0.7702 (t0) REVERT: D 536 MET cc_start: 0.6713 (tpp) cc_final: 0.6466 (tpt) REVERT: A 41 MET cc_start: 0.7575 (tpp) cc_final: 0.7307 (tpp) REVERT: A 100 LYS cc_start: 0.9621 (mtmt) cc_final: 0.9367 (tptt) REVERT: A 116 MET cc_start: 0.9190 (tpt) cc_final: 0.8845 (mmm) REVERT: E 70 GLU cc_start: 0.8884 (pp20) cc_final: 0.8640 (tm-30) REVERT: E 75 MET cc_start: 0.9573 (mpp) cc_final: 0.9353 (mpp) REVERT: E 116 MET cc_start: 0.9697 (tpp) cc_final: 0.9263 (tpp) REVERT: E 122 TYR cc_start: 0.9290 (t80) cc_final: 0.8955 (t80) REVERT: E 123 MET cc_start: 0.9395 (mtm) cc_final: 0.9190 (mtm) outliers start: 50 outliers final: 28 residues processed: 156 average time/residue: 0.3343 time to fit residues: 86.5308 Evaluate side-chains 148 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 882 ASP Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 978 MET Chi-restraints excluded: chain C residue 1102 MET Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 107 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 97 optimal weight: 30.0000 chunk 260 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 289 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 24 optimal weight: 30.0000 chunk 95 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 GLN ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24638 Z= 0.225 Angle : 0.549 13.024 33411 Z= 0.273 Chirality : 0.040 0.286 3657 Planarity : 0.003 0.048 4403 Dihedral : 4.052 42.852 3315 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.37 % Favored : 96.56 % Rotamer: Outliers : 1.72 % Allowed : 10.53 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.15), residues: 2996 helix: 1.74 (0.13), residues: 1557 sheet: 0.18 (0.30), residues: 279 loop : -0.50 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 841 HIS 0.005 0.001 HIS E 119 PHE 0.010 0.001 PHE C 421 TYR 0.015 0.001 TYR B1111 ARG 0.004 0.000 ARG C 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 123 time to evaluate : 2.734 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: B 311 GLU cc_start: 0.9520 (tt0) cc_final: 0.9318 (mt-10) REVERT: B 504 MET cc_start: 0.8299 (tpp) cc_final: 0.7990 (tpp) REVERT: B 1015 ARG cc_start: 0.8307 (mmt90) cc_final: 0.7914 (tmm-80) REVERT: B 1021 MET cc_start: 0.6317 (tmm) cc_final: 0.5031 (tmm) REVERT: B 1061 MET cc_start: 0.8208 (mmm) cc_final: 0.7338 (mmm) REVERT: B 1098 MET cc_start: 0.4807 (OUTLIER) cc_final: 0.2221 (ttt) REVERT: B 1135 PHE cc_start: 0.8720 (t80) cc_final: 0.8413 (t80) REVERT: B 1171 MET cc_start: 0.8369 (ptm) cc_final: 0.8071 (ppp) REVERT: C 667 MET cc_start: 0.9235 (mmt) cc_final: 0.9013 (mmp) REVERT: C 752 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8594 (mt) REVERT: C 787 MET cc_start: 0.8560 (mpp) cc_final: 0.8102 (mpp) REVERT: D 295 LEU cc_start: 0.8910 (mt) cc_final: 0.8613 (tp) REVERT: D 462 MET cc_start: 0.3968 (ppp) cc_final: 0.3620 (ppp) REVERT: D 483 MET cc_start: 0.5959 (ppp) cc_final: 0.5690 (ppp) REVERT: D 518 ASN cc_start: 0.7882 (m-40) cc_final: 0.7583 (t0) REVERT: D 536 MET cc_start: 0.6689 (tpp) cc_final: 0.6418 (tpt) REVERT: A 41 MET cc_start: 0.7566 (tpp) cc_final: 0.7272 (tpp) REVERT: A 100 LYS cc_start: 0.9623 (mtmt) cc_final: 0.9379 (tptt) REVERT: A 116 MET cc_start: 0.9208 (tpt) cc_final: 0.8847 (mmm) REVERT: E 70 GLU cc_start: 0.8926 (pp20) cc_final: 0.8570 (tm-30) REVERT: E 116 MET cc_start: 0.9592 (tpp) cc_final: 0.9018 (mmm) REVERT: E 122 TYR cc_start: 0.9302 (t80) cc_final: 0.8952 (t80) outliers start: 44 outliers final: 29 residues processed: 158 average time/residue: 0.3382 time to fit residues: 88.0894 Evaluate side-chains 147 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 882 ASP Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 1102 MET Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 126 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 278 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 163 optimal weight: 0.0670 chunk 243 optimal weight: 20.0000 chunk 161 optimal weight: 7.9990 chunk 288 optimal weight: 0.7980 chunk 180 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 overall best weight: 3.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 485 GLN ** B 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 757 GLN C 792 GLN E 119 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24638 Z= 0.196 Angle : 0.546 13.958 33411 Z= 0.269 Chirality : 0.039 0.236 3657 Planarity : 0.003 0.049 4403 Dihedral : 3.962 42.310 3315 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.37 % Favored : 96.56 % Rotamer: Outliers : 1.44 % Allowed : 11.43 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.16), residues: 2996 helix: 1.89 (0.13), residues: 1555 sheet: 0.29 (0.30), residues: 279 loop : -0.49 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 164 HIS 0.004 0.001 HIS E 91 PHE 0.013 0.001 PHE C 62 TYR 0.016 0.001 TYR B1111 ARG 0.010 0.000 ARG C 272 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 2.634 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: B 264 LYS cc_start: 0.9104 (ptmm) cc_final: 0.8821 (pttp) REVERT: B 311 GLU cc_start: 0.9500 (tt0) cc_final: 0.9297 (mp0) REVERT: B 518 MET cc_start: 0.9234 (mmm) cc_final: 0.8784 (mmm) REVERT: B 1015 ARG cc_start: 0.8258 (mmt90) cc_final: 0.7859 (tmm-80) REVERT: B 1021 MET cc_start: 0.6326 (tmm) cc_final: 0.4485 (tmm) REVERT: B 1061 MET cc_start: 0.8176 (mmm) cc_final: 0.7280 (mmm) REVERT: B 1098 MET cc_start: 0.4837 (OUTLIER) cc_final: 0.2649 (mtp) REVERT: B 1135 PHE cc_start: 0.8730 (t80) cc_final: 0.8426 (t80) REVERT: B 1168 MET cc_start: 0.7385 (ttm) cc_final: 0.7109 (ttm) REVERT: B 1171 MET cc_start: 0.8434 (ptm) cc_final: 0.8166 (ppp) REVERT: C 59 ASN cc_start: 0.7778 (m-40) cc_final: 0.7496 (t0) REVERT: C 667 MET cc_start: 0.9219 (mmt) cc_final: 0.8972 (mmt) REVERT: C 787 MET cc_start: 0.8533 (mpp) cc_final: 0.8065 (mpp) REVERT: D 273 MET cc_start: 0.7730 (mpp) cc_final: 0.7122 (mpp) REVERT: D 295 LEU cc_start: 0.8932 (mt) cc_final: 0.8622 (tp) REVERT: D 462 MET cc_start: 0.3939 (ppp) cc_final: 0.3600 (ppp) REVERT: D 483 MET cc_start: 0.5977 (ppp) cc_final: 0.5699 (ppp) REVERT: D 518 ASN cc_start: 0.7839 (m-40) cc_final: 0.7527 (t0) REVERT: D 536 MET cc_start: 0.6706 (tpp) cc_final: 0.6435 (tpt) REVERT: A 41 MET cc_start: 0.7573 (tpp) cc_final: 0.7298 (tpp) REVERT: A 100 LYS cc_start: 0.9616 (mtmt) cc_final: 0.9361 (tptt) REVERT: A 116 MET cc_start: 0.9153 (tpt) cc_final: 0.8725 (mmm) REVERT: E 70 GLU cc_start: 0.8937 (pp20) cc_final: 0.8601 (tm-30) REVERT: E 75 MET cc_start: 0.9540 (mpp) cc_final: 0.8922 (mpp) REVERT: E 116 MET cc_start: 0.9588 (tpp) cc_final: 0.9031 (mmm) REVERT: E 122 TYR cc_start: 0.9306 (t80) cc_final: 0.8928 (t80) outliers start: 37 outliers final: 28 residues processed: 152 average time/residue: 0.3479 time to fit residues: 86.4335 Evaluate side-chains 150 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 1102 MET Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 107 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 86 optimal weight: 0.0370 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 226 optimal weight: 0.7980 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 496 GLN B 911 GLN ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.5420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24638 Z= 0.151 Angle : 0.524 18.177 33411 Z= 0.255 Chirality : 0.039 0.292 3657 Planarity : 0.003 0.047 4403 Dihedral : 3.793 41.644 3315 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 1.29 % Allowed : 11.71 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.16), residues: 2996 helix: 2.06 (0.13), residues: 1559 sheet: 0.38 (0.31), residues: 279 loop : -0.47 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 164 HIS 0.004 0.001 HIS E 91 PHE 0.012 0.001 PHE C 62 TYR 0.018 0.001 TYR D 108 ARG 0.009 0.000 ARG C 272 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9092 (ptmm) cc_final: 0.8793 (pttp) REVERT: B 311 GLU cc_start: 0.9479 (tt0) cc_final: 0.9276 (mp0) REVERT: B 504 MET cc_start: 0.8285 (tpp) cc_final: 0.7955 (tpp) REVERT: B 660 MET cc_start: 0.8459 (ttp) cc_final: 0.7910 (tmm) REVERT: B 1015 ARG cc_start: 0.8237 (mmt90) cc_final: 0.7786 (tmm-80) REVERT: B 1021 MET cc_start: 0.6449 (tmm) cc_final: 0.4560 (tmm) REVERT: B 1061 MET cc_start: 0.8242 (mmm) cc_final: 0.7274 (mmm) REVERT: B 1098 MET cc_start: 0.4768 (OUTLIER) cc_final: 0.2252 (ttt) REVERT: B 1135 PHE cc_start: 0.8742 (t80) cc_final: 0.8441 (t80) REVERT: B 1171 MET cc_start: 0.8471 (ptm) cc_final: 0.8193 (ppp) REVERT: C 59 ASN cc_start: 0.7653 (m-40) cc_final: 0.7447 (t0) REVERT: C 667 MET cc_start: 0.9178 (mmt) cc_final: 0.8845 (mmt) REVERT: C 787 MET cc_start: 0.8498 (mpp) cc_final: 0.8036 (mpp) REVERT: D 273 MET cc_start: 0.7705 (mpp) cc_final: 0.7107 (mpp) REVERT: D 279 MET cc_start: 0.9608 (tpp) cc_final: 0.9029 (tpp) REVERT: D 295 LEU cc_start: 0.8926 (mt) cc_final: 0.8635 (tp) REVERT: D 462 MET cc_start: 0.4063 (ppp) cc_final: 0.3820 (ppp) REVERT: D 483 MET cc_start: 0.5940 (ppp) cc_final: 0.5716 (ppp) REVERT: D 518 ASN cc_start: 0.7943 (m-40) cc_final: 0.7608 (t0) REVERT: A 100 LYS cc_start: 0.9625 (mtmt) cc_final: 0.9342 (tptt) REVERT: A 116 MET cc_start: 0.9207 (tpt) cc_final: 0.8880 (mmm) REVERT: E 70 GLU cc_start: 0.8975 (pp20) cc_final: 0.8691 (tm-30) REVERT: E 116 MET cc_start: 0.9563 (tpp) cc_final: 0.9040 (mmm) REVERT: E 122 TYR cc_start: 0.9289 (t80) cc_final: 0.8912 (t80) outliers start: 33 outliers final: 24 residues processed: 152 average time/residue: 0.3524 time to fit residues: 87.0724 Evaluate side-chains 144 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 1102 MET Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 262 optimal weight: 4.9990 chunk 276 optimal weight: 20.0000 chunk 251 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 253 optimal weight: 1.9990 chunk 267 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.5653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24638 Z= 0.231 Angle : 0.569 12.589 33411 Z= 0.282 Chirality : 0.040 0.299 3657 Planarity : 0.003 0.047 4403 Dihedral : 3.927 42.544 3315 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 1.33 % Allowed : 11.78 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.16), residues: 2996 helix: 2.00 (0.13), residues: 1550 sheet: 0.35 (0.31), residues: 284 loop : -0.48 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 574 HIS 0.003 0.001 HIS C 784 PHE 0.015 0.001 PHE C 277 TYR 0.016 0.001 TYR D 580 ARG 0.008 0.000 ARG C 272 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9109 (ptmm) cc_final: 0.8815 (pttp) REVERT: B 504 MET cc_start: 0.8395 (tpp) cc_final: 0.7801 (tpp) REVERT: B 660 MET cc_start: 0.8532 (ttp) cc_final: 0.7946 (tmm) REVERT: B 1015 ARG cc_start: 0.8223 (mmt90) cc_final: 0.7792 (tmm-80) REVERT: B 1021 MET cc_start: 0.6472 (tmm) cc_final: 0.4877 (tmm) REVERT: B 1061 MET cc_start: 0.8320 (mmm) cc_final: 0.7412 (mmm) REVERT: B 1098 MET cc_start: 0.5032 (OUTLIER) cc_final: 0.2877 (mtp) REVERT: B 1135 PHE cc_start: 0.8749 (t80) cc_final: 0.8439 (t80) REVERT: B 1168 MET cc_start: 0.7360 (ttm) cc_final: 0.7086 (ttm) REVERT: B 1171 MET cc_start: 0.8465 (ptm) cc_final: 0.8195 (ppp) REVERT: C 667 MET cc_start: 0.9166 (mmt) cc_final: 0.8823 (mmt) REVERT: C 787 MET cc_start: 0.8537 (mpp) cc_final: 0.8082 (mpp) REVERT: C 1079 MET cc_start: 0.9237 (pmm) cc_final: 0.8894 (ppp) REVERT: D 273 MET cc_start: 0.7620 (mpp) cc_final: 0.7055 (mpp) REVERT: D 279 MET cc_start: 0.9639 (tpp) cc_final: 0.9193 (tpp) REVERT: D 295 LEU cc_start: 0.8839 (mt) cc_final: 0.8550 (tt) REVERT: D 462 MET cc_start: 0.4125 (ppp) cc_final: 0.3878 (ppp) REVERT: D 483 MET cc_start: 0.5884 (ppp) cc_final: 0.5648 (ppp) REVERT: D 536 MET cc_start: 0.6569 (tpp) cc_final: 0.6347 (tpt) REVERT: D 596 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7728 (ptt-90) REVERT: A 41 MET cc_start: 0.7597 (tpp) cc_final: 0.7292 (tpp) REVERT: A 100 LYS cc_start: 0.9624 (mtmt) cc_final: 0.9345 (tptt) REVERT: A 116 MET cc_start: 0.9209 (tpt) cc_final: 0.8846 (mmm) REVERT: E 70 GLU cc_start: 0.8963 (pp20) cc_final: 0.8687 (tm-30) REVERT: E 75 MET cc_start: 0.9549 (mpp) cc_final: 0.9114 (mpp) REVERT: E 116 MET cc_start: 0.9617 (tpp) cc_final: 0.8994 (mmm) REVERT: E 122 TYR cc_start: 0.9304 (t80) cc_final: 0.8897 (t80) outliers start: 34 outliers final: 24 residues processed: 146 average time/residue: 0.3362 time to fit residues: 80.4847 Evaluate side-chains 143 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 1102 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 596 ARG Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 176 optimal weight: 9.9990 chunk 283 optimal weight: 7.9990 chunk 173 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 chunk 297 optimal weight: 1.9990 chunk 274 optimal weight: 7.9990 chunk 237 optimal weight: 0.0870 chunk 24 optimal weight: 30.0000 chunk 183 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 GLN ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24638 Z= 0.133 Angle : 0.525 11.565 33411 Z= 0.257 Chirality : 0.039 0.280 3657 Planarity : 0.003 0.050 4403 Dihedral : 3.716 40.883 3315 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.06 % Rotamer: Outliers : 1.01 % Allowed : 12.25 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.16), residues: 2996 helix: 2.19 (0.14), residues: 1551 sheet: 0.53 (0.32), residues: 273 loop : -0.39 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 164 HIS 0.005 0.001 HIS B1133 PHE 0.013 0.001 PHE C 277 TYR 0.014 0.001 TYR B1111 ARG 0.008 0.000 ARG C 272 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 2.176 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: B 259 ARG cc_start: 0.9622 (ttp80) cc_final: 0.9121 (ttt180) REVERT: B 264 LYS cc_start: 0.9072 (ptmm) cc_final: 0.8779 (pttp) REVERT: B 311 GLU cc_start: 0.9473 (tt0) cc_final: 0.9270 (mp0) REVERT: B 504 MET cc_start: 0.8247 (tpp) cc_final: 0.7581 (tpp) REVERT: B 660 MET cc_start: 0.8425 (ttp) cc_final: 0.7894 (tmm) REVERT: B 1015 ARG cc_start: 0.8228 (mmt90) cc_final: 0.7782 (tmm-80) REVERT: B 1021 MET cc_start: 0.5753 (tmm) cc_final: 0.4693 (tmm) REVERT: B 1061 MET cc_start: 0.8258 (mmm) cc_final: 0.7398 (mmm) REVERT: B 1098 MET cc_start: 0.4841 (OUTLIER) cc_final: 0.2650 (mtp) REVERT: B 1135 PHE cc_start: 0.8782 (t80) cc_final: 0.8465 (t80) REVERT: B 1171 MET cc_start: 0.8633 (ptm) cc_final: 0.8342 (ppp) REVERT: C 667 MET cc_start: 0.9139 (mmt) cc_final: 0.8744 (mmt) REVERT: C 787 MET cc_start: 0.8493 (mpp) cc_final: 0.8052 (mpp) REVERT: D 273 MET cc_start: 0.7630 (mpp) cc_final: 0.7033 (mpp) REVERT: D 279 MET cc_start: 0.9646 (tpp) cc_final: 0.9197 (tpp) REVERT: D 295 LEU cc_start: 0.8880 (mt) cc_final: 0.8678 (tp) REVERT: D 462 MET cc_start: 0.4403 (ppp) cc_final: 0.4184 (ppp) REVERT: D 483 MET cc_start: 0.5867 (ppp) cc_final: 0.5629 (ppp) REVERT: D 536 MET cc_start: 0.6545 (tpp) cc_final: 0.6313 (tpt) REVERT: A 100 LYS cc_start: 0.9597 (mtmt) cc_final: 0.9293 (tptt) REVERT: A 104 ARG cc_start: 0.9251 (ttm170) cc_final: 0.8955 (ttm170) REVERT: A 116 MET cc_start: 0.9202 (tpt) cc_final: 0.8865 (mmm) REVERT: E 70 GLU cc_start: 0.8983 (pp20) cc_final: 0.8691 (tm-30) REVERT: E 75 MET cc_start: 0.9541 (mpp) cc_final: 0.9157 (mpp) REVERT: E 116 MET cc_start: 0.9561 (tpp) cc_final: 0.9117 (tpp) REVERT: E 122 TYR cc_start: 0.9297 (t80) cc_final: 0.8898 (t80) outliers start: 26 outliers final: 21 residues processed: 143 average time/residue: 0.3731 time to fit residues: 86.8279 Evaluate side-chains 141 residues out of total 2563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 333 ASN Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 1102 MET Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 188 optimal weight: 20.0000 chunk 252 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 237 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 243 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1153 GLN ** C 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 749 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.057720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.043271 restraints weight = 135286.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.044402 restraints weight = 76126.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.045069 restraints weight = 52980.077| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24638 Z= 0.262 Angle : 0.587 11.067 33411 Z= 0.293 Chirality : 0.041 0.295 3657 Planarity : 0.004 0.049 4403 Dihedral : 3.956 42.694 3315 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 1.33 % Allowed : 12.06 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.16), residues: 2996 helix: 2.02 (0.13), residues: 1548 sheet: 0.43 (0.31), residues: 275 loop : -0.45 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 574 HIS 0.007 0.001 HIS E 119 PHE 0.016 0.001 PHE C 277 TYR 0.016 0.001 TYR D 108 ARG 0.007 0.000 ARG C 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3522.87 seconds wall clock time: 65 minutes 27.97 seconds (3927.97 seconds total)