Starting phenix.real_space_refine on Sat Mar 23 05:46:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asv_15622/03_2024/8asv_15622_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asv_15622/03_2024/8asv_15622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asv_15622/03_2024/8asv_15622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asv_15622/03_2024/8asv_15622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asv_15622/03_2024/8asv_15622_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asv_15622/03_2024/8asv_15622_updated.pdb" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 147 5.16 5 C 22720 2.51 5 N 6063 2.21 5 O 6855 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 538": "OD1" <-> "OD2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A ASP 777": "OD1" <-> "OD2" Residue "A TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 914": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1005": "OD1" <-> "OD2" Residue "A TYR 1106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 425": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B GLU 597": "OE1" <-> "OE2" Residue "B TYR 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 788": "OE1" <-> "OE2" Residue "C PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 547": "OE1" <-> "OE2" Residue "D TYR 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1053": "OE1" <-> "OE2" Residue "D GLU 1137": "OE1" <-> "OE2" Residue "D PHE 1151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 180": "OD1" <-> "OD2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 112": "OE1" <-> "OE2" Residue "G ASP 138": "OD1" <-> "OD2" Residue "G PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H ASP 172": "OD1" <-> "OD2" Residue "H PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 63": "OE1" <-> "OE2" Residue "I TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 194": "OE1" <-> "OE2" Residue "I PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35789 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 9844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1235, 9844 Classifications: {'peptide': 1235} Link IDs: {'PTRANS': 39, 'TRANS': 1195} Chain breaks: 1 Chain: "B" Number of atoms: 6286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6286 Classifications: {'peptide': 786} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 759} Chain: "C" Number of atoms: 3730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3730 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 442} Chain: "D" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2769 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 9, 'TRANS': 333} Chain: "E" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1871 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2129 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain: "G" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2346 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 277} Chain breaks: 1 Chain: "H" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1865 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain: "I" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2129 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain: "J" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2812 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 331} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16336 SG CYS C 121 61.749 72.793 63.212 1.00 55.00 S ATOM 16236 SG CYS C 108 56.173 72.226 59.603 1.00 56.86 S ATOM 16311 SG CYS C 118 59.720 77.063 62.489 1.00 49.05 S Time building chain proxies: 16.69, per 1000 atoms: 0.47 Number of scatterers: 35789 At special positions: 0 Unit cell: (157.38, 165.12, 226.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 147 16.00 O 6855 8.00 N 6063 7.00 C 22720 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: 13.24 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 601 " pdb="FE3 SF4 C 601 " - pdb=" SG CYS C 118 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 121 " pdb="FE2 SF4 C 601 " - pdb=" SG CYS C 108 " Number of angles added : 9 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8530 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 46 sheets defined 26.0% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.36 Creating SS restraints... Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 742 through 755 removed outlier: 3.583A pdb=" N ALA A 755 " --> pdb=" O LYS A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 772 through 775 Processing helix chain 'A' and resid 780 through 793 removed outlier: 6.091A pdb=" N GLU A 788 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL A 789 " --> pdb=" O GLU A 785 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 805 Processing helix chain 'A' and resid 812 through 815 No H-bonds generated for 'chain 'A' and resid 812 through 815' Processing helix chain 'A' and resid 819 through 821 No H-bonds generated for 'chain 'A' and resid 819 through 821' Processing helix chain 'A' and resid 838 through 840 No H-bonds generated for 'chain 'A' and resid 838 through 840' Processing helix chain 'A' and resid 842 through 847 Processing helix chain 'A' and resid 854 through 868 removed outlier: 3.951A pdb=" N SER A 868 " --> pdb=" O ASN A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 885 removed outlier: 7.947A pdb=" N GLN A 878 " --> pdb=" O LYS A 874 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR A 879 " --> pdb=" O LYS A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 901 removed outlier: 3.814A pdb=" N GLU A 901 " --> pdb=" O LYS A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 918 removed outlier: 3.663A pdb=" N LEU A 918 " --> pdb=" O TYR A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 930 Processing helix chain 'A' and resid 935 through 943 removed outlier: 4.426A pdb=" N LYS A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 958 Proline residue: A 953 - end of helix Processing helix chain 'A' and resid 963 through 974 Processing helix chain 'A' and resid 977 through 987 removed outlier: 3.918A pdb=" N GLU A 986 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 987 " --> pdb=" O HIS A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1004 Processing helix chain 'A' and resid 1007 through 1012 Processing helix chain 'A' and resid 1018 through 1035 removed outlier: 4.832A pdb=" N VAL A1023 " --> pdb=" O GLU A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1048 Processing helix chain 'A' and resid 1051 through 1060 Processing helix chain 'A' and resid 1064 through 1073 Processing helix chain 'A' and resid 1076 through 1093 removed outlier: 4.525A pdb=" N GLU A1080 " --> pdb=" O GLU A1077 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A1082 " --> pdb=" O VAL A1079 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA A1083 " --> pdb=" O GLU A1080 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU A1084 " --> pdb=" O SER A1081 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A1090 " --> pdb=" O ILE A1087 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A1093 " --> pdb=" O LEU A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1105 removed outlier: 4.401A pdb=" N ILE A1102 " --> pdb=" O ASP A1098 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN A1103 " --> pdb=" O ALA A1099 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU A1104 " --> pdb=" O ALA A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1119 removed outlier: 4.520A pdb=" N LEU A1116 " --> pdb=" O GLU A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1132 Processing helix chain 'A' and resid 1138 through 1141 No H-bonds generated for 'chain 'A' and resid 1138 through 1141' Processing helix chain 'A' and resid 1143 through 1170 Processing helix chain 'A' and resid 1254 through 1268 Processing helix chain 'A' and resid 1272 through 1282 Processing helix chain 'A' and resid 1286 through 1303 Processing helix chain 'B' and resid 470 through 477 Processing helix chain 'B' and resid 486 through 488 No H-bonds generated for 'chain 'B' and resid 486 through 488' Processing helix chain 'B' and resid 539 through 545 removed outlier: 3.916A pdb=" N GLN B 543 " --> pdb=" O GLU B 539 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ARG B 544 " --> pdb=" O ASP B 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 153 through 167 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 188 through 203 removed outlier: 4.282A pdb=" N LEU C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 273 through 286 removed outlier: 4.167A pdb=" N CYS C 277 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 315 removed outlier: 3.547A pdb=" N PHE C 310 " --> pdb=" O ASP C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.872A pdb=" N LEU C 340 " --> pdb=" O GLY C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 removed outlier: 4.057A pdb=" N LEU C 364 " --> pdb=" O ARG C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 403 removed outlier: 4.161A pdb=" N ALA C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 413 No H-bonds generated for 'chain 'C' and resid 410 through 413' Processing helix chain 'C' and resid 508 through 522 removed outlier: 3.736A pdb=" N LEU C 512 " --> pdb=" O PHE C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 537 No H-bonds generated for 'chain 'C' and resid 535 through 537' Processing helix chain 'D' and resid 1007 through 1014 removed outlier: 3.723A pdb=" N TYR D1014 " --> pdb=" O GLY D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1018 through 1035 removed outlier: 5.779A pdb=" N LYS D1030 " --> pdb=" O ASN D1026 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N HIS D1031 " --> pdb=" O ILE D1027 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1048 Processing helix chain 'D' and resid 1053 through 1060 Processing helix chain 'D' and resid 1065 through 1074 Processing helix chain 'D' and resid 1076 through 1078 No H-bonds generated for 'chain 'D' and resid 1076 through 1078' Processing helix chain 'D' and resid 1081 through 1093 removed outlier: 3.532A pdb=" N GLU D1085 " --> pdb=" O SER D1081 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D1086 " --> pdb=" O VAL D1082 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER D1088 " --> pdb=" O GLU D1084 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N SER D1089 " --> pdb=" O GLU D1085 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU D1093 " --> pdb=" O SER D1089 " (cutoff:3.500A) Processing helix chain 'D' and resid 1096 through 1106 Processing helix chain 'D' and resid 1111 through 1119 Processing helix chain 'D' and resid 1123 through 1132 Processing helix chain 'D' and resid 1137 through 1141 removed outlier: 3.602A pdb=" N GLU D1140 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU D1141 " --> pdb=" O LEU D1138 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1137 through 1141' Processing helix chain 'D' and resid 1143 through 1158 Processing helix chain 'D' and resid 1160 through 1165 removed outlier: 3.657A pdb=" N GLN D1164 " --> pdb=" O ASP D1160 " (cutoff:3.500A) Processing helix chain 'D' and resid 1254 through 1282 removed outlier: 4.198A pdb=" N VAL D1259 " --> pdb=" O LEU D1255 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY D1260 " --> pdb=" O VAL D1256 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU D1262 " --> pdb=" O SER D1258 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU D1264 " --> pdb=" O GLY D1260 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG D1265 " --> pdb=" O ARG D1261 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU D1266 " --> pdb=" O LEU D1262 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN D1267 " --> pdb=" O ILE D1263 " (cutoff:3.500A) Proline residue: D1271 - end of helix Processing helix chain 'D' and resid 1288 through 1309 removed outlier: 3.700A pdb=" N LYS D1308 " --> pdb=" O LYS D1304 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU D1309 " --> pdb=" O ALA D1305 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 16 Processing helix chain 'E' and resid 37 through 48 removed outlier: 3.529A pdb=" N LYS E 47 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER E 48 " --> pdb=" O HIS E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 88 removed outlier: 3.818A pdb=" N ILE E 87 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 121 removed outlier: 5.503A pdb=" N THR E 118 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 163 Processing helix chain 'E' and resid 181 through 189 Processing helix chain 'F' and resid 21 through 24 Processing helix chain 'F' and resid 43 through 53 removed outlier: 4.174A pdb=" N ALA F 48 " --> pdb=" O TRP F 44 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL F 50 " --> pdb=" O ILE F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 96 removed outlier: 3.687A pdb=" N LYS F 95 " --> pdb=" O ASN F 91 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU F 96 " --> pdb=" O SER F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 102 No H-bonds generated for 'chain 'F' and resid 100 through 102' Processing helix chain 'F' and resid 112 through 115 No H-bonds generated for 'chain 'F' and resid 112 through 115' Processing helix chain 'F' and resid 122 through 138 removed outlier: 4.175A pdb=" N GLN F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 157 Processing helix chain 'F' and resid 163 through 169 Processing helix chain 'F' and resid 171 through 176 Processing helix chain 'F' and resid 202 through 214 removed outlier: 3.810A pdb=" N PHE F 212 " --> pdb=" O TYR F 208 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE F 213 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS F 214 " --> pdb=" O SER F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'G' and resid 118 through 135 removed outlier: 3.994A pdb=" N LEU G 122 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE G 126 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA G 127 " --> pdb=" O GLY G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 162 Processing helix chain 'G' and resid 265 through 279 removed outlier: 3.508A pdb=" N GLU G 273 " --> pdb=" O LEU G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 320 removed outlier: 3.645A pdb=" N ILE G 308 " --> pdb=" O SER G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 345 Processing helix chain 'G' and resid 359 through 368 Processing helix chain 'G' and resid 388 through 392 removed outlier: 3.625A pdb=" N ARG G 392 " --> pdb=" O PHE G 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 16 Processing helix chain 'H' and resid 36 through 49 removed outlier: 3.643A pdb=" N SER H 48 " --> pdb=" O HIS H 44 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS H 49 " --> pdb=" O GLN H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 89 removed outlier: 4.339A pdb=" N LYS H 85 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE H 88 " --> pdb=" O VAL H 84 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER H 89 " --> pdb=" O LYS H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 123 removed outlier: 5.500A pdb=" N THR H 118 " --> pdb=" O GLU H 115 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG H 119 " --> pdb=" O TYR H 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER H 122 " --> pdb=" O ARG H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 145 No H-bonds generated for 'chain 'H' and resid 143 through 145' Processing helix chain 'H' and resid 157 through 164 Processing helix chain 'H' and resid 181 through 189 Processing helix chain 'I' and resid 21 through 24 No H-bonds generated for 'chain 'I' and resid 21 through 24' Processing helix chain 'I' and resid 42 through 54 removed outlier: 4.347A pdb=" N ASN I 47 " --> pdb=" O TRP I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 95 Processing helix chain 'I' and resid 122 through 136 removed outlier: 4.127A pdb=" N PHE I 133 " --> pdb=" O VAL I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 157 Processing helix chain 'I' and resid 163 through 177 removed outlier: 5.395A pdb=" N THR I 172 " --> pdb=" O ASN I 168 " (cutoff:3.500A) Proline residue: I 173 - end of helix Processing helix chain 'I' and resid 202 through 214 removed outlier: 3.691A pdb=" N PHE I 207 " --> pdb=" O ASN I 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 97 Processing helix chain 'J' and resid 118 through 135 removed outlier: 3.791A pdb=" N LEU J 122 " --> pdb=" O HIS J 119 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY J 123 " --> pdb=" O SER J 120 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N PHE J 126 " --> pdb=" O GLY J 123 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN J 129 " --> pdb=" O PHE J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 162 removed outlier: 3.656A pdb=" N LYS J 162 " --> pdb=" O MET J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 231 through 233 No H-bonds generated for 'chain 'J' and resid 231 through 233' Processing helix chain 'J' and resid 265 through 277 removed outlier: 3.703A pdb=" N SER J 270 " --> pdb=" O SER J 266 " (cutoff:3.500A) Processing helix chain 'J' and resid 299 through 302 Processing helix chain 'J' and resid 306 through 320 Processing helix chain 'J' and resid 338 through 344 Processing helix chain 'J' and resid 362 through 368 Processing helix chain 'J' and resid 388 through 390 No H-bonds generated for 'chain 'J' and resid 388 through 390' Processing sheet with id= A, first strand: chain 'A' and resid 20 through 23 Processing sheet with id= B, first strand: chain 'A' and resid 26 through 30 removed outlier: 3.558A pdb=" N PHE A 413 " --> pdb=" O ASN A 420 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 46 through 50 removed outlier: 7.097A pdb=" N VAL A 62 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER A 50 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N THR A 60 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 86 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN A 75 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL A 84 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N MET A 77 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG A 82 " --> pdb=" O MET A 77 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 134 through 136 removed outlier: 3.996A pdb=" N SER A 99 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 145 through 150 removed outlier: 6.970A pdb=" N VAL A 160 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA A 148 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ALA A 158 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 252 through 255 removed outlier: 3.908A pdb=" N THR A 252 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER A 296 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 317 through 323 removed outlier: 4.691A pdb=" N VAL A 332 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 360 through 362 removed outlier: 3.750A pdb=" N GLN A 391 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR A 381 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU A 389 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 441 through 446 Processing sheet with id= J, first strand: chain 'A' and resid 477 through 480 removed outlier: 3.967A pdb=" N ASP A 477 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA A 499 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE A 514 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 533 through 536 Processing sheet with id= L, first strand: chain 'A' and resid 579 through 581 removed outlier: 3.896A pdb=" N VAL A 589 " --> pdb=" O ARG A 580 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLN A 599 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU A 608 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 621 through 625 Processing sheet with id= N, first strand: chain 'A' and resid 708 through 710 removed outlier: 4.371A pdb=" N ASN A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 677 " --> pdb=" O SER A 666 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER A 666 " --> pdb=" O THR A 677 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 736 through 739 removed outlier: 5.359A pdb=" N GLN A 730 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU A 717 " --> pdb=" O GLN A 730 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 30 through 34 removed outlier: 4.366A pdb=" N ALA B 53 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 62 through 67 removed outlier: 6.692A pdb=" N ALA B 77 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL B 65 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL B 75 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE B 67 " --> pdb=" O PHE B 73 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE B 73 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL B 83 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN B 98 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LYS B 87 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N CYS B 96 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 107 through 113 removed outlier: 6.660A pdb=" N GLY B 120 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU B 110 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N SER B 118 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA B 112 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ARG B 130 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B 140 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 153 through 160 removed outlier: 7.169A pdb=" N GLY B 171 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU B 156 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA B 169 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU B 158 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU B 167 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LYS B 160 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LYS B 165 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER B 181 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL B 194 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 259 through 262 removed outlier: 3.557A pdb=" N CYS B 222 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 209 " --> pdb=" O CYS B 222 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B 224 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 207 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 284 through 288 removed outlier: 6.784A pdb=" N ALA B 299 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU B 287 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU B 297 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 321 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLU B 309 " --> pdb=" O CYS B 319 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N CYS B 319 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 345 through 348 removed outlier: 3.834A pdb=" N ILE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 588 through 591 Processing sheet with id= X, first strand: chain 'B' and resid 609 through 614 removed outlier: 7.166A pdb=" N VAL B 624 " --> pdb=" O THR B 610 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU B 612 " --> pdb=" O LEU B 622 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU B 622 " --> pdb=" O LEU B 612 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N PHE B 614 " --> pdb=" O PHE B 620 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N PHE B 620 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLU B 634 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU B 644 " --> pdb=" O GLU B 634 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 656 through 660 removed outlier: 7.003A pdb=" N ALA B 673 " --> pdb=" O TRP B 657 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA B 659 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 671 " --> pdb=" O ALA B 659 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 696 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ARG B 683 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU B 694 " --> pdb=" O ARG B 683 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLN B 685 " --> pdb=" O TYR B 692 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR B 692 " --> pdb=" O GLN B 685 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 704 through 709 removed outlier: 6.983A pdb=" N GLY B 723 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE B 707 " --> pdb=" O SER B 721 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER B 721 " --> pdb=" O ILE B 707 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE B 709 " --> pdb=" O LEU B 719 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU B 719 " --> pdb=" O ILE B 709 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N SER B 733 " --> pdb=" O LEU B 741 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 741 " --> pdb=" O SER B 733 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR B 735 " --> pdb=" O PHE B 739 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE B 739 " --> pdb=" O THR B 735 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 5 through 11 removed outlier: 3.561A pdb=" N THR B 6 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 782 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE B 10 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR B 780 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER B 779 " --> pdb=" O SER B 775 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 775 " --> pdb=" O SER B 779 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 411 through 415 removed outlier: 6.133A pdb=" N ALA B 413 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU B 431 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP B 415 " --> pdb=" O TRP B 429 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TRP B 429 " --> pdb=" O TRP B 415 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 444 through 449 removed outlier: 6.831A pdb=" N ARG B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 462 through 465 Processing sheet with id= AE, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.814A pdb=" N LYS C 173 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL C 99 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU C 175 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL C 101 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL C 177 " --> pdb=" O VAL C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'C' and resid 228 through 230 removed outlier: 6.809A pdb=" N ARG C 251 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS C 289 " --> pdb=" O LEU C 252 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'C' and resid 430 through 437 removed outlier: 3.823A pdb=" N GLY C 458 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASP C 450 " --> pdb=" O LEU C 456 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU C 456 " --> pdb=" O ASP C 450 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU C 485 " --> pdb=" O ARG C 461 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 481 through 483 Processing sheet with id= AI, first strand: chain 'E' and resid 229 through 231 removed outlier: 7.084A pdb=" N PHE E 24 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N VAL E 169 " --> pdb=" O PHE E 24 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU E 26 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE E 171 " --> pdb=" O LEU E 26 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU E 28 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N VAL E 173 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N MET E 131 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N CYS E 27 " --> pdb=" O MET E 131 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA E 133 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASP E 29 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR E 135 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL E 104 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N THR E 134 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE E 106 " --> pdb=" O THR E 134 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N HIS E 136 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 217 through 221 removed outlier: 3.937A pdb=" N ILE F 217 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL F 146 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N VAL F 184 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE F 148 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N ASN F 186 " --> pdb=" O ILE F 148 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 77 through 81 removed outlier: 3.595A pdb=" N SER F 81 " --> pdb=" O LEU F 106 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'F' and resid 234 through 236 Processing sheet with id= AM, first strand: chain 'G' and resid 411 through 415 removed outlier: 3.796A pdb=" N SER G 400 " --> pdb=" O VAL G 381 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL G 381 " --> pdb=" O SER G 400 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N TRP G 402 " --> pdb=" O GLY G 379 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLY G 379 " --> pdb=" O TRP G 402 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL G 351 " --> pdb=" O LEU G 384 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL G 108 " --> pdb=" O LEU G 327 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA G 329 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL G 110 " --> pdb=" O ALA G 329 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER G 330 " --> pdb=" O ILE G 288 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 151 through 154 Processing sheet with id= AO, first strand: chain 'H' and resid 214 through 219 removed outlier: 4.106A pdb=" N LEU H 216 " --> pdb=" O ASN H 208 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASN H 208 " --> pdb=" O LEU H 216 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE H 171 " --> pdb=" O LEU H 28 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'H' and resid 220 through 223 Processing sheet with id= AQ, first strand: chain 'I' and resid 267 through 271 removed outlier: 3.574A pdb=" N ILE I 217 " --> pdb=" O LEU I 31 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL I 146 " --> pdb=" O ILE I 182 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL I 184 " --> pdb=" O VAL I 146 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE I 148 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N ASN I 186 " --> pdb=" O ILE I 148 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL I 78 " --> pdb=" O ILE I 147 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N GLU I 149 " --> pdb=" O VAL I 78 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA I 80 " --> pdb=" O GLU I 149 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'J' and resid 107 through 112 removed outlier: 7.040A pdb=" N LEU J 327 " --> pdb=" O VAL J 108 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL J 110 " --> pdb=" O LEU J 327 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA J 329 " --> pdb=" O VAL J 110 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N GLU J 112 " --> pdb=" O ALA J 329 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE J 331 " --> pdb=" O GLU J 112 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'J' and resid 283 through 286 Processing sheet with id= AT, first strand: chain 'J' and resid 412 through 415 removed outlier: 6.236A pdb=" N VAL J 381 " --> pdb=" O SER J 400 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP J 402 " --> pdb=" O GLY J 379 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY J 379 " --> pdb=" O TRP J 402 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL J 351 " --> pdb=" O LEU J 384 " (cutoff:3.500A) 1043 hydrogen bonds defined for protein. 2835 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: 13.83 Time building geometry restraints manager: 14.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.44: 15518 1.44 - 1.65: 20758 1.65 - 1.86: 231 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 36519 Sorted by residual: bond pdb=" C VAL C 493 " pdb=" N PRO C 494 " ideal model delta sigma weight residual 1.329 1.360 -0.031 1.22e-02 6.72e+03 6.26e+00 bond pdb=" CA ILE G 252 " pdb=" C ILE G 252 " ideal model delta sigma weight residual 1.524 1.504 0.020 8.60e-03 1.35e+04 5.40e+00 bond pdb=" C MET G 248 " pdb=" O MET G 248 " ideal model delta sigma weight residual 1.244 1.227 0.017 9.30e-03 1.16e+04 3.22e+00 bond pdb=" CA ASN A 992 " pdb=" C ASN A 992 " ideal model delta sigma weight residual 1.523 1.504 0.019 1.21e-02 6.83e+03 2.58e+00 bond pdb=" C PRO J 338 " pdb=" N PRO J 339 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.03e+00 ... (remaining 36514 not shown) Histogram of bond angle deviations from ideal: 73.63 - 85.73: 12 85.73 - 97.83: 0 97.83 - 109.93: 5002 109.93 - 122.03: 36862 122.03 - 134.13: 7589 Bond angle restraints: 49465 Sorted by residual: angle pdb=" N VAL J 75 " pdb=" CA VAL J 75 " pdb=" C VAL J 75 " ideal model delta sigma weight residual 111.91 107.08 4.83 8.90e-01 1.26e+00 2.94e+01 angle pdb=" N SER F 64 " pdb=" CA SER F 64 " pdb=" C SER F 64 " ideal model delta sigma weight residual 108.19 114.36 -6.17 1.29e+00 6.01e-01 2.29e+01 angle pdb=" C SER D1314 " pdb=" CA SER D1314 " pdb=" CB SER D1314 " ideal model delta sigma weight residual 116.63 111.18 5.45 1.16e+00 7.43e-01 2.21e+01 angle pdb=" N ASN I 102 " pdb=" CA ASN I 102 " pdb=" C ASN I 102 " ideal model delta sigma weight residual 112.97 108.00 4.97 1.06e+00 8.90e-01 2.19e+01 angle pdb=" N TYR A1038 " pdb=" CA TYR A1038 " pdb=" C TYR A1038 " ideal model delta sigma weight residual 110.97 115.43 -4.46 1.09e+00 8.42e-01 1.68e+01 ... (remaining 49460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 19733 17.79 - 35.59: 2001 35.59 - 53.38: 293 53.38 - 71.17: 73 71.17 - 88.96: 63 Dihedral angle restraints: 22163 sinusoidal: 8997 harmonic: 13166 Sorted by residual: dihedral pdb=" CA ASN J 191 " pdb=" C ASN J 191 " pdb=" N LEU J 192 " pdb=" CA LEU J 192 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA LYS I 225 " pdb=" C LYS I 225 " pdb=" N THR I 226 " pdb=" CA THR I 226 " ideal model delta harmonic sigma weight residual 180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ASP B 528 " pdb=" C ASP B 528 " pdb=" N PRO B 529 " pdb=" CA PRO B 529 " ideal model delta harmonic sigma weight residual -180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 22160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3882 0.040 - 0.081: 1254 0.081 - 0.121: 393 0.121 - 0.162: 60 0.162 - 0.202: 6 Chirality restraints: 5595 Sorted by residual: chirality pdb=" CB ILE F 217 " pdb=" CA ILE F 217 " pdb=" CG1 ILE F 217 " pdb=" CG2 ILE F 217 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLU C 308 " pdb=" N GLU C 308 " pdb=" C GLU C 308 " pdb=" CB GLU C 308 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA PHE B 355 " pdb=" N PHE B 355 " pdb=" C PHE B 355 " pdb=" CB PHE B 355 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.60e-01 ... (remaining 5592 not shown) Planarity restraints: 6353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 831 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C MET A 831 " 0.038 2.00e-02 2.50e+03 pdb=" O MET A 831 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 832 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1296 " -0.010 2.00e-02 2.50e+03 1.62e-02 4.61e+00 pdb=" CG PHE A1296 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A1296 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A1296 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A1296 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1296 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A1296 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU J 386 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO J 387 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO J 387 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 387 " 0.028 5.00e-02 4.00e+02 ... (remaining 6350 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 948 2.68 - 3.24: 35477 3.24 - 3.79: 52911 3.79 - 4.35: 71940 4.35 - 4.90: 116040 Nonbonded interactions: 277316 Sorted by model distance: nonbonded pdb=" OG1 THR I 35 " pdb=" OD1 ASN I 220 " model vdw 2.128 2.440 nonbonded pdb=" OE1 GLU E 41 " pdb=" OH TYR E 229 " model vdw 2.135 2.440 nonbonded pdb=" OG1 THR B 369 " pdb=" O ILE B 374 " model vdw 2.149 2.440 nonbonded pdb=" OG1 THR A 592 " pdb=" OD1 ASP A 594 " model vdw 2.171 2.440 nonbonded pdb=" O ASP A 185 " pdb=" NH2 ARG A 286 " model vdw 2.171 2.520 ... (remaining 277311 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'E' and resid 2 through 232) selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 16.640 Check model and map are aligned: 0.520 Set scattering table: 0.300 Process input model: 95.930 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36519 Z= 0.172 Angle : 0.680 11.733 49465 Z= 0.398 Chirality : 0.044 0.202 5595 Planarity : 0.004 0.050 6353 Dihedral : 15.093 88.964 13633 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.00 % Favored : 90.93 % Rotamer: Outliers : 0.02 % Allowed : 0.42 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.14 (0.12), residues: 4454 helix: -0.53 (0.15), residues: 1163 sheet: -0.64 (0.17), residues: 1020 loop : -2.32 (0.12), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1064 HIS 0.005 0.001 HIS D1345 PHE 0.037 0.001 PHE A1296 TYR 0.024 0.001 TYR G 237 ARG 0.006 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 4.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 605 GLN cc_start: 0.7922 (mp10) cc_final: 0.7498 (mp10) REVERT: A 993 VAL cc_start: 0.5235 (OUTLIER) cc_final: 0.5030 (m) REVERT: A 1285 MET cc_start: 0.4030 (mtp) cc_final: 0.3700 (mmm) REVERT: C 234 ASP cc_start: 0.8127 (t70) cc_final: 0.7907 (t0) REVERT: C 400 MET cc_start: 0.7332 (mpp) cc_final: 0.7012 (mpp) REVERT: H 78 MET cc_start: 0.7242 (ppp) cc_final: 0.6700 (ppp) outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.4292 time to fit residues: 190.9436 Evaluate side-chains 198 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 3.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 374 optimal weight: 0.9990 chunk 335 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 chunk 179 optimal weight: 0.0570 chunk 347 optimal weight: 0.5980 chunk 134 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 258 optimal weight: 9.9990 chunk 402 optimal weight: 6.9990 overall best weight: 2.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 83 ASN A 459 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1293 GLN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.0536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36519 Z= 0.194 Angle : 0.573 7.817 49465 Z= 0.306 Chirality : 0.044 0.160 5595 Planarity : 0.004 0.052 6353 Dihedral : 5.442 30.206 4853 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.70 % Favored : 90.26 % Rotamer: Outliers : 0.02 % Allowed : 5.49 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.10 (0.12), residues: 4454 helix: -0.42 (0.15), residues: 1157 sheet: -0.65 (0.17), residues: 1020 loop : -2.32 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 310 HIS 0.005 0.001 HIS B 652 PHE 0.029 0.002 PHE A1151 TYR 0.020 0.001 TYR G 237 ARG 0.004 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 4.605 Fit side-chains revert: symmetry clash REVERT: A 605 GLN cc_start: 0.7951 (mp10) cc_final: 0.7536 (mp10) REVERT: A 1285 MET cc_start: 0.3928 (mtp) cc_final: 0.3662 (mmm) REVERT: C 234 ASP cc_start: 0.8217 (t70) cc_final: 0.7930 (t0) REVERT: G 175 MET cc_start: 0.1375 (mpp) cc_final: 0.1032 (mpp) REVERT: H 78 MET cc_start: 0.7216 (ppp) cc_final: 0.6603 (ppp) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.4274 time to fit residues: 186.3624 Evaluate side-chains 188 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 4.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 223 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 334 optimal weight: 0.9990 chunk 273 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 403 optimal weight: 7.9990 chunk 435 optimal weight: 3.9990 chunk 358 optimal weight: 9.9990 chunk 399 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 323 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN I 30 ASN I 237 HIS I 257 ASN ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 36519 Z= 0.348 Angle : 0.713 8.776 49465 Z= 0.379 Chirality : 0.048 0.211 5595 Planarity : 0.005 0.055 6353 Dihedral : 6.175 32.623 4853 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.10 % Favored : 87.83 % Rotamer: Outliers : 0.12 % Allowed : 6.63 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.51 (0.12), residues: 4454 helix: -0.79 (0.15), residues: 1152 sheet: -0.82 (0.17), residues: 999 loop : -2.58 (0.12), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 633 HIS 0.010 0.002 HIS C 271 PHE 0.023 0.002 PHE A1151 TYR 0.025 0.002 TYR C 436 ARG 0.010 0.001 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 244 time to evaluate : 4.424 Fit side-chains revert: symmetry clash REVERT: A 605 GLN cc_start: 0.8020 (mp10) cc_final: 0.7779 (mp10) REVERT: C 234 ASP cc_start: 0.8208 (t70) cc_final: 0.7928 (t0) REVERT: I 103 TYR cc_start: 0.6937 (t80) cc_final: 0.6487 (t80) outliers start: 5 outliers final: 3 residues processed: 249 average time/residue: 0.4619 time to fit residues: 197.0766 Evaluate side-chains 178 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 4.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 398 optimal weight: 3.9990 chunk 303 optimal weight: 4.9990 chunk 209 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 192 optimal weight: 0.1980 chunk 270 optimal weight: 10.0000 chunk 404 optimal weight: 5.9990 chunk 428 optimal weight: 8.9990 chunk 211 optimal weight: 0.9980 chunk 383 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS I 257 ASN ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36519 Z= 0.164 Angle : 0.577 9.343 49465 Z= 0.308 Chirality : 0.044 0.287 5595 Planarity : 0.004 0.052 6353 Dihedral : 5.630 29.534 4853 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.64 % Favored : 91.31 % Rotamer: Outliers : 0.05 % Allowed : 3.57 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.20 (0.12), residues: 4454 helix: -0.53 (0.15), residues: 1165 sheet: -0.70 (0.17), residues: 996 loop : -2.36 (0.12), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 633 HIS 0.006 0.001 HIS B 652 PHE 0.024 0.001 PHE A1151 TYR 0.023 0.001 TYR E 218 ARG 0.005 0.000 ARG A1065 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 268 time to evaluate : 4.465 Fit side-chains REVERT: A 605 GLN cc_start: 0.8028 (mp10) cc_final: 0.7586 (mp10) REVERT: C 234 ASP cc_start: 0.8201 (t70) cc_final: 0.7972 (t0) REVERT: E 87 ILE cc_start: 0.8600 (mt) cc_final: 0.8349 (tt) REVERT: G 175 MET cc_start: 0.1969 (mpp) cc_final: 0.1638 (mpp) outliers start: 2 outliers final: 1 residues processed: 270 average time/residue: 0.4247 time to fit residues: 196.5832 Evaluate side-chains 185 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 4.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 356 optimal weight: 6.9990 chunk 243 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 318 optimal weight: 8.9990 chunk 176 optimal weight: 0.9980 chunk 365 optimal weight: 10.0000 chunk 295 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 384 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN G 150 HIS G 271 GLN G 378 HIS I 177 GLN ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 36519 Z= 0.366 Angle : 0.733 9.783 49465 Z= 0.388 Chirality : 0.048 0.244 5595 Planarity : 0.005 0.053 6353 Dihedral : 6.332 33.082 4853 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.62 % Favored : 87.31 % Rotamer: Outliers : 0.05 % Allowed : 3.97 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.56 (0.12), residues: 4454 helix: -0.91 (0.15), residues: 1152 sheet: -0.79 (0.17), residues: 971 loop : -2.59 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 633 HIS 0.009 0.001 HIS C 271 PHE 0.023 0.003 PHE B 670 TYR 0.029 0.002 TYR D1025 ARG 0.007 0.001 ARG A1065 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 243 time to evaluate : 4.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 GLN cc_start: 0.8102 (mp10) cc_final: 0.7868 (mp10) REVERT: B 481 ILE cc_start: 0.7989 (mm) cc_final: 0.7629 (tt) REVERT: C 234 ASP cc_start: 0.8154 (t70) cc_final: 0.7891 (t0) REVERT: G 175 MET cc_start: 0.1394 (mpp) cc_final: 0.1133 (mpp) REVERT: I 103 TYR cc_start: 0.7060 (t80) cc_final: 0.6650 (t80) outliers start: 2 outliers final: 0 residues processed: 245 average time/residue: 0.4301 time to fit residues: 180.7615 Evaluate side-chains 184 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 4.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 144 optimal weight: 7.9990 chunk 385 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 251 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 428 optimal weight: 7.9990 chunk 355 optimal weight: 0.0370 chunk 198 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 225 optimal weight: 2.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 83 ASN A 202 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 ASN ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1293 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS H 44 HIS H 98 GLN ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36519 Z= 0.192 Angle : 0.609 12.001 49465 Z= 0.324 Chirality : 0.045 0.226 5595 Planarity : 0.004 0.074 6353 Dihedral : 5.878 30.101 4853 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.82 % Favored : 91.13 % Rotamer: Outliers : 0.05 % Allowed : 2.34 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.32 (0.12), residues: 4454 helix: -0.66 (0.15), residues: 1159 sheet: -0.73 (0.17), residues: 987 loop : -2.43 (0.12), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 442 HIS 0.007 0.001 HIS G 133 PHE 0.016 0.002 PHE B 670 TYR 0.024 0.001 TYR D1014 ARG 0.017 0.000 ARG D1320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 249 time to evaluate : 3.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.5031 (pm20) REVERT: A 77 MET cc_start: 0.6735 (mmm) cc_final: 0.6144 (mmm) REVERT: A 605 GLN cc_start: 0.7952 (mp10) cc_final: 0.7494 (mp10) REVERT: C 234 ASP cc_start: 0.8181 (t70) cc_final: 0.7913 (t0) REVERT: C 308 GLU cc_start: 0.7955 (mp0) cc_final: 0.7717 (mp0) REVERT: C 400 MET cc_start: 0.7711 (mpp) cc_final: 0.7272 (mpp) REVERT: C 553 MET cc_start: 0.8249 (mmm) cc_final: 0.7690 (mmm) REVERT: D 1047 MET cc_start: 0.1931 (mmt) cc_final: 0.1669 (mmt) REVERT: G 175 MET cc_start: 0.1766 (mpp) cc_final: 0.1478 (mpp) REVERT: H 42 PHE cc_start: 0.7201 (m-80) cc_final: 0.5601 (t80) REVERT: I 45 MET cc_start: 0.7954 (ttm) cc_final: 0.7633 (ttp) outliers start: 2 outliers final: 0 residues processed: 251 average time/residue: 0.4468 time to fit residues: 192.3086 Evaluate side-chains 189 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 4.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 413 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 313 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 360 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 426 optimal weight: 4.9990 chunk 267 optimal weight: 20.0000 chunk 260 optimal weight: 5.9990 chunk 197 optimal weight: 0.1980 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 ASN ** D1168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS ** H 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 ASN ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36519 Z= 0.271 Angle : 0.663 10.606 49465 Z= 0.352 Chirality : 0.046 0.182 5595 Planarity : 0.005 0.053 6353 Dihedral : 6.068 31.335 4853 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.63 % Favored : 88.33 % Rotamer: Outliers : 0.02 % Allowed : 2.29 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.45 (0.12), residues: 4454 helix: -0.75 (0.15), residues: 1156 sheet: -0.83 (0.17), residues: 998 loop : -2.52 (0.12), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 633 HIS 0.007 0.001 HIS C 271 PHE 0.019 0.002 PHE B 670 TYR 0.020 0.002 TYR C 120 ARG 0.007 0.000 ARG D1320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 241 time to evaluate : 3.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.5970 (tm-30) cc_final: 0.5035 (pm20) REVERT: A 605 GLN cc_start: 0.8054 (mp10) cc_final: 0.7637 (mp10) REVERT: C 234 ASP cc_start: 0.8142 (t70) cc_final: 0.7879 (t0) REVERT: C 308 GLU cc_start: 0.8148 (mp0) cc_final: 0.7867 (mp0) REVERT: C 400 MET cc_start: 0.7333 (mpp) cc_final: 0.6873 (mpp) REVERT: D 1025 TYR cc_start: 0.4422 (m-10) cc_final: 0.4165 (m-80) REVERT: D 1047 MET cc_start: 0.2104 (mmt) cc_final: 0.1596 (mmt) REVERT: G 175 MET cc_start: 0.1547 (mpp) cc_final: 0.1008 (mpp) REVERT: I 45 MET cc_start: 0.7974 (ttm) cc_final: 0.7727 (ttp) REVERT: I 103 TYR cc_start: 0.7142 (t80) cc_final: 0.6581 (t80) outliers start: 1 outliers final: 0 residues processed: 242 average time/residue: 0.4408 time to fit residues: 181.9529 Evaluate side-chains 186 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 4.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 264 optimal weight: 9.9990 chunk 170 optimal weight: 8.9990 chunk 255 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 83 optimal weight: 0.0020 chunk 82 optimal weight: 5.9990 chunk 271 optimal weight: 9.9990 chunk 290 optimal weight: 0.2980 chunk 211 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 335 optimal weight: 9.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1166 ASN ** D1168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS H 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 36519 Z= 0.209 Angle : 0.624 12.116 49465 Z= 0.330 Chirality : 0.045 0.221 5595 Planarity : 0.004 0.058 6353 Dihedral : 5.881 30.132 4853 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.59 % Favored : 90.37 % Rotamer: Outliers : 0.02 % Allowed : 1.22 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.36 (0.12), residues: 4454 helix: -0.71 (0.15), residues: 1167 sheet: -0.78 (0.17), residues: 998 loop : -2.45 (0.12), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1064 HIS 0.006 0.001 HIS B 652 PHE 0.025 0.002 PHE A 917 TYR 0.028 0.001 TYR G 237 ARG 0.007 0.000 ARG D1095 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 253 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ILE cc_start: 0.8777 (mm) cc_final: 0.8476 (mm) REVERT: A 605 GLN cc_start: 0.7984 (mp10) cc_final: 0.7584 (mp10) REVERT: C 234 ASP cc_start: 0.8134 (t70) cc_final: 0.7856 (t0) REVERT: C 308 GLU cc_start: 0.8124 (mp0) cc_final: 0.7897 (mp0) REVERT: C 400 MET cc_start: 0.7386 (mpp) cc_final: 0.7035 (mpp) REVERT: D 1047 MET cc_start: 0.2158 (mmt) cc_final: 0.1658 (mmt) REVERT: D 1068 MET cc_start: 0.6559 (mpp) cc_final: 0.6025 (mmp) REVERT: G 175 MET cc_start: 0.1656 (mpp) cc_final: 0.1329 (mpp) REVERT: I 45 MET cc_start: 0.7953 (ttm) cc_final: 0.7655 (ttp) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.4308 time to fit residues: 186.7073 Evaluate side-chains 194 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 4.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 388 optimal weight: 3.9990 chunk 409 optimal weight: 2.9990 chunk 373 optimal weight: 4.9990 chunk 397 optimal weight: 2.9990 chunk 408 optimal weight: 3.9990 chunk 239 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 312 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 359 optimal weight: 5.9990 chunk 376 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS H 44 HIS ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36519 Z= 0.258 Angle : 0.657 12.976 49465 Z= 0.347 Chirality : 0.046 0.217 5595 Planarity : 0.004 0.053 6353 Dihedral : 5.993 30.790 4853 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.63 % Favored : 88.33 % Rotamer: Outliers : 0.02 % Allowed : 0.70 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.45 (0.12), residues: 4454 helix: -0.76 (0.15), residues: 1158 sheet: -0.82 (0.17), residues: 978 loop : -2.51 (0.12), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1064 HIS 0.008 0.001 HIS A1290 PHE 0.021 0.002 PHE A 917 TYR 0.031 0.002 TYR I 88 ARG 0.007 0.000 ARG A 713 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 241 time to evaluate : 4.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 605 GLN cc_start: 0.7978 (mp10) cc_final: 0.7589 (mp10) REVERT: C 234 ASP cc_start: 0.8133 (t70) cc_final: 0.7864 (t0) REVERT: C 400 MET cc_start: 0.7416 (mpp) cc_final: 0.6955 (mpp) REVERT: D 1053 GLU cc_start: 0.2476 (tp30) cc_final: 0.2260 (tp30) outliers start: 1 outliers final: 0 residues processed: 242 average time/residue: 0.4392 time to fit residues: 180.9747 Evaluate side-chains 188 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 4.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 396 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 420 optimal weight: 7.9990 chunk 256 optimal weight: 20.0000 chunk 199 optimal weight: 0.8980 chunk 292 optimal weight: 3.9990 chunk 441 optimal weight: 9.9990 chunk 406 optimal weight: 4.9990 chunk 351 optimal weight: 0.0050 chunk 36 optimal weight: 6.9990 chunk 271 optimal weight: 0.0670 overall best weight: 1.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS H 98 GLN I 94 ASN ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36519 Z= 0.166 Angle : 0.600 13.440 49465 Z= 0.315 Chirality : 0.045 0.229 5595 Planarity : 0.004 0.051 6353 Dihedral : 5.650 29.374 4853 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.85 % Favored : 91.11 % Rotamer: Outliers : 0.02 % Allowed : 0.40 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.23 (0.12), residues: 4454 helix: -0.59 (0.15), residues: 1173 sheet: -0.73 (0.17), residues: 1004 loop : -2.36 (0.12), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1064 HIS 0.007 0.001 HIS B 652 PHE 0.023 0.001 PHE A 917 TYR 0.026 0.001 TYR G 237 ARG 0.006 0.000 ARG A 713 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 252 time to evaluate : 4.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 ILE cc_start: 0.8684 (mm) cc_final: 0.8446 (mm) REVERT: A 605 GLN cc_start: 0.7993 (mp10) cc_final: 0.7587 (mp10) REVERT: C 234 ASP cc_start: 0.8139 (t70) cc_final: 0.7913 (t0) REVERT: C 400 MET cc_start: 0.7426 (mpp) cc_final: 0.7013 (mpp) REVERT: G 175 MET cc_start: 0.1345 (mpp) cc_final: 0.1009 (mpp) REVERT: G 395 MET cc_start: 0.7091 (tpt) cc_final: 0.6230 (tpt) REVERT: H 42 PHE cc_start: 0.7175 (m-80) cc_final: 0.5591 (t80) REVERT: H 78 MET cc_start: 0.7274 (ppp) cc_final: 0.6528 (ppp) REVERT: I 45 MET cc_start: 0.7801 (ttm) cc_final: 0.7521 (ttp) outliers start: 1 outliers final: 0 residues processed: 253 average time/residue: 0.4344 time to fit residues: 188.9149 Evaluate side-chains 190 residues out of total 4010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 3.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 215 optimal weight: 3.9990 chunk 279 optimal weight: 5.9990 chunk 374 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 324 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 352 optimal weight: 0.0470 chunk 147 optimal weight: 6.9990 chunk 361 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 2.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1193 GLN ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.082416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.069365 restraints weight = 201258.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.068998 restraints weight = 164344.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.069391 restraints weight = 137046.553| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 36519 Z= 0.229 Angle : 0.634 14.028 49465 Z= 0.334 Chirality : 0.045 0.205 5595 Planarity : 0.004 0.052 6353 Dihedral : 5.789 30.445 4853 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.93 % Favored : 89.02 % Rotamer: Outliers : 0.02 % Allowed : 0.35 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.29 (0.12), residues: 4454 helix: -0.64 (0.15), residues: 1171 sheet: -0.75 (0.17), residues: 998 loop : -2.40 (0.12), residues: 2285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1064 HIS 0.006 0.001 HIS C 271 PHE 0.019 0.002 PHE A 917 TYR 0.018 0.002 TYR I 261 ARG 0.006 0.000 ARG A 713 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6266.25 seconds wall clock time: 115 minutes 49.13 seconds (6949.13 seconds total)