Starting phenix.real_space_refine on Tue Feb 20 00:05:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7c_30604/02_2024/7d7c_30604.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7c_30604/02_2024/7d7c_30604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7c_30604/02_2024/7d7c_30604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7c_30604/02_2024/7d7c_30604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7c_30604/02_2024/7d7c_30604.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7c_30604/02_2024/7d7c_30604.pdb" } resolution = 3.6 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 48 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 16335 2.51 5 N 4625 2.21 5 O 5128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 17": "OE1" <-> "OE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "C TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 7": "OE1" <-> "OE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C ASP 393": "OD1" <-> "OD2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 423": "OD1" <-> "OD2" Residue "C ASP 434": "OD1" <-> "OD2" Residue "C GLU 441": "OE1" <-> "OE2" Residue "C ASP 483": "OD1" <-> "OD2" Residue "C TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 625": "OE1" <-> "OE2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 675": "OD1" <-> "OD2" Residue "C ASP 696": "OD1" <-> "OD2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 781": "OD1" <-> "OD2" Residue "C ASP 785": "OD1" <-> "OD2" Residue "C ASP 790": "OD1" <-> "OD2" Residue "C GLU 849": "OE1" <-> "OE2" Residue "C TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 881": "OD1" <-> "OD2" Residue "C GLU 949": "OE1" <-> "OE2" Residue "C GLU 985": "OE1" <-> "OE2" Residue "C ASP 995": "OD1" <-> "OD2" Residue "C GLU 1012": "OE1" <-> "OE2" Residue "C TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1026": "OE1" <-> "OE2" Residue "C GLU 1030": "OE1" <-> "OE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1089": "OE1" <-> "OE2" Residue "C ASP 1095": "OD1" <-> "OD2" Residue "C TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1310": "OD1" <-> "OD2" Residue "C GLU 1316": "OE1" <-> "OE2" Residue "C GLU 1338": "OE1" <-> "OE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D GLU 295": "OE1" <-> "OE2" Residue "D ASP 308": "OD1" <-> "OD2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D ASP 462": "OD1" <-> "OD2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D ASP 505": "OD1" <-> "OD2" Residue "D TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 558": "OD1" <-> "OD2" Residue "D TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D ASP 691": "OD1" <-> "OD2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 785": "OD1" <-> "OD2" Residue "D ASP 806": "OD1" <-> "OD2" Residue "D ASP 847": "OD1" <-> "OD2" Residue "D ASP 855": "OD1" <-> "OD2" Residue "D GLU 873": "OE1" <-> "OE2" Residue "D ASP 889": "OD1" <-> "OD2" Residue "D ASP 902": "OD1" <-> "OD2" Residue "D GLU 1009": "OE1" <-> "OE2" Residue "D PHE 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1039": "OD1" <-> "OD2" Residue "D ASP 1042": "OD1" <-> "OD2" Residue "D ASP 1073": "OD1" <-> "OD2" Residue "D PHE 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1184": "OD1" <-> "OD2" Residue "D ASP 1239": "OD1" <-> "OD2" Residue "D GLU 1281": "OE1" <-> "OE2" Residue "D GLU 1291": "OE1" <-> "OE2" Residue "D TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 15": "OE1" <-> "OE2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 135": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26249 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1686 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1681 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Chain: "D" Number of atoms: 10384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10384 Classifications: {'peptide': 1335} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1279} Chain breaks: 2 Chain: "T" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 467 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "F" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1128 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "N" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 519 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20031 SG CYS D 814 86.451 67.375 129.517 1.00115.32 S ATOM 20596 SG CYS D 888 85.667 67.560 125.979 1.00104.77 S ATOM 20647 SG CYS D 895 84.746 64.207 127.826 1.00105.89 S ATOM 20668 SG CYS D 898 83.177 67.277 128.309 1.00103.24 S Time building chain proxies: 13.68, per 1000 atoms: 0.52 Number of scatterers: 26249 At special positions: 0 Unit cell: (133.314, 160.761, 167.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 110 16.00 P 48 15.00 Mg 1 11.99 O 5128 8.00 N 4625 7.00 C 16335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.31 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " Number of angles added : 6 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5960 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 46 sheets defined 36.4% alpha, 13.7% beta 18 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 8.45 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.635A pdb=" N ASP A 114 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.957A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 4.270A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.710A pdb=" N THR B 157 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 28 through 37 removed outlier: 3.581A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 4.290A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.621A pdb=" N ARG C 245 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.869A pdb=" N THR C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 391 removed outlier: 3.776A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER C 391 " --> pdb=" O ASN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 478 removed outlier: 3.502A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 481 No H-bonds generated for 'chain 'C' and resid 479 through 481' Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 521 through 527 Processing helix chain 'C' and resid 610 through 614 removed outlier: 3.877A pdb=" N ASN C 613 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 687 Processing helix chain 'C' and resid 705 through 710 removed outlier: 3.693A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.838A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 980 removed outlier: 4.131A pdb=" N LYS C 958 " --> pdb=" O LYS C 954 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP C 959 " --> pdb=" O GLN C 955 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 972 " --> pdb=" O GLU C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.621A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.689A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.606A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1101 through 1106' Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.859A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.831A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.736A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1177 removed outlier: 3.524A pdb=" N ARG C1171 " --> pdb=" O GLU C1167 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.627A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.701A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1290 removed outlier: 3.592A pdb=" N GLN C1288 " --> pdb=" O ALA C1284 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1321 through 1331 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 114 through 117 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.884A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.549A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 211 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 264 through 283 removed outlier: 3.540A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.637A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 407 through 416 Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.730A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.795A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.757A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 594 removed outlier: 3.641A pdb=" N ASN D 593 " --> pdb=" O TYR D 589 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN D 594 " --> pdb=" O SER D 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 589 through 594' Processing helix chain 'D' and resid 597 through 613 removed outlier: 3.829A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.606A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.560A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.629A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.521A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.597A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.911A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.596A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1069 through 1074 removed outlier: 4.611A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D1074 " --> pdb=" O GLY D1070 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1069 through 1074' Processing helix chain 'D' and resid 1137 through 1147 removed outlier: 3.847A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 Processing helix chain 'D' and resid 1225 through 1241 removed outlier: 4.299A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1282 through 1293 Processing helix chain 'D' and resid 1308 through 1315 removed outlier: 3.995A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1325 removed outlier: 3.910A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.749A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 3.823A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 28 removed outlier: 3.859A pdb=" N LEU F 17 " --> pdb=" O ASN F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 55 removed outlier: 3.502A pdb=" N GLY F 44 " --> pdb=" O ASN F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 83 removed outlier: 3.709A pdb=" N GLN F 69 " --> pdb=" O GLN F 65 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU F 70 " --> pdb=" O SER F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 125 Processing helix chain 'F' and resid 137 through 142 Processing helix chain 'F' and resid 142 through 150 removed outlier: 3.599A pdb=" N ASP F 150 " --> pdb=" O GLN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 153 No H-bonds generated for 'chain 'F' and resid 151 through 153' Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 5.073A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 61 removed outlier: 5.448A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.804A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 18 removed outlier: 4.195A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N HIS B 23 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR B 207 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 101 removed outlier: 6.686A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.814A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.626A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB6, first strand: chain 'C' and resid 228 through 230 Processing sheet with id=AB7, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.623A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.073A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.747A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.594A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.594A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.757A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 751 removed outlier: 5.662A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY C 722 " --> pdb=" O VAL C 777 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1065 through 1067 removed outlier: 7.316A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 832 Processing sheet with id=AD1, first strand: chain 'C' and resid 835 through 839 Processing sheet with id=AD2, first strand: chain 'C' and resid 842 through 843 removed outlier: 3.754A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 876 through 877 Processing sheet with id=AD4, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD5, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.305A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD7, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.729A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD9, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.415A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 11.253A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AE2, first strand: chain 'D' and resid 526 through 527 removed outlier: 6.885A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'D' and resid 825 through 826 removed outlier: 6.579A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.727A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.852A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN D1019 " --> pdb=" O VAL D1002 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL D1002 " --> pdb=" O ASN D1019 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 958 through 961 removed outlier: 6.564A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1078 through 1079 removed outlier: 3.653A pdb=" N LEU D1078 " --> pdb=" O TYR D1099 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 1162 through 1165 removed outlier: 4.294A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.800A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 973 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 11.59 Time building geometry restraints manager: 10.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7003 1.33 - 1.45: 4364 1.45 - 1.57: 15096 1.57 - 1.69: 92 1.69 - 1.81: 191 Bond restraints: 26746 Sorted by residual: bond pdb=" N TYR C 47 " pdb=" CA TYR C 47 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.44e+00 bond pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.26e-02 6.30e+03 7.51e+00 bond pdb=" C THR C 563 " pdb=" N PRO C 564 " ideal model delta sigma weight residual 1.335 1.312 0.023 8.70e-03 1.32e+04 7.16e+00 bond pdb=" N GLU A 72 " pdb=" CA GLU A 72 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.31e-02 5.83e+03 6.59e+00 bond pdb=" N HIS F 126 " pdb=" CA HIS F 126 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 6.09e+00 ... (remaining 26741 not shown) Histogram of bond angle deviations from ideal: 97.69 - 104.99: 618 104.99 - 112.28: 13900 112.28 - 119.57: 8873 119.57 - 126.86: 12571 126.86 - 134.16: 357 Bond angle restraints: 36319 Sorted by residual: angle pdb=" C SER D 503 " pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta sigma weight residual 121.52 111.32 10.20 1.74e+00 3.30e-01 3.44e+01 angle pdb=" N GLY C 162 " pdb=" CA GLY C 162 " pdb=" C GLY C 162 " ideal model delta sigma weight residual 111.67 116.59 -4.92 9.20e-01 1.18e+00 2.86e+01 angle pdb=" N VAL D 839 " pdb=" CA VAL D 839 " pdb=" C VAL D 839 " ideal model delta sigma weight residual 113.20 108.29 4.91 9.60e-01 1.09e+00 2.62e+01 angle pdb=" C VAL D 244 " pdb=" N LEU D 245 " pdb=" CA LEU D 245 " ideal model delta sigma weight residual 120.94 128.01 -7.07 1.90e+00 2.77e-01 1.39e+01 angle pdb=" CA ARG D1345 " pdb=" C ARG D1345 " pdb=" O ARG D1345 " ideal model delta sigma weight residual 122.36 118.17 4.19 1.21e+00 6.83e-01 1.20e+01 ... (remaining 36314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 15798 35.04 - 70.09: 473 70.09 - 105.13: 39 105.13 - 140.17: 0 140.17 - 175.22: 1 Dihedral angle restraints: 16311 sinusoidal: 7044 harmonic: 9267 Sorted by residual: dihedral pdb=" CA GLY D 852 " pdb=" C GLY D 852 " pdb=" N THR D 853 " pdb=" CA THR D 853 " ideal model delta harmonic sigma weight residual -180.00 -151.89 -28.11 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ARG F 132 " pdb=" C ARG F 132 " pdb=" N ASP F 133 " pdb=" CA ASP F 133 " ideal model delta harmonic sigma weight residual 180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA SER B 20 " pdb=" C SER B 20 " pdb=" N SER B 21 " pdb=" CA SER B 21 " ideal model delta harmonic sigma weight residual -180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 16308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2482 0.037 - 0.074: 1174 0.074 - 0.111: 375 0.111 - 0.147: 90 0.147 - 0.184: 16 Chirality restraints: 4137 Sorted by residual: chirality pdb=" CA LEU C 27 " pdb=" N LEU C 27 " pdb=" C LEU C 27 " pdb=" CB LEU C 27 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CB ILE C 176 " pdb=" CA ILE C 176 " pdb=" CG1 ILE C 176 " pdb=" CG2 ILE C 176 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CB ILE C1079 " pdb=" CA ILE C1079 " pdb=" CG1 ILE C1079 " pdb=" CG2 ILE C1079 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.97e-01 ... (remaining 4134 not shown) Planarity restraints: 4580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 42 " -0.094 5.00e-02 4.00e+02 1.44e-01 3.33e+01 pdb=" N PRO C 43 " 0.250 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC N 51 " -0.002 2.00e-02 2.50e+03 1.75e-02 6.88e+00 pdb=" N1 DC N 51 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DC N 51 " -0.042 2.00e-02 2.50e+03 pdb=" O2 DC N 51 " 0.023 2.00e-02 2.50e+03 pdb=" N3 DC N 51 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DC N 51 " -0.015 2.00e-02 2.50e+03 pdb=" N4 DC N 51 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC N 51 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC N 51 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 25 " 0.016 2.00e-02 2.50e+03 1.48e-02 6.55e+00 pdb=" N9 DG N 25 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DG N 25 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG N 25 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG N 25 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG N 25 " 0.020 2.00e-02 2.50e+03 pdb=" O6 DG N 25 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG N 25 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG N 25 " 0.030 2.00e-02 2.50e+03 pdb=" N2 DG N 25 " -0.022 2.00e-02 2.50e+03 pdb=" N3 DG N 25 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG N 25 " -0.003 2.00e-02 2.50e+03 ... (remaining 4577 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 337 2.55 - 3.14: 22913 3.14 - 3.73: 39723 3.73 - 4.31: 54469 4.31 - 4.90: 89067 Nonbonded interactions: 206509 Sorted by model distance: nonbonded pdb=" OD2 ASP D 460 " pdb="MG MG D1501 " model vdw 1.967 2.170 nonbonded pdb=" NH1 ARG C 267 " pdb=" O ARG C 268 " model vdw 2.179 2.520 nonbonded pdb=" OG1 THR D 816 " pdb=" OE1 GLU D 818 " model vdw 2.198 2.440 nonbonded pdb=" O ALA D 741 " pdb=" ND2 ASN D 762 " model vdw 2.201 2.520 nonbonded pdb=" OD1 ASP C1214 " pdb=" N GLY C1215 " model vdw 2.202 2.520 ... (remaining 206504 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 232)) selection = (chain 'B' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.150 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 78.150 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.007 0.126 26746 Z= 0.479 Angle : 0.789 13.191 36319 Z= 0.457 Chirality : 0.047 0.184 4137 Planarity : 0.005 0.144 4580 Dihedral : 16.349 175.217 10351 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.71 % Favored : 88.20 % Rotamer: Outliers : 0.29 % Allowed : 9.32 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -4.31 (0.12), residues: 3203 helix: -1.89 (0.13), residues: 1073 sheet: -2.61 (0.21), residues: 437 loop : -3.71 (0.12), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 115 HIS 0.011 0.002 HIS D 777 PHE 0.014 0.002 PHE A 231 TYR 0.020 0.002 TYR A 177 ARG 0.005 0.000 ARG C 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 315 time to evaluate : 3.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 LYS cc_start: 0.8852 (tttt) cc_final: 0.8411 (tppt) REVERT: C 267 ARG cc_start: 0.7762 (tpt90) cc_final: 0.7373 (ttp80) REVERT: C 366 ILE cc_start: 0.9148 (mt) cc_final: 0.8918 (mm) REVERT: C 370 MET cc_start: 0.9145 (mmm) cc_final: 0.8584 (mmm) REVERT: C 403 MET cc_start: 0.8670 (tmm) cc_final: 0.8380 (tmm) REVERT: C 503 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8708 (mptt) REVERT: C 951 MET cc_start: 0.8466 (mmt) cc_final: 0.8113 (tpp) REVERT: D 42 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7911 (mm-30) REVERT: D 45 ASN cc_start: 0.8935 (t0) cc_final: 0.8731 (t0) REVERT: D 180 MET cc_start: 0.8226 (ptt) cc_final: 0.7874 (ptt) REVERT: D 301 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7959 (tm-30) REVERT: D 325 LYS cc_start: 0.9347 (mtpt) cc_final: 0.9058 (mtpp) REVERT: D 462 ASP cc_start: 0.8493 (m-30) cc_final: 0.8125 (m-30) REVERT: D 617 THR cc_start: 0.9163 (m) cc_final: 0.8876 (p) REVERT: D 625 MET cc_start: 0.8849 (ttp) cc_final: 0.8582 (ttp) REVERT: D 869 CYS cc_start: 0.8055 (m) cc_final: 0.7723 (m) REVERT: D 1369 ARG cc_start: 0.8707 (ttt-90) cc_final: 0.8457 (ttp80) REVERT: F 52 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8339 (tm-30) REVERT: F 65 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8104 (mm-40) REVERT: F 74 ASP cc_start: 0.8833 (t0) cc_final: 0.8550 (t0) REVERT: F 91 TYR cc_start: 0.8303 (m-80) cc_final: 0.7845 (m-80) outliers start: 8 outliers final: 6 residues processed: 322 average time/residue: 0.4483 time to fit residues: 216.3935 Evaluate side-chains 240 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 234 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain F residue 133 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 117 HIS A 147 GLN B 23 HIS B 117 HIS ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN C 343 HIS C 618 GLN C 856 ASN ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 GLN C1038 GLN C1134 GLN C1136 GLN D 320 ASN D 340 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** D 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN D 929 GLN D 962 ASN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 26746 Z= 0.402 Angle : 0.687 8.471 36319 Z= 0.363 Chirality : 0.045 0.166 4137 Planarity : 0.005 0.073 4580 Dihedral : 13.316 168.897 4065 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.46 % Favored : 90.51 % Rotamer: Outliers : 2.33 % Allowed : 16.45 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.13), residues: 3203 helix: -0.52 (0.15), residues: 1100 sheet: -2.20 (0.22), residues: 427 loop : -3.15 (0.13), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D1193 HIS 0.011 0.002 HIS D 777 PHE 0.022 0.002 PHE F 58 TYR 0.018 0.002 TYR D 772 ARG 0.006 0.000 ARG C 478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 251 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.8276 (m-80) cc_final: 0.7961 (m-80) REVERT: B 142 MET cc_start: 0.7763 (ptp) cc_final: 0.7559 (ptp) REVERT: B 145 LYS cc_start: 0.8719 (tttt) cc_final: 0.8329 (tppt) REVERT: C 46 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7810 (mm-40) REVERT: C 267 ARG cc_start: 0.7737 (tpt90) cc_final: 0.7422 (ttp80) REVERT: C 403 MET cc_start: 0.8624 (tmm) cc_final: 0.8323 (tmm) REVERT: C 492 MET cc_start: 0.7572 (mmt) cc_final: 0.7355 (tpt) REVERT: C 848 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6625 (mp0) REVERT: C 1119 MET cc_start: 0.8070 (tpp) cc_final: 0.7819 (tpp) REVERT: C 1134 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8725 (pp30) REVERT: C 1304 MET cc_start: 0.8190 (tpt) cc_final: 0.7924 (tpp) REVERT: D 45 ASN cc_start: 0.8974 (t0) cc_final: 0.8693 (t0) REVERT: D 180 MET cc_start: 0.8225 (ptt) cc_final: 0.7604 (ptt) REVERT: D 301 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7910 (tm-30) REVERT: D 322 ARG cc_start: 0.7906 (ppt170) cc_final: 0.7610 (ppt170) REVERT: D 398 LYS cc_start: 0.9501 (mtpp) cc_final: 0.9278 (mtpp) REVERT: D 462 ASP cc_start: 0.8468 (m-30) cc_final: 0.8082 (m-30) REVERT: D 625 MET cc_start: 0.8869 (ttp) cc_final: 0.8584 (ttp) REVERT: D 697 MET cc_start: 0.8430 (tmm) cc_final: 0.8207 (tmm) REVERT: D 795 TYR cc_start: 0.8929 (t80) cc_final: 0.8694 (t80) REVERT: D 822 MET cc_start: 0.8673 (mmp) cc_final: 0.8367 (mmt) REVERT: D 869 CYS cc_start: 0.8081 (m) cc_final: 0.7600 (m) REVERT: D 1144 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9201 (mp) REVERT: D 1215 GLU cc_start: 0.8350 (tp30) cc_final: 0.8117 (mm-30) REVERT: F 52 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8323 (tm-30) REVERT: F 65 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8126 (mm-40) REVERT: F 74 ASP cc_start: 0.8813 (t0) cc_final: 0.8520 (t0) REVERT: F 91 TYR cc_start: 0.8256 (m-80) cc_final: 0.7902 (m-80) outliers start: 64 outliers final: 46 residues processed: 298 average time/residue: 0.4001 time to fit residues: 190.9592 Evaluate side-chains 268 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 219 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1134 GLN Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1241 ASP Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 133 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 163 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 199 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 293 optimal weight: 1.9990 chunk 317 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 291 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26746 Z= 0.198 Angle : 0.584 11.631 36319 Z= 0.308 Chirality : 0.042 0.164 4137 Planarity : 0.004 0.050 4580 Dihedral : 13.001 171.243 4063 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.84 % Favored : 93.13 % Rotamer: Outliers : 2.73 % Allowed : 19.29 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.19 (0.14), residues: 3203 helix: 0.37 (0.16), residues: 1100 sheet: -1.83 (0.24), residues: 390 loop : -2.73 (0.13), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D1193 HIS 0.006 0.001 HIS D 777 PHE 0.010 0.001 PHE C 972 TYR 0.013 0.001 TYR D 772 ARG 0.009 0.000 ARG D1372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 266 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.8275 (m-80) cc_final: 0.7941 (m-80) REVERT: B 145 LYS cc_start: 0.8665 (tttt) cc_final: 0.8313 (tppt) REVERT: B 186 ASN cc_start: 0.8450 (t0) cc_final: 0.8075 (p0) REVERT: C 46 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7885 (mm-40) REVERT: C 369 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7936 (ppp) REVERT: C 473 ARG cc_start: 0.8234 (mmm160) cc_final: 0.8027 (tpp80) REVERT: C 848 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: C 951 MET cc_start: 0.8472 (mmt) cc_final: 0.7983 (tpt) REVERT: D 180 MET cc_start: 0.8171 (ptt) cc_final: 0.7463 (ptt) REVERT: D 301 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7857 (tm-30) REVERT: D 322 ARG cc_start: 0.7931 (ppt170) cc_final: 0.7563 (ppt170) REVERT: D 462 ASP cc_start: 0.8238 (m-30) cc_final: 0.7935 (m-30) REVERT: D 587 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8967 (mp) REVERT: D 625 MET cc_start: 0.8873 (ttp) cc_final: 0.8581 (ttp) REVERT: D 795 TYR cc_start: 0.8843 (t80) cc_final: 0.8623 (t80) REVERT: D 822 MET cc_start: 0.8766 (mmp) cc_final: 0.8447 (mmt) REVERT: D 869 CYS cc_start: 0.8030 (m) cc_final: 0.7487 (m) REVERT: D 1138 LEU cc_start: 0.9470 (tt) cc_final: 0.9163 (pp) REVERT: D 1215 GLU cc_start: 0.8262 (tp30) cc_final: 0.8001 (mm-30) REVERT: F 52 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8336 (tm-30) REVERT: F 65 GLN cc_start: 0.8522 (mm-40) cc_final: 0.7924 (mm-40) REVERT: F 74 ASP cc_start: 0.8797 (t0) cc_final: 0.8370 (t0) REVERT: F 91 TYR cc_start: 0.8245 (m-80) cc_final: 0.7903 (m-80) outliers start: 75 outliers final: 49 residues processed: 321 average time/residue: 0.3827 time to fit residues: 198.7945 Evaluate side-chains 283 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 231 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1241 ASP Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 133 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 290 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 32 optimal weight: 0.0970 chunk 140 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 294 optimal weight: 2.9990 chunk 312 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 279 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN C1013 GLN D 45 ASN D 320 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 26746 Z= 0.246 Angle : 0.587 9.999 36319 Z= 0.308 Chirality : 0.042 0.244 4137 Planarity : 0.004 0.048 4580 Dihedral : 12.869 173.652 4063 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.71 % Favored : 92.26 % Rotamer: Outliers : 3.71 % Allowed : 21.07 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3203 helix: 0.65 (0.16), residues: 1100 sheet: -1.50 (0.24), residues: 392 loop : -2.56 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1193 HIS 0.008 0.001 HIS F 84 PHE 0.009 0.001 PHE C 405 TYR 0.017 0.001 TYR D 772 ARG 0.006 0.000 ARG C 841 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 241 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.8143 (m-80) cc_final: 0.7700 (m-80) REVERT: B 145 LYS cc_start: 0.8589 (tttt) cc_final: 0.8266 (tppt) REVERT: C 46 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7860 (mm-40) REVERT: C 369 MET cc_start: 0.8374 (ppp) cc_final: 0.7937 (ppp) REVERT: C 848 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: C 951 MET cc_start: 0.8409 (mmt) cc_final: 0.7902 (tpt) REVERT: C 1059 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6449 (ptm-80) REVERT: C 1304 MET cc_start: 0.8168 (tpt) cc_final: 0.7788 (tpp) REVERT: C 1319 MET cc_start: 0.7566 (tmm) cc_final: 0.7364 (tmm) REVERT: D 42 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7524 (mm-30) REVERT: D 180 MET cc_start: 0.8223 (ptt) cc_final: 0.7561 (ptt) REVERT: D 301 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7848 (tm-30) REVERT: D 322 ARG cc_start: 0.7891 (ppt170) cc_final: 0.7475 (ppt170) REVERT: D 462 ASP cc_start: 0.8200 (m-30) cc_final: 0.7873 (m-30) REVERT: D 587 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8984 (mp) REVERT: D 625 MET cc_start: 0.8838 (ttp) cc_final: 0.8534 (ttp) REVERT: D 822 MET cc_start: 0.8789 (mmp) cc_final: 0.8468 (mmt) REVERT: D 869 CYS cc_start: 0.8080 (m) cc_final: 0.7480 (m) REVERT: D 898 CYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7572 (m) REVERT: D 1215 GLU cc_start: 0.8312 (tp30) cc_final: 0.7989 (mm-30) REVERT: F 52 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8291 (tm-30) REVERT: F 65 GLN cc_start: 0.8496 (mm-40) cc_final: 0.7965 (mm-40) REVERT: F 74 ASP cc_start: 0.8741 (t0) cc_final: 0.8380 (t0) REVERT: F 91 TYR cc_start: 0.8237 (m-80) cc_final: 0.7883 (m-80) outliers start: 102 outliers final: 81 residues processed: 318 average time/residue: 0.3505 time to fit residues: 182.5725 Evaluate side-chains 306 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 221 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1059 ARG Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1241 ASP Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 133 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 260 optimal weight: 0.0030 chunk 177 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 266 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 280 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 26746 Z= 0.383 Angle : 0.663 11.805 36319 Z= 0.345 Chirality : 0.043 0.259 4137 Planarity : 0.005 0.058 4580 Dihedral : 12.927 174.175 4062 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.12 % Favored : 90.85 % Rotamer: Outliers : 4.66 % Allowed : 22.63 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.14), residues: 3203 helix: 0.62 (0.16), residues: 1100 sheet: -1.58 (0.24), residues: 429 loop : -2.50 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D1193 HIS 0.010 0.001 HIS D 777 PHE 0.012 0.001 PHE C 405 TYR 0.025 0.002 TYR D 772 ARG 0.006 0.000 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 232 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.8067 (m-80) cc_final: 0.7693 (m-80) REVERT: B 145 LYS cc_start: 0.8572 (tttt) cc_final: 0.8276 (tppt) REVERT: B 212 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7560 (t0) REVERT: C 848 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: C 951 MET cc_start: 0.8431 (mmt) cc_final: 0.8058 (tpt) REVERT: C 1059 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6537 (ptm-80) REVERT: C 1304 MET cc_start: 0.8197 (tpt) cc_final: 0.7875 (tpp) REVERT: D 180 MET cc_start: 0.8088 (ptt) cc_final: 0.7634 (ptt) REVERT: D 301 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7870 (tm-30) REVERT: D 322 ARG cc_start: 0.7887 (ppt170) cc_final: 0.7515 (ppt170) REVERT: D 462 ASP cc_start: 0.8422 (m-30) cc_final: 0.8016 (m-30) REVERT: D 587 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.8997 (mp) REVERT: D 625 MET cc_start: 0.8817 (ttp) cc_final: 0.8501 (ttp) REVERT: D 822 MET cc_start: 0.8791 (mmp) cc_final: 0.8475 (mmt) REVERT: D 869 CYS cc_start: 0.8181 (m) cc_final: 0.7521 (m) REVERT: D 898 CYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7477 (m) REVERT: D 1144 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9167 (mp) REVERT: D 1189 MET cc_start: 0.7970 (tpp) cc_final: 0.7667 (tpt) REVERT: D 1215 GLU cc_start: 0.8428 (tp30) cc_final: 0.8094 (mm-30) REVERT: F 52 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8321 (tm-30) REVERT: F 65 GLN cc_start: 0.8536 (mm-40) cc_final: 0.7996 (mm-40) REVERT: F 74 ASP cc_start: 0.8778 (t0) cc_final: 0.8386 (t0) REVERT: F 91 TYR cc_start: 0.8258 (m-80) cc_final: 0.7935 (m-80) outliers start: 128 outliers final: 100 residues processed: 330 average time/residue: 0.3420 time to fit residues: 187.3701 Evaluate side-chains 328 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 222 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1059 ARG Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1241 ASP Chi-restraints excluded: chain C residue 1315 MET Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 892 PHE Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 133 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 105 optimal weight: 8.9990 chunk 281 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 183 optimal weight: 0.0020 chunk 77 optimal weight: 0.0970 chunk 312 optimal weight: 7.9990 chunk 259 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 overall best weight: 1.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26746 Z= 0.191 Angle : 0.573 9.177 36319 Z= 0.298 Chirality : 0.041 0.223 4137 Planarity : 0.004 0.058 4580 Dihedral : 12.715 174.288 4062 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.24 % Favored : 93.72 % Rotamer: Outliers : 4.00 % Allowed : 23.36 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 3203 helix: 0.96 (0.16), residues: 1093 sheet: -1.18 (0.26), residues: 388 loop : -2.29 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D1193 HIS 0.006 0.001 HIS D 777 PHE 0.009 0.001 PHE F 58 TYR 0.022 0.001 TYR D 795 ARG 0.010 0.000 ARG C1034 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 248 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.8096 (m-80) cc_final: 0.7696 (m-80) REVERT: B 145 LYS cc_start: 0.8484 (tttt) cc_final: 0.8241 (tppt) REVERT: B 212 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7539 (t0) REVERT: C 848 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: C 1059 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6469 (ptm-80) REVERT: C 1304 MET cc_start: 0.8187 (tpt) cc_final: 0.7802 (tpp) REVERT: C 1319 MET cc_start: 0.7381 (tmm) cc_final: 0.7090 (tmm) REVERT: D 42 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7612 (mm-30) REVERT: D 130 MET cc_start: 0.8112 (ptm) cc_final: 0.7814 (tmm) REVERT: D 180 MET cc_start: 0.7942 (ptt) cc_final: 0.7447 (ptt) REVERT: D 301 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7835 (tm-30) REVERT: D 308 ASP cc_start: 0.8904 (t0) cc_final: 0.8483 (m-30) REVERT: D 322 ARG cc_start: 0.8006 (ppt170) cc_final: 0.7598 (ppt170) REVERT: D 462 ASP cc_start: 0.8145 (m-30) cc_final: 0.7816 (m-30) REVERT: D 587 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8955 (mp) REVERT: D 625 MET cc_start: 0.8863 (ttp) cc_final: 0.8560 (ttp) REVERT: D 698 MET cc_start: 0.9303 (tpt) cc_final: 0.8788 (tpp) REVERT: D 822 MET cc_start: 0.8773 (mmp) cc_final: 0.8442 (mmt) REVERT: D 869 CYS cc_start: 0.8050 (m) cc_final: 0.7376 (m) REVERT: D 898 CYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7604 (m) REVERT: D 1040 MET cc_start: -0.1819 (mtp) cc_final: -0.2177 (mtt) REVERT: D 1144 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9116 (mp) REVERT: D 1189 MET cc_start: 0.8019 (tpp) cc_final: 0.7664 (tpt) REVERT: D 1215 GLU cc_start: 0.8338 (tp30) cc_final: 0.8040 (mm-30) REVERT: F 52 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8204 (tm-30) REVERT: F 65 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8027 (mm-40) REVERT: F 74 ASP cc_start: 0.8778 (t0) cc_final: 0.8377 (t0) REVERT: F 91 TYR cc_start: 0.8253 (m-10) cc_final: 0.7907 (m-80) outliers start: 110 outliers final: 77 residues processed: 337 average time/residue: 0.3477 time to fit residues: 193.7913 Evaluate side-chains 317 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 234 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1059 ARG Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1241 ASP Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1094 ASP Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 150 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 178 optimal weight: 0.0870 chunk 228 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 263 optimal weight: 0.7980 chunk 174 optimal weight: 8.9990 chunk 311 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 684 ASN ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26746 Z= 0.156 Angle : 0.554 8.485 36319 Z= 0.288 Chirality : 0.041 0.205 4137 Planarity : 0.004 0.054 4580 Dihedral : 12.526 175.754 4062 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer: Outliers : 3.28 % Allowed : 24.85 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 3203 helix: 1.17 (0.16), residues: 1095 sheet: -0.91 (0.27), residues: 377 loop : -2.11 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D1193 HIS 0.005 0.001 HIS D 777 PHE 0.008 0.001 PHE D 461 TYR 0.010 0.001 TYR D1232 ARG 0.007 0.000 ARG C1033 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 262 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 GLN cc_start: 0.8797 (pt0) cc_final: 0.8532 (pp30) REVERT: B 68 TYR cc_start: 0.8087 (m-80) cc_final: 0.7709 (m-80) REVERT: B 145 LYS cc_start: 0.8391 (tttt) cc_final: 0.8123 (tppt) REVERT: B 182 ARG cc_start: 0.8126 (ttt90) cc_final: 0.7791 (ttt-90) REVERT: B 212 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7420 (t0) REVERT: C 176 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7677 (tp) REVERT: C 315 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6906 (mtm) REVERT: C 1059 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.6363 (ptm-80) REVERT: C 1304 MET cc_start: 0.8209 (tpt) cc_final: 0.7871 (tpp) REVERT: C 1329 GLU cc_start: 0.8097 (tt0) cc_final: 0.7768 (tt0) REVERT: D 180 MET cc_start: 0.6835 (ptt) cc_final: 0.6454 (ptt) REVERT: D 301 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7801 (tm-30) REVERT: D 322 ARG cc_start: 0.7994 (ppt170) cc_final: 0.7556 (ppt170) REVERT: D 462 ASP cc_start: 0.7959 (m-30) cc_final: 0.7678 (m-30) REVERT: D 587 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9078 (mp) REVERT: D 625 MET cc_start: 0.8852 (ttp) cc_final: 0.8543 (ttp) REVERT: D 698 MET cc_start: 0.9289 (tpt) cc_final: 0.8706 (tpp) REVERT: D 869 CYS cc_start: 0.8149 (m) cc_final: 0.7518 (m) REVERT: D 898 CYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7735 (m) REVERT: D 1040 MET cc_start: -0.2028 (mtp) cc_final: -0.2434 (mtt) REVERT: D 1144 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9083 (mp) REVERT: D 1189 MET cc_start: 0.8019 (tpp) cc_final: 0.7689 (tpt) REVERT: D 1215 GLU cc_start: 0.8246 (tp30) cc_final: 0.7937 (mm-30) REVERT: F 52 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8247 (tm-30) REVERT: F 65 GLN cc_start: 0.8469 (mm-40) cc_final: 0.7992 (mm-40) REVERT: F 74 ASP cc_start: 0.8760 (t0) cc_final: 0.8303 (t0) REVERT: F 91 TYR cc_start: 0.8248 (m-10) cc_final: 0.7915 (m-80) outliers start: 90 outliers final: 66 residues processed: 330 average time/residue: 0.3413 time to fit residues: 185.5356 Evaluate side-chains 310 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 237 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1059 ARG Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1241 ASP Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 150 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 192 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 93 optimal weight: 0.1980 chunk 61 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 580 GLN ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 26746 Z= 0.330 Angle : 0.638 11.106 36319 Z= 0.331 Chirality : 0.043 0.208 4137 Planarity : 0.004 0.055 4580 Dihedral : 12.639 176.067 4061 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.77 % Favored : 92.19 % Rotamer: Outliers : 4.40 % Allowed : 24.49 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 3203 helix: 1.11 (0.16), residues: 1098 sheet: -1.10 (0.25), residues: 414 loop : -2.10 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D1193 HIS 0.009 0.001 HIS D 419 PHE 0.028 0.002 PHE C1270 TYR 0.023 0.002 TYR D 795 ARG 0.005 0.000 ARG C 687 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 231 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 GLN cc_start: 0.8829 (pt0) cc_final: 0.8597 (pp30) REVERT: B 68 TYR cc_start: 0.8125 (m-80) cc_final: 0.7723 (m-80) REVERT: B 212 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7731 (t0) REVERT: C 315 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6242 (mtm) REVERT: C 488 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7399 (tpt) REVERT: C 848 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: C 1059 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.6371 (ptm-80) REVERT: C 1304 MET cc_start: 0.8235 (tpt) cc_final: 0.7918 (tpp) REVERT: D 122 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7754 (p) REVERT: D 180 MET cc_start: 0.7247 (ptt) cc_final: 0.6934 (ptt) REVERT: D 301 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7854 (tm-30) REVERT: D 308 ASP cc_start: 0.9066 (t0) cc_final: 0.8793 (m-30) REVERT: D 322 ARG cc_start: 0.8051 (ppt170) cc_final: 0.7551 (ppt170) REVERT: D 462 ASP cc_start: 0.8272 (m-30) cc_final: 0.7875 (m-30) REVERT: D 698 MET cc_start: 0.9292 (tpt) cc_final: 0.8776 (tpp) REVERT: D 822 MET cc_start: 0.8704 (mmt) cc_final: 0.8395 (mmt) REVERT: D 869 CYS cc_start: 0.8086 (m) cc_final: 0.7398 (m) REVERT: D 898 CYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7735 (m) REVERT: D 1040 MET cc_start: -0.1917 (mtp) cc_final: -0.2336 (mtt) REVERT: D 1144 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9105 (mp) REVERT: D 1189 MET cc_start: 0.8037 (tpp) cc_final: 0.7745 (tpp) REVERT: D 1215 GLU cc_start: 0.8408 (tp30) cc_final: 0.8045 (mm-30) REVERT: F 52 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8222 (tm-30) REVERT: F 65 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8093 (mm-40) REVERT: F 74 ASP cc_start: 0.8755 (t0) cc_final: 0.8375 (t0) REVERT: F 91 TYR cc_start: 0.8273 (m-10) cc_final: 0.7907 (m-80) outliers start: 121 outliers final: 93 residues processed: 323 average time/residue: 0.3281 time to fit residues: 177.4459 Evaluate side-chains 326 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 225 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1059 ARG Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1241 ASP Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1094 ASP Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1332 LEU Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain D residue 1370 MET Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 150 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 283 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 chunk 272 optimal weight: 3.9990 chunk 290 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 262 optimal weight: 0.8980 chunk 274 optimal weight: 9.9990 chunk 289 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 26746 Z= 0.292 Angle : 0.630 11.502 36319 Z= 0.326 Chirality : 0.043 0.236 4137 Planarity : 0.004 0.055 4580 Dihedral : 12.665 175.395 4061 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.34 % Favored : 92.63 % Rotamer: Outliers : 4.11 % Allowed : 24.85 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 3203 helix: 1.07 (0.16), residues: 1100 sheet: -1.04 (0.26), residues: 395 loop : -2.08 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1193 HIS 0.009 0.001 HIS D 777 PHE 0.022 0.001 PHE D 172 TYR 0.026 0.001 TYR D 795 ARG 0.005 0.000 ARG C1034 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 235 time to evaluate : 3.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 GLN cc_start: 0.8793 (pt0) cc_final: 0.8565 (pp30) REVERT: B 68 TYR cc_start: 0.8180 (m-80) cc_final: 0.7720 (m-80) REVERT: B 212 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7659 (t0) REVERT: C 488 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.6573 (tpt) REVERT: C 848 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: C 1059 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6362 (ptm-80) REVERT: C 1304 MET cc_start: 0.8228 (tpt) cc_final: 0.7896 (tpp) REVERT: D 122 SER cc_start: 0.7993 (OUTLIER) cc_final: 0.7737 (p) REVERT: D 180 MET cc_start: 0.7511 (ptt) cc_final: 0.7298 (ptt) REVERT: D 301 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7878 (tm-30) REVERT: D 308 ASP cc_start: 0.9040 (t0) cc_final: 0.8793 (m-30) REVERT: D 322 ARG cc_start: 0.8031 (ppt170) cc_final: 0.7603 (ppt170) REVERT: D 462 ASP cc_start: 0.8298 (m-30) cc_final: 0.7912 (m-30) REVERT: D 698 MET cc_start: 0.9301 (tpt) cc_final: 0.8806 (tpp) REVERT: D 725 MET cc_start: 0.8550 (mtm) cc_final: 0.8348 (mtm) REVERT: D 822 MET cc_start: 0.8671 (mmt) cc_final: 0.8282 (mmt) REVERT: D 869 CYS cc_start: 0.8100 (m) cc_final: 0.7401 (m) REVERT: D 898 CYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7635 (m) REVERT: D 1040 MET cc_start: -0.2118 (mtp) cc_final: -0.2495 (mtt) REVERT: D 1144 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9109 (mp) REVERT: D 1189 MET cc_start: 0.7943 (tpp) cc_final: 0.7684 (tpp) REVERT: D 1215 GLU cc_start: 0.8402 (tp30) cc_final: 0.8021 (mm-30) REVERT: D 1349 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8158 (pt0) REVERT: F 52 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8217 (tm-30) REVERT: F 65 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8080 (mm-40) REVERT: F 74 ASP cc_start: 0.8801 (t0) cc_final: 0.8345 (t0) REVERT: F 91 TYR cc_start: 0.8270 (m-10) cc_final: 0.7902 (m-80) outliers start: 113 outliers final: 95 residues processed: 321 average time/residue: 0.3395 time to fit residues: 183.5381 Evaluate side-chains 335 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 232 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1059 ARG Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1241 ASP Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1094 ASP Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1236 GLU Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1332 LEU Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 150 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 190 optimal weight: 4.9990 chunk 306 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 213 optimal weight: 0.6980 chunk 321 optimal weight: 10.0000 chunk 296 optimal weight: 9.9990 chunk 256 optimal weight: 0.2980 chunk 26 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 26746 Z= 0.263 Angle : 0.622 11.456 36319 Z= 0.321 Chirality : 0.042 0.234 4137 Planarity : 0.004 0.054 4580 Dihedral : 12.640 175.614 4061 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.43 % Favored : 92.54 % Rotamer: Outliers : 3.89 % Allowed : 25.29 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.15), residues: 3203 helix: 1.13 (0.16), residues: 1094 sheet: -1.01 (0.26), residues: 395 loop : -2.01 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1193 HIS 0.008 0.001 HIS D 777 PHE 0.023 0.001 PHE C1270 TYR 0.018 0.001 TYR D 772 ARG 0.006 0.000 ARG C1034 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6406 Ramachandran restraints generated. 3203 Oldfield, 0 Emsley, 3203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 237 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6954 (p90) REVERT: B 68 TYR cc_start: 0.8177 (m-80) cc_final: 0.7745 (m-80) REVERT: B 212 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7702 (t0) REVERT: C 488 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.6937 (tpt) REVERT: C 848 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: C 951 MET cc_start: 0.8464 (mmt) cc_final: 0.7945 (tpp) REVERT: C 954 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8694 (mptt) REVERT: C 1059 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6359 (ptm-80) REVERT: C 1304 MET cc_start: 0.8222 (tpt) cc_final: 0.7876 (tpp) REVERT: D 122 SER cc_start: 0.7977 (OUTLIER) cc_final: 0.7736 (p) REVERT: D 180 MET cc_start: 0.7549 (ptt) cc_final: 0.7234 (ptt) REVERT: D 301 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7881 (tm-30) REVERT: D 308 ASP cc_start: 0.8985 (t0) cc_final: 0.8720 (m-30) REVERT: D 322 ARG cc_start: 0.8072 (ppt170) cc_final: 0.7654 (ppt170) REVERT: D 462 ASP cc_start: 0.8238 (m-30) cc_final: 0.7868 (m-30) REVERT: D 698 MET cc_start: 0.9301 (tpt) cc_final: 0.8803 (tpp) REVERT: D 725 MET cc_start: 0.8543 (mtm) cc_final: 0.8337 (mtm) REVERT: D 822 MET cc_start: 0.8663 (mmt) cc_final: 0.8264 (mmt) REVERT: D 869 CYS cc_start: 0.8094 (m) cc_final: 0.7394 (m) REVERT: D 898 CYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7622 (m) REVERT: D 1040 MET cc_start: -0.2134 (mtp) cc_final: -0.2505 (mtt) REVERT: D 1144 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9102 (mp) REVERT: D 1189 MET cc_start: 0.7953 (tpp) cc_final: 0.7697 (tpp) REVERT: D 1215 GLU cc_start: 0.8411 (tp30) cc_final: 0.8041 (mm-30) REVERT: D 1349 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: F 52 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8172 (tm-30) REVERT: F 65 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8072 (mm-40) REVERT: F 74 ASP cc_start: 0.8780 (t0) cc_final: 0.8338 (t0) REVERT: F 91 TYR cc_start: 0.8268 (m-10) cc_final: 0.7901 (m-80) outliers start: 107 outliers final: 94 residues processed: 319 average time/residue: 0.3326 time to fit residues: 178.3920 Evaluate side-chains 334 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 231 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 777 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 848 GLU Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1059 ARG Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1072 ASN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1113 LEU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1241 ASP Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 419 HIS Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 789 LYS Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 898 CYS Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1094 ASP Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1257 VAL Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain D residue 1331 VAL Chi-restraints excluded: chain D residue 1332 LEU Chi-restraints excluded: chain D residue 1349 GLU Chi-restraints excluded: chain D residue 1361 THR Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 150 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 203 optimal weight: 4.9990 chunk 272 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 256 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 263 optimal weight: 0.1980 chunk 32 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.087065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.062659 restraints weight = 80718.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.064717 restraints weight = 40542.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.066105 restraints weight = 25940.349| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26746 Z= 0.219 Angle : 0.602 11.868 36319 Z= 0.311 Chirality : 0.042 0.245 4137 Planarity : 0.004 0.054 4580 Dihedral : 12.573 175.864 4061 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.49 % Favored : 93.47 % Rotamer: Outliers : 4.04 % Allowed : 25.29 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 3203 helix: 1.22 (0.16), residues: 1091 sheet: -0.93 (0.26), residues: 395 loop : -1.94 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1193 HIS 0.008 0.001 HIS F 84 PHE 0.019 0.001 PHE D 172 TYR 0.031 0.001 TYR D 795 ARG 0.006 0.000 ARG C1034 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5000.50 seconds wall clock time: 96 minutes 48.13 seconds (5808.13 seconds total)