Starting phenix.real_space_refine on Sun Mar 24 09:50:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/03_2024/7en1_31199_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/03_2024/7en1_31199.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/03_2024/7en1_31199_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/03_2024/7en1_31199_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/03_2024/7en1_31199_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/03_2024/7en1_31199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/03_2024/7en1_31199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/03_2024/7en1_31199_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en1_31199/03_2024/7en1_31199_neut_trim_updated.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 69 5.16 5 C 12880 2.51 5 N 3772 2.21 5 O 3716 1.98 5 H 20419 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 122": "OE1" <-> "OE2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A ARG 276": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 374": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 377": "OD1" <-> "OD2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A GLU 774": "OE1" <-> "OE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A GLU 831": "OE1" <-> "OE2" Residue "A PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 944": "OD1" <-> "OD2" Residue "A GLU 958": "OE1" <-> "OE2" Residue "A GLU 997": "OE1" <-> "OE2" Residue "A GLU 1117": "OE1" <-> "OE2" Residue "A PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "A PHE 1200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1234": "OE1" <-> "OE2" Residue "A GLU 1310": "OE1" <-> "OE2" Residue "A GLU 1356": "OE1" <-> "OE2" Residue "A GLU 1361": "OE1" <-> "OE2" Residue "A ARG 1372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 1375": "OE1" <-> "OE2" Residue "A PHE 1379": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1399": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 530": "OD1" <-> "OD2" Residue "B TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 820": "OD1" <-> "OD2" Residue "B GLU 831": "OE1" <-> "OE2" Residue "B ARG 901": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 914": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1015": "OE1" <-> "OE2" Residue "B ASP 1034": "OD1" <-> "OD2" Residue "B GLU 1159": "OE1" <-> "OE2" Residue "B PHE 1200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1207": "OE1" <-> "OE2" Residue "B ASP 1291": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40862 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 20280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1320, 20280 Classifications: {'peptide': 1320} Link IDs: {'PCIS': 1, 'PTRANS': 83, 'TRANS': 1235} Chain breaks: 1 Chain: "B" Number of atoms: 20444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 20444 Classifications: {'peptide': 1334} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 1248} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 71 Unusual residues: {' MG': 1, 'J9F': 1, 'PNS': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'NH1NOTPRO': 1, 'rna2p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'J9F:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {' MG': 1, 'PNS': 1, 'SAL': 1} Classifications: {'RNA': 1, 'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH1NOTPRO': 1, 'rna2p': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Planarities with less than four sites: {'SAL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C28 PNS A1501 " occ=0.00 ... (19 atoms not shown) pdb=" S44 PNS A1501 " occ=0.00 residue: pdb=" C1 SAL B1502 " occ=0.00 ... (7 atoms not shown) pdb=" O2 SAL B1502 " occ=0.00 Time building chain proxies: 18.00, per 1000 atoms: 0.44 Number of scatterers: 40862 At special positions: 0 Unit cell: (133, 148, 137, 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) S 69 16.00 P 4 15.00 Mg 2 11.99 O 3716 8.00 N 3772 7.00 C 12880 6.00 H 20419 1.00 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 36.91 Conformation dependent library (CDL) restraints added in 4.4 seconds 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4906 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 117 helices and 28 sheets defined 40.6% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.79 Creating SS restraints... Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 142 through 155 Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 189 through 205 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 241 through 256 removed outlier: 4.135A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.948A pdb=" N ALA A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 297 Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 327 through 339 Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 404 through 423 removed outlier: 4.016A pdb=" N ASP A 420 " --> pdb=" O HIS A 416 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N HIS A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 458 through 463 removed outlier: 3.723A pdb=" N ALA A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 521 Processing helix chain 'A' and resid 535 through 545 Processing helix chain 'A' and resid 558 through 566 Processing helix chain 'A' and resid 582 through 598 Processing helix chain 'A' and resid 615 through 626 Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 671 through 675 Processing helix chain 'A' and resid 711 through 725 removed outlier: 4.319A pdb=" N LEU A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 749 removed outlier: 3.702A pdb=" N LEU A 748 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 749 " --> pdb=" O PHE A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'A' and resid 769 through 779 Processing helix chain 'A' and resid 788 through 795 Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 907 through 913 Processing helix chain 'A' and resid 943 through 945 No H-bonds generated for 'chain 'A' and resid 943 through 945' Processing helix chain 'A' and resid 956 through 964 Processing helix chain 'A' and resid 1009 through 1032 removed outlier: 4.168A pdb=" N ALA A1029 " --> pdb=" O ALA A1025 " (cutoff:3.500A) Proline residue: A1030 - end of helix Processing helix chain 'A' and resid 1035 through 1047 removed outlier: 4.367A pdb=" N ALA A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1063 Processing helix chain 'A' and resid 1067 through 1082 Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1108 through 1116 Processing helix chain 'A' and resid 1120 through 1124 Processing helix chain 'A' and resid 1139 through 1147 removed outlier: 3.522A pdb=" N GLY A1144 " --> pdb=" O TRP A1140 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA A1146 " --> pdb=" O ASP A1142 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER A1147 " --> pdb=" O GLN A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1171 removed outlier: 3.728A pdb=" N ALA A1167 " --> pdb=" O VAL A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1184 No H-bonds generated for 'chain 'A' and resid 1182 through 1184' Processing helix chain 'A' and resid 1188 through 1190 No H-bonds generated for 'chain 'A' and resid 1188 through 1190' Processing helix chain 'A' and resid 1203 through 1205 No H-bonds generated for 'chain 'A' and resid 1203 through 1205' Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1236 through 1245 Processing helix chain 'A' and resid 1249 through 1251 No H-bonds generated for 'chain 'A' and resid 1249 through 1251' Processing helix chain 'A' and resid 1255 through 1264 Processing helix chain 'A' and resid 1292 through 1302 Processing helix chain 'A' and resid 1305 through 1307 No H-bonds generated for 'chain 'A' and resid 1305 through 1307' Processing helix chain 'A' and resid 1328 through 1338 Processing helix chain 'A' and resid 1354 through 1367 Processing helix chain 'A' and resid 1378 through 1381 No H-bonds generated for 'chain 'A' and resid 1378 through 1381' Processing helix chain 'A' and resid 1385 through 1398 removed outlier: 3.589A pdb=" N ARG A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1410 Processing helix chain 'A' and resid 1414 through 1422 removed outlier: 4.667A pdb=" N HIS A1420 " --> pdb=" O GLY A1416 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A1421 " --> pdb=" O LEU A1417 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 22 Processing helix chain 'B' and resid 27 through 31 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 65 through 70 Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.692A pdb=" N CYS B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'B' and resid 142 through 155 Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.525A pdb=" N HIS B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 241 through 256 Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 269 through 297 removed outlier: 4.781A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ALA B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 327 through 339 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 404 through 423 removed outlier: 4.381A pdb=" N ASP B 420 " --> pdb=" O HIS B 416 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N HIS B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 458 through 461 No H-bonds generated for 'chain 'B' and resid 458 through 461' Processing helix chain 'B' and resid 505 through 522 Processing helix chain 'B' and resid 535 through 545 Processing helix chain 'B' and resid 558 through 566 Processing helix chain 'B' and resid 582 through 598 Processing helix chain 'B' and resid 615 through 626 Processing helix chain 'B' and resid 640 through 649 Processing helix chain 'B' and resid 671 through 676 Processing helix chain 'B' and resid 711 through 725 removed outlier: 3.898A pdb=" N LEU B 724 " --> pdb=" O ALA B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 749 removed outlier: 3.693A pdb=" N LEU B 748 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE B 749 " --> pdb=" O PHE B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'B' and resid 769 through 779 Processing helix chain 'B' and resid 788 through 796 Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 842 through 844 No H-bonds generated for 'chain 'B' and resid 842 through 844' Processing helix chain 'B' and resid 907 through 913 Processing helix chain 'B' and resid 956 through 964 Processing helix chain 'B' and resid 1009 through 1028 removed outlier: 3.842A pdb=" N GLU B1028 " --> pdb=" O GLY B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1032 No H-bonds generated for 'chain 'B' and resid 1030 through 1032' Processing helix chain 'B' and resid 1035 through 1047 removed outlier: 3.589A pdb=" N ASP B1043 " --> pdb=" O ARG B1039 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ALA B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1063 Processing helix chain 'B' and resid 1067 through 1082 Processing helix chain 'B' and resid 1088 through 1092 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1108 through 1115 removed outlier: 3.897A pdb=" N ARG B1114 " --> pdb=" O GLU B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1124 No H-bonds generated for 'chain 'B' and resid 1121 through 1124' Processing helix chain 'B' and resid 1141 through 1143 No H-bonds generated for 'chain 'B' and resid 1141 through 1143' Processing helix chain 'B' and resid 1145 through 1148 No H-bonds generated for 'chain 'B' and resid 1145 through 1148' Processing helix chain 'B' and resid 1162 through 1169 Processing helix chain 'B' and resid 1182 through 1184 No H-bonds generated for 'chain 'B' and resid 1182 through 1184' Processing helix chain 'B' and resid 1188 through 1190 No H-bonds generated for 'chain 'B' and resid 1188 through 1190' Processing helix chain 'B' and resid 1203 through 1205 No H-bonds generated for 'chain 'B' and resid 1203 through 1205' Processing helix chain 'B' and resid 1209 through 1219 Processing helix chain 'B' and resid 1236 through 1245 Processing helix chain 'B' and resid 1249 through 1251 No H-bonds generated for 'chain 'B' and resid 1249 through 1251' Processing helix chain 'B' and resid 1255 through 1264 Processing helix chain 'B' and resid 1292 through 1302 Processing helix chain 'B' and resid 1328 through 1339 Processing sheet with id= A, first strand: chain 'A' and resid 469 through 472 Processing sheet with id= B, first strand: chain 'A' and resid 161 through 164 Processing sheet with id= C, first strand: chain 'A' and resid 318 through 325 removed outlier: 3.943A pdb=" N ARG A 485 " --> pdb=" O ASN A 449 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 364 through 372 Processing sheet with id= E, first strand: chain 'A' and resid 630 through 633 removed outlier: 6.814A pdb=" N LEU A 654 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 732 through 734 removed outlier: 6.606A pdb=" N SER A 757 " --> pdb=" O LEU A 733 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 783 through 787 removed outlier: 7.021A pdb=" N ALA A 809 " --> pdb=" O TRP A 784 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N SER A 786 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 811 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 835 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN A 849 " --> pdb=" O GLY A 839 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 872 through 877 removed outlier: 3.615A pdb=" N GLY A 896 " --> pdb=" O ARG A 921 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ARG A 921 " --> pdb=" O GLY A 896 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 929 through 931 Processing sheet with id= J, first strand: chain 'A' and resid 946 through 949 removed outlier: 3.631A pdb=" N VAL A 947 " --> pdb=" O ILE A 954 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1311 through 1314 removed outlier: 3.668A pdb=" N ARG A1311 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 971 " --> pdb=" O VAL A 989 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1268 through 1273 removed outlier: 6.187A pdb=" N LEU A1280 " --> pdb=" O LEU A1272 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU A1159 " --> pdb=" O GLN A1179 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 571 through 574 removed outlier: 6.599A pdb=" N VAL A 580 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.742A pdb=" N VAL A 709 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 694 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL A 707 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 469 through 471 Processing sheet with id= P, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= Q, first strand: chain 'B' and resid 318 through 325 Processing sheet with id= R, first strand: chain 'B' and resid 364 through 372 Processing sheet with id= S, first strand: chain 'B' and resid 732 through 734 removed outlier: 6.625A pdb=" N SER B 757 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 580 " --> pdb=" O ALA B 572 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B 574 " --> pdb=" O GLN B 578 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 630 through 633 removed outlier: 6.719A pdb=" N LEU B 654 " --> pdb=" O GLU B 608 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 783 through 787 removed outlier: 6.792A pdb=" N ALA B 809 " --> pdb=" O TRP B 784 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N SER B 786 " --> pdb=" O ALA B 809 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 811 " --> pdb=" O SER B 786 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN B 849 " --> pdb=" O GLY B 839 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 872 through 877 Processing sheet with id= W, first strand: chain 'B' and resid 915 through 917 Processing sheet with id= X, first strand: chain 'B' and resid 929 through 931 Processing sheet with id= Y, first strand: chain 'B' and resid 946 through 949 Processing sheet with id= Z, first strand: chain 'B' and resid 1311 through 1314 removed outlier: 3.793A pdb=" N ARG B1311 " --> pdb=" O LEU B 984 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 1153 through 1157 removed outlier: 6.101A pdb=" N LEU B1128 " --> pdb=" O GLU B1154 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N THR B1156 " --> pdb=" O LEU B1128 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B1130 " --> pdb=" O THR B1156 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG B1196 " --> pdb=" O ALA B1131 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG B1225 " --> pdb=" O VAL B1197 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER B1199 " --> pdb=" O ARG B1225 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B1227 " --> pdb=" O SER B1199 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP B1230 " --> pdb=" O ALA B1279 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B1279 " --> pdb=" O ASP B1230 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU B1282 " --> pdb=" O CYS B1271 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N CYS B1271 " --> pdb=" O GLU B1282 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B1284 " --> pdb=" O PRO B1269 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 691 through 697 removed outlier: 6.704A pdb=" N VAL B 709 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL B 694 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL B 707 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR B 696 " --> pdb=" O LYS B 705 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LYS B 705 " --> pdb=" O TYR B 696 " (cutoff:3.500A) 821 hydrogen bonds defined for protein. 2343 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.66 Time building geometry restraints manager: 38.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.89 - 1.08: 7353 1.08 - 1.28: 16500 1.28 - 1.47: 7948 1.47 - 1.66: 9393 1.66 - 1.86: 94 Bond restraints: 41288 Sorted by residual: bond pdb=" N CYS A1505 " pdb=" H CYS A1505 " ideal model delta sigma weight residual 0.860 1.018 -0.158 2.00e-02 2.50e+03 6.24e+01 bond pdb=" N CYS B1505 " pdb=" H CYS B1505 " ideal model delta sigma weight residual 0.860 1.017 -0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" C4 AMP A1504 " pdb=" C5 AMP A1504 " ideal model delta sigma weight residual 1.490 1.338 0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" N ALA A 794 " pdb=" H ALA A 794 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N TYR B 804 " pdb=" H TYR B 804 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 41283 not shown) Histogram of bond angle deviations from ideal: 72.32 - 84.96: 3 84.96 - 97.60: 34 97.60 - 110.24: 37049 110.24 - 122.88: 34406 122.88 - 135.52: 3209 Bond angle restraints: 74701 Sorted by residual: angle pdb=" N GLN B 689 " pdb=" CA GLN B 689 " pdb=" HA GLN B 689 " ideal model delta sigma weight residual 110.00 72.32 37.68 3.00e+00 1.11e-01 1.58e+02 angle pdb=" C GLN B 689 " pdb=" CA GLN B 689 " pdb=" HA GLN B 689 " ideal model delta sigma weight residual 109.00 77.63 31.37 3.00e+00 1.11e-01 1.09e+02 angle pdb=" CB GLN B 689 " pdb=" CA GLN B 689 " pdb=" HA GLN B 689 " ideal model delta sigma weight residual 109.00 78.51 30.49 3.00e+00 1.11e-01 1.03e+02 angle pdb=" CA PHE A 741 " pdb=" CB PHE A 741 " pdb=" CG PHE A 741 " ideal model delta sigma weight residual 113.80 122.27 -8.47 1.00e+00 1.00e+00 7.17e+01 angle pdb=" N PRO B 174 " pdb=" CA PRO B 174 " pdb=" CB PRO B 174 " ideal model delta sigma weight residual 103.22 107.09 -3.87 5.20e-01 3.70e+00 5.53e+01 ... (remaining 74696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.16: 17525 21.16 - 42.33: 1085 42.33 - 63.49: 545 63.49 - 84.65: 118 84.65 - 105.82: 8 Dihedral angle restraints: 19281 sinusoidal: 10721 harmonic: 8560 Sorted by residual: dihedral pdb=" CA VAL A 486 " pdb=" C VAL A 486 " pdb=" N GLY A 487 " pdb=" CA GLY A 487 " ideal model delta harmonic sigma weight residual -180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA VAL B 486 " pdb=" C VAL B 486 " pdb=" N GLY B 487 " pdb=" CA GLY B 487 " ideal model delta harmonic sigma weight residual -180.00 -150.98 -29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA SER B 813 " pdb=" C SER B 813 " pdb=" N GLY B 814 " pdb=" CA GLY B 814 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 19278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2115 0.094 - 0.189: 886 0.189 - 0.283: 145 0.283 - 0.377: 28 0.377 - 0.472: 5 Chirality restraints: 3179 Sorted by residual: chirality pdb=" CA GLN B 689 " pdb=" N GLN B 689 " pdb=" C GLN B 689 " pdb=" CB GLN B 689 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CA ASP B 742 " pdb=" N ASP B 742 " pdb=" C ASP B 742 " pdb=" CB ASP B 742 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ASP A1246 " pdb=" N ASP A1246 " pdb=" C ASP A1246 " pdb=" CB ASP A1246 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 3176 not shown) Planarity restraints: 6264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 953 " 0.572 9.50e-02 1.11e+02 2.83e-01 1.02e+03 pdb=" NE ARG B 953 " 0.142 2.00e-02 2.50e+03 pdb=" CZ ARG B 953 " 0.126 2.00e-02 2.50e+03 pdb=" NH1 ARG B 953 " 0.176 2.00e-02 2.50e+03 pdb=" NH2 ARG B 953 " -0.017 2.00e-02 2.50e+03 pdb="HH11 ARG B 953 " -0.486 2.00e-02 2.50e+03 pdb="HH12 ARG B 953 " 0.247 2.00e-02 2.50e+03 pdb="HH21 ARG B 953 " -0.156 2.00e-02 2.50e+03 pdb="HH22 ARG B 953 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 816 " -0.356 2.00e-02 2.50e+03 1.27e-01 6.43e+02 pdb=" CG TRP A 816 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 816 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TRP A 816 " 0.074 2.00e-02 2.50e+03 pdb=" NE1 TRP A 816 " 0.128 2.00e-02 2.50e+03 pdb=" CE2 TRP A 816 " 0.042 2.00e-02 2.50e+03 pdb=" CE3 TRP A 816 " 0.112 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 816 " -0.060 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 816 " 0.057 2.00e-02 2.50e+03 pdb=" CH2 TRP A 816 " -0.062 2.00e-02 2.50e+03 pdb=" HD1 TRP A 816 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP A 816 " 0.116 2.00e-02 2.50e+03 pdb=" HE3 TRP A 816 " 0.141 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 816 " -0.138 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 816 " 0.059 2.00e-02 2.50e+03 pdb=" HH2 TRP A 816 " -0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 602 " -0.285 9.50e-02 1.11e+02 1.79e-01 5.24e+02 pdb=" NE ARG A 602 " -0.117 2.00e-02 2.50e+03 pdb=" CZ ARG A 602 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 602 " 0.037 2.00e-02 2.50e+03 pdb=" NH2 ARG A 602 " 0.004 2.00e-02 2.50e+03 pdb="HH11 ARG A 602 " 0.261 2.00e-02 2.50e+03 pdb="HH12 ARG A 602 " -0.316 2.00e-02 2.50e+03 pdb="HH21 ARG A 602 " 0.013 2.00e-02 2.50e+03 pdb="HH22 ARG A 602 " 0.149 2.00e-02 2.50e+03 ... (remaining 6261 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 3141 2.16 - 2.77: 75841 2.77 - 3.38: 130253 3.38 - 3.99: 173783 3.99 - 4.60: 254871 Nonbonded interactions: 637889 Sorted by model distance: nonbonded pdb=" OE2 GLU A 608 " pdb=" HG SER A 610 " model vdw 1.552 1.850 nonbonded pdb=" HG1 THR B 343 " pdb=" O26 PNS B1501 " model vdw 1.572 1.850 nonbonded pdb=" OE1 GLU B1015 " pdb=" HG SER B1235 " model vdw 1.580 1.850 nonbonded pdb=" HG SER A 472 " pdb=" OD2 ASP A 480 " model vdw 1.586 1.850 nonbonded pdb=" OD2 ASP B1134 " pdb=" HG SER B1199 " model vdw 1.593 1.850 ... (remaining 637884 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 99 through 1340 or resid 1501 or resid 1503 through 1505)) \ selection = (chain 'B' and (resid 99 through 1340 or resid 1501 or resid 1503 through 1504 o \ r (resid 1505 and (name N or name CA or name C or name O or name CB or name SG o \ r name H or name H2 or name HA or name HB2 or name HB3 or name HG )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.700 Extract box with map and model: 5.560 Check model and map are aligned: 0.610 Set scattering table: 0.340 Process input model: 137.320 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.140 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.013 0.152 20869 Z= 0.857 Angle : 1.970 21.372 28429 Z= 1.290 Chirality : 0.101 0.472 3179 Planarity : 0.022 0.206 3782 Dihedral : 15.106 105.818 7716 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.17 % Favored : 94.56 % Rotamer: Outliers : 1.72 % Allowed : 5.72 % Favored : 92.56 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 1.18 % 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: -2.33 (0.15), residues: 2648 helix: -1.68 (0.13), residues: 1092 sheet: -1.98 (0.24), residues: 422 loop : -0.97 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.229 0.035 TRP A 816 HIS 0.028 0.006 HIS A 711 PHE 0.132 0.024 PHE B 372 TYR 0.205 0.034 TYR B 923 ARG 0.019 0.002 ARG B 953 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 237 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1055 SER cc_start: 0.1741 (OUTLIER) cc_final: 0.1354 (t) REVERT: A 1073 MET cc_start: 0.5360 (mtp) cc_final: 0.4996 (mtm) REVERT: A 1207 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7273 (mm-30) REVERT: A 1296 GLN cc_start: 0.7324 (tp40) cc_final: 0.6952 (mm-40) REVERT: B 295 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8795 (mt) REVERT: B 715 ILE cc_start: 0.9224 (tp) cc_final: 0.8907 (tp) REVERT: B 1000 MET cc_start: 0.5895 (tmm) cc_final: 0.5601 (tmm) outliers start: 35 outliers final: 10 residues processed: 266 average time/residue: 1.0858 time to fit residues: 395.5867 Evaluate side-chains 148 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 1109 ARG Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1230 ASP Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 223 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 GLN A 946 GLN B 449 ASN ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20869 Z= 0.247 Angle : 0.747 7.620 28429 Z= 0.382 Chirality : 0.041 0.414 3179 Planarity : 0.007 0.057 3782 Dihedral : 9.344 83.214 3045 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.53 % Allowed : 8.33 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: -1.28 (0.16), residues: 2648 helix: -0.42 (0.15), residues: 1090 sheet: -1.86 (0.23), residues: 438 loop : -0.64 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 196 HIS 0.007 0.001 HIS B 916 PHE 0.022 0.002 PHE B 372 TYR 0.019 0.002 TYR A 290 ARG 0.007 0.001 ARG A1210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1055 SER cc_start: 0.2102 (OUTLIER) cc_final: 0.1637 (t) REVERT: A 1073 MET cc_start: 0.5286 (mtp) cc_final: 0.5024 (mtm) REVERT: A 1207 GLU cc_start: 0.7531 (mp0) cc_final: 0.7189 (mm-30) REVERT: B 1505 CYS cc_start: 0.4986 (m) cc_final: 0.4763 (m) outliers start: 31 outliers final: 20 residues processed: 185 average time/residue: 0.9926 time to fit residues: 262.3036 Evaluate side-chains 143 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 587 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1308 ARG Chi-restraints excluded: chain A residue 1334 SER Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1230 ASP Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 241 optimal weight: 20.0000 chunk 260 optimal weight: 8.9990 chunk 214 optimal weight: 3.9990 chunk 239 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20869 Z= 0.344 Angle : 0.675 7.197 28429 Z= 0.344 Chirality : 0.040 0.403 3179 Planarity : 0.005 0.067 3782 Dihedral : 8.486 78.257 3034 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.08 % Allowed : 9.12 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.16), residues: 2648 helix: 0.04 (0.15), residues: 1093 sheet: -1.96 (0.22), residues: 468 loop : -0.52 (0.20), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B1140 HIS 0.007 0.001 HIS A 340 PHE 0.021 0.002 PHE B1200 TYR 0.025 0.002 TYR A1194 ARG 0.006 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8689 (tt) REVERT: A 1073 MET cc_start: 0.5384 (mtp) cc_final: 0.5137 (mtm) REVERT: A 1145 MET cc_start: 0.5991 (ttt) cc_final: 0.5307 (ppp) REVERT: A 1207 GLU cc_start: 0.7321 (mp0) cc_final: 0.7056 (mm-30) REVERT: B 715 ILE cc_start: 0.9221 (tp) cc_final: 0.8898 (tp) REVERT: B 1073 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7543 (mtp) outliers start: 22 outliers final: 16 residues processed: 141 average time/residue: 1.0633 time to fit residues: 214.3077 Evaluate side-chains 130 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1308 ARG Chi-restraints excluded: chain A residue 1334 SER Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1073 MET Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1215 LEU Chi-restraints excluded: chain B residue 1230 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 238 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 chunk 241 optimal weight: 20.0000 chunk 256 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20869 Z= 0.305 Angle : 0.632 6.365 28429 Z= 0.319 Chirality : 0.038 0.402 3179 Planarity : 0.005 0.054 3782 Dihedral : 7.885 81.414 3025 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.38 % Allowed : 9.51 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2648 helix: 0.35 (0.16), residues: 1091 sheet: -1.97 (0.22), residues: 466 loop : -0.44 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 535 HIS 0.006 0.001 HIS A 340 PHE 0.017 0.002 PHE B 372 TYR 0.015 0.002 TYR B 290 ARG 0.007 0.000 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8552 (mmm) cc_final: 0.8230 (mmp) REVERT: A 394 LEU cc_start: 0.8948 (tp) cc_final: 0.8745 (tt) REVERT: A 849 ASN cc_start: 0.7382 (m110) cc_final: 0.7014 (m110) REVERT: A 865 TYR cc_start: 0.8499 (m-10) cc_final: 0.8102 (m-10) REVERT: A 1073 MET cc_start: 0.5507 (mtp) cc_final: 0.5279 (mtm) REVERT: A 1145 MET cc_start: 0.5993 (ttt) cc_final: 0.5349 (ppp) REVERT: A 1207 GLU cc_start: 0.7336 (mp0) cc_final: 0.7048 (mm-30) REVERT: B 346 SER cc_start: 0.8604 (OUTLIER) cc_final: 0.8038 (p) outliers start: 28 outliers final: 20 residues processed: 147 average time/residue: 0.9611 time to fit residues: 204.6240 Evaluate side-chains 133 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 883 ASP Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1230 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 213 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 218 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20869 Z= 0.331 Angle : 0.624 6.019 28429 Z= 0.313 Chirality : 0.038 0.398 3179 Planarity : 0.005 0.053 3782 Dihedral : 7.598 81.129 3025 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.33 % Allowed : 9.86 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.17), residues: 2648 helix: 0.52 (0.16), residues: 1110 sheet: -2.02 (0.22), residues: 477 loop : -0.37 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 535 HIS 0.006 0.001 HIS A 340 PHE 0.023 0.002 PHE B1200 TYR 0.014 0.002 TYR B 290 ARG 0.012 0.001 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 3.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 1073 MET cc_start: 0.5484 (mtp) cc_final: 0.5253 (mtm) REVERT: A 1145 MET cc_start: 0.6223 (ttt) cc_final: 0.5556 (ppp) REVERT: A 1207 GLU cc_start: 0.7360 (mp0) cc_final: 0.7109 (mm-30) REVERT: B 346 SER cc_start: 0.8582 (OUTLIER) cc_final: 0.8136 (p) outliers start: 27 outliers final: 21 residues processed: 134 average time/residue: 0.9931 time to fit residues: 191.9500 Evaluate side-chains 130 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1308 ARG Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1230 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 86 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 20869 Z= 0.395 Angle : 0.639 6.535 28429 Z= 0.322 Chirality : 0.039 0.398 3179 Planarity : 0.005 0.050 3782 Dihedral : 7.482 81.527 3025 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.33 % Allowed : 10.35 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2648 helix: 0.57 (0.16), residues: 1106 sheet: -2.10 (0.22), residues: 479 loop : -0.41 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 535 HIS 0.006 0.001 HIS A 340 PHE 0.015 0.002 PHE B 372 TYR 0.022 0.002 TYR B 865 ARG 0.007 0.001 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 865 TYR cc_start: 0.8472 (m-10) cc_final: 0.8092 (m-10) REVERT: A 1055 SER cc_start: 0.2071 (OUTLIER) cc_final: 0.1595 (t) REVERT: A 1073 MET cc_start: 0.5489 (mtp) cc_final: 0.5240 (mtm) REVERT: A 1145 MET cc_start: 0.6322 (ttt) cc_final: 0.5830 (ppp) REVERT: A 1207 GLU cc_start: 0.7322 (mp0) cc_final: 0.7091 (mm-30) REVERT: B 346 SER cc_start: 0.8628 (OUTLIER) cc_final: 0.8109 (p) outliers start: 27 outliers final: 22 residues processed: 132 average time/residue: 0.9842 time to fit residues: 187.9195 Evaluate side-chains 124 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1109 ARG Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1230 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 247 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 255 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 20869 Z= 0.390 Angle : 0.636 6.343 28429 Z= 0.318 Chirality : 0.039 0.397 3179 Planarity : 0.005 0.051 3782 Dihedral : 7.330 80.551 3025 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.48 % Allowed : 10.65 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2648 helix: 0.61 (0.16), residues: 1102 sheet: -2.12 (0.22), residues: 480 loop : -0.44 (0.20), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 535 HIS 0.005 0.001 HIS B 375 PHE 0.018 0.002 PHE B 372 TYR 0.018 0.002 TYR B 865 ARG 0.006 0.001 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 3.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 865 TYR cc_start: 0.8462 (m-10) cc_final: 0.7997 (m-10) REVERT: A 1055 SER cc_start: 0.2062 (OUTLIER) cc_final: 0.1597 (t) REVERT: A 1073 MET cc_start: 0.5486 (mtp) cc_final: 0.5232 (mtm) REVERT: A 1207 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7162 (mm-30) REVERT: B 346 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.8198 (p) outliers start: 30 outliers final: 21 residues processed: 130 average time/residue: 0.9300 time to fit residues: 176.0383 Evaluate side-chains 124 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 3.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1109 ARG Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1230 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 158 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 162 optimal weight: 0.0770 chunk 174 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 GLN B 421 HIS B1223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20869 Z= 0.226 Angle : 0.582 5.991 28429 Z= 0.288 Chirality : 0.038 0.386 3179 Planarity : 0.005 0.053 3782 Dihedral : 7.011 80.204 3021 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.94 % Allowed : 11.58 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2648 helix: 0.96 (0.16), residues: 1104 sheet: -1.85 (0.23), residues: 435 loop : -0.35 (0.20), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 535 HIS 0.005 0.001 HIS A 340 PHE 0.014 0.002 PHE B 372 TYR 0.014 0.002 TYR B 865 ARG 0.006 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 736 VAL cc_start: 0.9133 (m) cc_final: 0.8908 (p) REVERT: A 1055 SER cc_start: 0.2362 (OUTLIER) cc_final: 0.1871 (t) REVERT: A 1073 MET cc_start: 0.5377 (mtp) cc_final: 0.5102 (mtm) REVERT: A 1207 GLU cc_start: 0.7345 (mp0) cc_final: 0.7137 (mm-30) REVERT: B 346 SER cc_start: 0.8551 (m) cc_final: 0.8105 (p) outliers start: 19 outliers final: 17 residues processed: 133 average time/residue: 0.9835 time to fit residues: 190.3437 Evaluate side-chains 120 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1230 ASP Chi-restraints excluded: chain B residue 1284 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 232 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 223 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 186 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 237 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20869 Z= 0.319 Angle : 0.600 5.947 28429 Z= 0.298 Chirality : 0.038 0.388 3179 Planarity : 0.005 0.051 3782 Dihedral : 7.028 80.882 3021 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.23 % Allowed : 11.63 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2648 helix: 0.97 (0.16), residues: 1101 sheet: -1.94 (0.23), residues: 453 loop : -0.33 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 535 HIS 0.005 0.001 HIS B 375 PHE 0.015 0.002 PHE B 372 TYR 0.017 0.002 TYR B 865 ARG 0.005 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 3.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 736 VAL cc_start: 0.9163 (m) cc_final: 0.8945 (p) REVERT: A 1055 SER cc_start: 0.2380 (OUTLIER) cc_final: 0.1889 (t) REVERT: A 1073 MET cc_start: 0.5391 (mtp) cc_final: 0.5124 (mtm) REVERT: A 1207 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7133 (mm-30) REVERT: B 346 SER cc_start: 0.8630 (m) cc_final: 0.8170 (p) outliers start: 25 outliers final: 22 residues processed: 126 average time/residue: 1.0260 time to fit residues: 186.7760 Evaluate side-chains 125 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1207 GLU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1109 ARG Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1230 ASP Chi-restraints excluded: chain B residue 1284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 156 optimal weight: 6.9990 chunk 251 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 174 optimal weight: 0.6980 chunk 264 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 210 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20869 Z= 0.239 Angle : 0.575 6.021 28429 Z= 0.284 Chirality : 0.038 0.383 3179 Planarity : 0.005 0.052 3782 Dihedral : 6.914 80.282 3021 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.03 % Allowed : 12.03 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2648 helix: 1.18 (0.16), residues: 1090 sheet: -1.88 (0.23), residues: 441 loop : -0.31 (0.20), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1041 HIS 0.004 0.001 HIS A 340 PHE 0.013 0.001 PHE B 372 TYR 0.024 0.002 TYR B 865 ARG 0.006 0.000 ARG B 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5296 Ramachandran restraints generated. 2648 Oldfield, 0 Emsley, 2648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1385 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1055 SER cc_start: 0.2343 (OUTLIER) cc_final: 0.1858 (t) REVERT: A 1073 MET cc_start: 0.5516 (mtp) cc_final: 0.5221 (mtm) REVERT: A 1207 GLU cc_start: 0.7387 (mp0) cc_final: 0.7167 (mm-30) REVERT: B 346 SER cc_start: 0.8611 (m) cc_final: 0.8119 (p) REVERT: B 1505 CYS cc_start: 0.4561 (m) cc_final: 0.4351 (m) outliers start: 21 outliers final: 18 residues processed: 126 average time/residue: 1.0064 time to fit residues: 183.1273 Evaluate side-chains 120 residues out of total 2029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 991 ARG Chi-restraints excluded: chain B residue 1008 PHE Chi-restraints excluded: chain B residue 1159 GLU Chi-restraints excluded: chain B residue 1284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 166 optimal weight: 1.9990 chunk 223 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.087159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.064988 restraints weight = 188731.176| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.94 r_work: 0.3114 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20869 Z= 0.215 Angle : 0.566 6.073 28429 Z= 0.277 Chirality : 0.037 0.379 3179 Planarity : 0.004 0.051 3782 Dihedral : 6.782 80.655 3019 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.03 % Allowed : 12.27 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2648 helix: 1.25 (0.16), residues: 1102 sheet: -1.79 (0.24), residues: 433 loop : -0.32 (0.20), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B1041 HIS 0.004 0.001 HIS B 375 PHE 0.014 0.001 PHE B 372 TYR 0.014 0.002 TYR B 874 ARG 0.005 0.000 ARG A1210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7924.65 seconds wall clock time: 140 minutes 55.00 seconds (8455.00 seconds total)