Starting phenix.real_space_refine on Sat Feb 24 06:34:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/02_2024/7en2_31200_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/02_2024/7en2_31200.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/02_2024/7en2_31200_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/02_2024/7en2_31200_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/02_2024/7en2_31200_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/02_2024/7en2_31200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/02_2024/7en2_31200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/02_2024/7en2_31200_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/02_2024/7en2_31200_neut_trim_updated.pdb" } resolution = 3.78 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 68 5.16 5 C 13237 2.51 5 N 3883 2.21 5 O 3817 1.98 5 H 21010 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 377": "OD1" <-> "OD2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A ASP 660": "OD1" <-> "OD2" Residue "A GLU 774": "OE1" <-> "OE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A GLU 908": "OE1" <-> "OE2" Residue "A ASP 944": "OD1" <-> "OD2" Residue "A ARG 950": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 958": "OE1" <-> "OE2" Residue "A GLU 997": "OE1" <-> "OE2" Residue "A GLU 1117": "OE1" <-> "OE2" Residue "A GLU 1159": "OE1" <-> "OE2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "A GLU 1207": "OE1" <-> "OE2" Residue "A GLU 1234": "OE1" <-> "OE2" Residue "A GLU 1310": "OE1" <-> "OE2" Residue "A GLU 1353": "OE1" <-> "OE2" Residue "A GLU 1356": "OE1" <-> "OE2" Residue "A GLU 1361": "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 GLU 150": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 377": "OD1" <-> "OD2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B ASP 488": "OD1" <-> "OD2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B ASP 530": "OD1" <-> "OD2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B GLU 587": "OE1" <-> "OE2" Residue "B PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B GLU 659": "OE1" <-> "OE2" Residue "B GLU 774": "OE1" <-> "OE2" Residue "B GLU 831": "OE1" <-> "OE2" Residue "B ASP 944": "OD1" <-> "OD2" Residue "B GLU 958": "OE1" <-> "OE2" Residue "B GLU 1015": "OE1" <-> "OE2" Residue "B ASP 1034": "OD1" <-> "OD2" Residue "B TYR 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1234": "OE1" <-> "OE2" Residue "B GLU 1310": "OE1" <-> "OE2" Residue "B GLU 1356": "OE1" <-> "OE2" Residue "B GLU 1361": "OE1" <-> "OE2" Residue "B PHE 1379": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1399": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 42019 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 20290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1321, 20290 Classifications: {'peptide': 1321} Link IDs: {'PCIS': 1, 'PTRANS': 83, 'TRANS': 1236} Chain breaks: 1 Chain: "B" Number of atoms: 21641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 21641 Classifications: {'peptide': 1410} Link IDs: {'PCIS': 1, 'PTRANS': 87, 'TRANS': 1321} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'PNS': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'PNS': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C28 PNS A1501 " occ=0.00 ... (19 atoms not shown) pdb=" S44 PNS A1501 " occ=0.00 Time building chain proxies: 18.87, per 1000 atoms: 0.45 Number of scatterers: 42019 At special positions: 0 Unit cell: (145, 158, 133, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 68 16.00 P 4 15.00 O 3817 8.00 N 3883 7.00 C 13237 6.00 H 21010 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 38.80 Conformation dependent library (CDL) restraints added in 4.9 seconds 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5044 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 122 helices and 27 sheets defined 40.7% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.31 Creating SS restraints... Processing helix chain 'A' and resid 109 through 118 removed outlier: 3.507A pdb=" N ALA A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 155 Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' 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 241 through 256 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 294 removed outlier: 4.269A pdb=" N ALA A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ALA A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) 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: 3.657A pdb=" N ASP A 420 " --> pdb=" O HIS A 416 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.447A 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 Processing helix chain 'A' and resid 505 through 522 Processing helix chain 'A' and resid 535 through 546 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 removed outlier: 3.797A pdb=" N LEU A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 699 through 701 No H-bonds generated for 'chain 'A' and resid 699 through 701' Processing helix chain 'A' and resid 711 through 725 removed outlier: 3.637A pdb=" N LEU A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 751 removed outlier: 3.773A pdb=" N LEU A 748 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 749 " --> pdb=" O PHE A 746 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY A 750 " --> pdb=" O ASP A 747 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY A 751 " --> pdb=" O LEU A 748 " (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 796 removed outlier: 3.511A pdb=" N MET A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) 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 956 through 964 Processing helix chain 'A' and resid 1009 through 1028 removed outlier: 4.690A pdb=" N GLU A1028 " --> pdb=" O GLY A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1032 No H-bonds generated for 'chain 'A' and resid 1030 through 1032' Processing helix chain 'A' and resid 1035 through 1046 Processing helix chain 'A' and resid 1049 through 1052 No H-bonds generated for 'chain 'A' and resid 1049 through 1052' Processing helix chain 'A' and resid 1057 through 1063 removed outlier: 3.802A pdb=" N LEU A1063 " --> pdb=" O LEU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1082 Processing helix chain 'A' and resid 1088 through 1091 No H-bonds generated for 'chain 'A' and resid 1088 through 1091' Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1108 through 1116 Processing helix chain 'A' and resid 1121 through 1124 No H-bonds generated for 'chain 'A' and resid 1121 through 1124' Processing helix chain 'A' and resid 1141 through 1148 removed outlier: 6.379A pdb=" N ALA A1146 " --> pdb=" O GLN A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1171 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 1209 through 1219 removed outlier: 3.717A pdb=" N ALA A1214 " --> pdb=" O ARG A1210 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1241 No H-bonds generated for 'chain 'A' and resid 1238 through 1241' Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 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 1300 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 1339 Processing helix chain 'A' and resid 1354 through 1367 Processing helix chain 'A' and resid 1378 through 1382 Processing helix chain 'A' and resid 1385 through 1399 removed outlier: 3.544A pdb=" N ARG A1390 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1408 No H-bonds generated for 'chain 'A' and resid 1405 through 1408' Processing helix chain 'A' and resid 1414 through 1422 removed outlier: 4.192A pdb=" N ARG A1419 " --> pdb=" O ALA A1415 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N HIS A1420 " --> pdb=" O GLY A1416 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 27 through 31 Processing helix chain 'B' and resid 46 through 58 removed outlier: 3.871A pdb=" N TYR B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 109 through 118 removed outlier: 3.685A pdb=" N ARG B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) 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 203 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 241 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 269 through 292 removed outlier: 3.561A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'B' and resid 327 through 339 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 404 through 423 removed outlier: 3.980A pdb=" N ASP B 420 " --> pdb=" O HIS B 416 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 436 Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 505 through 521 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 removed outlier: 3.558A pdb=" N LEU B 645 " --> pdb=" O ALA B 641 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 648 " --> pdb=" O ARG B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 675 Processing helix chain 'B' and resid 699 through 701 No H-bonds generated for 'chain 'B' and resid 699 through 701' Processing helix chain 'B' and resid 711 through 725 removed outlier: 4.247A pdb=" N LEU B 724 " --> pdb=" O ALA B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 753 removed outlier: 3.841A pdb=" N LEU B 748 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE B 749 " --> pdb=" O PHE B 746 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY B 750 " --> pdb=" O ASP B 747 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU B 752 " --> pdb=" O PHE B 749 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B 753 " --> pdb=" O GLY B 750 " (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 778 Processing helix chain 'B' and resid 788 through 795 Processing helix chain 'B' and resid 821 through 825 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 removed outlier: 3.970A pdb=" N ARG B 912 " --> pdb=" O GLU B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 964 Processing helix chain 'B' and resid 1009 through 1028 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: 4.409A pdb=" N ARG B1040 " --> pdb=" O GLY B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1063 removed outlier: 4.048A pdb=" N ARG B1062 " --> pdb=" O GLU B1058 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU B1063 " --> pdb=" O ALA B1059 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1082 Processing helix chain 'B' and resid 1090 through 1092 No H-bonds generated for 'chain 'B' and resid 1090 through 1092' Processing helix chain 'B' and resid 1098 through 1103 Processing helix chain 'B' and resid 1108 through 1116 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 1163 through 1171 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 1209 through 1219 removed outlier: 3.705A pdb=" N ALA B1214 " --> pdb=" O ARG B1210 " (cutoff:3.500A) Processing helix chain 'B' and resid 1238 through 1244 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 1275 through 1278 No H-bonds generated for 'chain 'B' and resid 1275 through 1278' Processing helix chain 'B' and resid 1292 through 1302 Processing helix chain 'B' and resid 1305 through 1307 No H-bonds generated for 'chain 'B' and resid 1305 through 1307' Processing helix chain 'B' and resid 1328 through 1339 Processing helix chain 'B' and resid 1354 through 1367 Processing helix chain 'B' and resid 1378 through 1381 No H-bonds generated for 'chain 'B' and resid 1378 through 1381' Processing helix chain 'B' and resid 1385 through 1399 removed outlier: 3.547A pdb=" N ALA B1393 " --> pdb=" O THR B1389 " (cutoff:3.500A) Processing helix chain 'B' and resid 1405 through 1408 No H-bonds generated for 'chain 'B' and resid 1405 through 1408' Processing helix chain 'B' and resid 1414 through 1422 removed outlier: 4.236A pdb=" N ARG B1419 " --> pdb=" O ALA B1415 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N HIS B1420 " --> pdb=" O GLY B1416 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU B1421 " --> pdb=" O LEU B1417 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 104 through 106 Processing sheet with id= B, first strand: chain 'A' and resid 179 through 182 removed outlier: 8.031A pdb=" N ASP A 180 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU A 218 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLN A 182 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU A 220 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 230 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 318 through 325 removed outlier: 4.061A 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 634 removed outlier: 6.475A pdb=" N LEU A 654 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N SER A 610 " --> pdb=" O LEU A 654 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE A 656 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N THR A 657 " --> pdb=" O PRO A 667 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU A 669 " --> pdb=" O THR A 657 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 732 through 734 removed outlier: 6.919A 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: 6.981A pdb=" N ALA A 809 " --> pdb=" O TRP A 784 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N SER A 786 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 811 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 835 " --> pdb=" O VAL A 853 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 872 through 877 Processing sheet with id= I, first strand: chain 'A' and resid 914 through 917 Processing sheet with id= J, first strand: chain 'A' and resid 929 through 931 Processing sheet with id= K, first strand: chain 'A' and resid 946 through 948 removed outlier: 4.010A pdb=" N VAL A 947 " --> pdb=" O ILE A 954 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1311 through 1315 removed outlier: 3.563A pdb=" N ARG A1311 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 986 " --> pdb=" O ARG A1311 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 971 " --> pdb=" O VAL A 989 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1153 through 1157 removed outlier: 6.096A pdb=" N LEU A1128 " --> pdb=" O GLU A1154 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N THR A1156 " --> pdb=" O LEU A1128 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A1130 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ARG A1196 " --> pdb=" O ALA A1131 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG A1225 " --> pdb=" O VAL A1197 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N SER A1199 " --> pdb=" O ARG A1225 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A1227 " --> pdb=" O SER A1199 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A1230 " --> pdb=" O ALA A1279 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TRP A1273 " --> pdb=" O LEU A1280 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU A1282 " --> pdb=" O CYS A1271 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N CYS A1271 " --> pdb=" O GLU A1282 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A1284 " --> pdb=" O PRO A1269 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 571 through 574 removed outlier: 6.646A pdb=" N VAL A 580 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.764A pdb=" N VAL A 709 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL A 694 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL A 707 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 179 through 184 removed outlier: 8.126A pdb=" N ASP B 180 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU B 218 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLN B 182 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU B 220 " --> pdb=" O GLN B 182 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TRP B 184 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG B 222 " --> pdb=" O TRP B 184 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= R, first strand: chain 'B' and resid 318 through 325 removed outlier: 4.204A pdb=" N ARG B 485 " --> pdb=" O ASN B 449 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 364 through 372 Processing sheet with id= T, first strand: chain 'B' and resid 630 through 633 removed outlier: 6.962A pdb=" N LEU B 654 " --> pdb=" O GLU B 608 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 757 through 759 removed outlier: 7.595A pdb=" N LEU B 783 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA B 809 " --> pdb=" O TRP B 784 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N SER B 786 " --> pdb=" O ALA B 809 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU B 811 " --> pdb=" O SER B 786 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 835 " --> pdb=" O VAL B 853 " (cutoff:3.500A) removed outlier: 3.920A 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 removed outlier: 3.754A pdb=" N GLY B 896 " --> pdb=" O ARG B 921 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ARG B 921 " --> pdb=" O GLY B 896 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 929 through 931 Processing sheet with id= X, first strand: chain 'B' and resid 1268 through 1273 removed outlier: 6.793A pdb=" N LEU B1280 " --> pdb=" O LEU B1272 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU B1154 " --> pdb=" O VAL B1130 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL B1132 " --> pdb=" O GLU B1154 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR B1156 " --> pdb=" O VAL B1132 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B1177 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N GLU B1159 " --> pdb=" O VAL B1177 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLN B1179 " --> pdb=" O GLU B1159 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 571 through 574 removed outlier: 6.723A pdb=" N VAL B 580 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 691 through 696 removed outlier: 6.705A pdb=" N VAL B 709 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL B 694 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL B 707 " --> pdb=" O VAL B 694 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 969 through 976 removed outlier: 7.168A pdb=" N VAL B 989 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA B 972 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 987 " --> pdb=" O ALA B 972 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA B 974 " --> pdb=" O GLY B 985 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY B 985 " --> pdb=" O ALA B 974 " (cutoff:3.500A) 795 hydrogen bonds defined for protein. 2295 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: 20.40 Time building geometry restraints manager: 39.69 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: 6706 1.08 - 1.27: 17834 1.27 - 1.46: 6642 1.46 - 1.65: 11183 1.65 - 1.84: 93 Bond restraints: 42458 Sorted by residual: bond pdb=" CZ3 TRP A 184 " pdb=" HZ3 TRP A 184 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" N GLY B 487 " pdb=" H GLY B 487 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" CZ2 TRP A1140 " pdb=" HZ2 TRP A1140 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" CD1 TRP A 847 " pdb=" HD1 TRP A 847 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" CD2 TYR A1206 " pdb=" HD2 TYR A1206 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.59e+01 ... (remaining 42453 not shown) Histogram of bond angle deviations from ideal: 73.12 - 85.57: 6 85.57 - 98.03: 42 98.03 - 110.49: 40430 110.49 - 122.95: 33064 122.95 - 135.41: 3283 Bond angle restraints: 76825 Sorted by residual: angle pdb=" N ALA B 84 " pdb=" CA ALA B 84 " pdb=" HA ALA B 84 " ideal model delta sigma weight residual 110.00 73.12 36.88 3.00e+00 1.11e-01 1.51e+02 angle pdb=" N GLN A 518 " pdb=" CA GLN A 518 " pdb=" HA GLN A 518 " ideal model delta sigma weight residual 110.00 76.52 33.48 3.00e+00 1.11e-01 1.25e+02 angle pdb=" C ALA B 84 " pdb=" CA ALA B 84 " pdb=" HA ALA B 84 " ideal model delta sigma weight residual 109.00 77.10 31.90 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CB GLN A 518 " pdb=" CA GLN A 518 " pdb=" HA GLN A 518 " ideal model delta sigma weight residual 109.00 77.61 31.39 3.00e+00 1.11e-01 1.10e+02 angle pdb=" C GLN A 518 " pdb=" CA GLN A 518 " pdb=" HA GLN A 518 " ideal model delta sigma weight residual 109.00 79.04 29.96 3.00e+00 1.11e-01 9.97e+01 ... (remaining 76820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.79: 18467 26.79 - 53.59: 964 53.59 - 80.38: 367 80.38 - 107.18: 18 107.18 - 133.97: 2 Dihedral angle restraints: 19818 sinusoidal: 11008 harmonic: 8810 Sorted by residual: dihedral pdb=" C ARG B1274 " pdb=" N ARG B1274 " pdb=" CA ARG B1274 " pdb=" CB ARG B1274 " ideal model delta harmonic sigma weight residual -122.60 -141.26 18.66 0 2.50e+00 1.60e-01 5.57e+01 dihedral pdb=" N ARG B1274 " pdb=" C ARG B1274 " pdb=" CA ARG B1274 " pdb=" CB ARG B1274 " ideal model delta harmonic sigma weight residual 122.80 141.12 -18.32 0 2.50e+00 1.60e-01 5.37e+01 dihedral pdb=" C GLN A 518 " pdb=" N GLN A 518 " pdb=" CA GLN A 518 " pdb=" CB GLN A 518 " ideal model delta harmonic sigma weight residual -122.60 -139.09 16.49 0 2.50e+00 1.60e-01 4.35e+01 ... (remaining 19815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 2881 0.151 - 0.302: 359 0.302 - 0.453: 21 0.453 - 0.604: 3 0.604 - 0.755: 2 Chirality restraints: 3266 Sorted by residual: chirality pdb=" CA ARG B1274 " pdb=" N ARG B1274 " pdb=" C ARG B1274 " pdb=" CB ARG B1274 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CA GLN A 518 " pdb=" N GLN A 518 " pdb=" C GLN A 518 " pdb=" CB GLN A 518 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA ARG A1274 " pdb=" N ARG A1274 " pdb=" C ARG A1274 " pdb=" CB ARG A1274 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.42e+00 ... (remaining 3263 not shown) Planarity restraints: 6442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 816 " -0.402 2.00e-02 2.50e+03 1.56e-01 9.74e+02 pdb=" CG TRP A 816 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP A 816 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 TRP A 816 " 0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP A 816 " 0.151 2.00e-02 2.50e+03 pdb=" CE2 TRP A 816 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP A 816 " 0.088 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 816 " -0.102 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 816 " 0.071 2.00e-02 2.50e+03 pdb=" CH2 TRP A 816 " -0.087 2.00e-02 2.50e+03 pdb=" HD1 TRP A 816 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 TRP A 816 " 0.197 2.00e-02 2.50e+03 pdb=" HE3 TRP A 816 " 0.144 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 816 " -0.182 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 816 " 0.189 2.00e-02 2.50e+03 pdb=" HH2 TRP A 816 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1273 " -0.379 2.00e-02 2.50e+03 1.30e-01 6.73e+02 pdb=" CG TRP A1273 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A1273 " 0.094 2.00e-02 2.50e+03 pdb=" CD2 TRP A1273 " 0.111 2.00e-02 2.50e+03 pdb=" NE1 TRP A1273 " 0.140 2.00e-02 2.50e+03 pdb=" CE2 TRP A1273 " 0.084 2.00e-02 2.50e+03 pdb=" CE3 TRP A1273 " 0.094 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1273 " -0.053 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1273 " 0.063 2.00e-02 2.50e+03 pdb=" CH2 TRP A1273 " -0.040 2.00e-02 2.50e+03 pdb=" HD1 TRP A1273 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 TRP A1273 " 0.048 2.00e-02 2.50e+03 pdb=" HE3 TRP A1273 " 0.080 2.00e-02 2.50e+03 pdb=" HZ2 TRP A1273 " -0.178 2.00e-02 2.50e+03 pdb=" HZ3 TRP A1273 " 0.052 2.00e-02 2.50e+03 pdb=" HH2 TRP A1273 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AMP A1502 " -0.377 2.00e-02 2.50e+03 1.55e-01 6.58e+02 pdb=" C2 AMP A1502 " 0.056 2.00e-02 2.50e+03 pdb=" C4 AMP A1502 " 0.119 2.00e-02 2.50e+03 pdb=" C5 AMP A1502 " 0.063 2.00e-02 2.50e+03 pdb=" C6 AMP A1502 " -0.038 2.00e-02 2.50e+03 pdb=" C8 AMP A1502 " 0.128 2.00e-02 2.50e+03 pdb=" N1 AMP A1502 " -0.069 2.00e-02 2.50e+03 pdb=" N3 AMP A1502 " 0.148 2.00e-02 2.50e+03 pdb=" N6 AMP A1502 " -0.200 2.00e-02 2.50e+03 pdb=" N7 AMP A1502 " 0.074 2.00e-02 2.50e+03 pdb=" N9 AMP A1502 " 0.096 2.00e-02 2.50e+03 ... (remaining 6439 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 3472 2.16 - 2.77: 78079 2.77 - 3.38: 134424 3.38 - 3.99: 178717 3.99 - 4.60: 260910 Nonbonded interactions: 655602 Sorted by model distance: nonbonded pdb=" OE2 GLU A1015 " pdb=" HG SER A1235 " model vdw 1.555 1.850 nonbonded pdb=" HG1 THR A 474 " pdb=" OD2 ASP A 480 " model vdw 1.572 1.850 nonbonded pdb=" HG1 THR B 343 " pdb=" O26 PNS B1501 " model vdw 1.584 1.850 nonbonded pdb=" OD2 ASP B1134 " pdb=" HG SER B1199 " model vdw 1.591 1.850 nonbonded pdb=" OE2 GLU A 843 " pdb=" HH TYR A 903 " model vdw 1.592 1.850 ... (remaining 655597 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' selection = (chain 'B' and (resid 98 through 1425 or resid 1501 through 1502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.730 Extract box with map and model: 6.020 Check model and map are aligned: 0.650 Set scattering table: 0.400 Process input model: 146.820 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.170 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 0.144 21448 Z= 0.854 Angle : 1.988 15.387 29212 Z= 1.304 Chirality : 0.103 0.755 3266 Planarity : 0.024 0.361 3888 Dihedral : 15.844 133.971 7925 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.17 % Favored : 92.32 % Rotamer: Outliers : 2.21 % Allowed : 6.57 % Favored : 91.23 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 1.16 % 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: -2.76 (0.14), residues: 2721 helix: -2.17 (0.12), residues: 1118 sheet: -1.61 (0.23), residues: 409 loop : -1.36 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.260 0.038 TRP A1273 HIS 0.025 0.005 HIS B 711 PHE 0.097 0.023 PHE B1200 TYR 0.224 0.034 TYR B 51 ARG 0.018 0.002 ARG A 901 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 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. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 238 time to evaluate : 2.952 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: symmetry clash revert: symmetry clash REVERT: A 1248 ARG cc_start: 0.8011 (mmp80) cc_final: 0.7222 (ptt90) REVERT: B 381 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.6999 (mp) REVERT: B 471 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8215 (mt) REVERT: B 850 LEU cc_start: 0.8884 (tt) cc_final: 0.8658 (tt) REVERT: B 1105 LEU cc_start: 0.5711 (mp) cc_final: 0.5322 (mp) REVERT: B 1402 ARG cc_start: 0.4549 (OUTLIER) cc_final: 0.4287 (mmt180) outliers start: 46 outliers final: 21 residues processed: 279 average time/residue: 1.0412 time to fit residues: 413.3566 Evaluate side-chains 158 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1109 ARG Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1402 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN A 919 GLN ** A1099 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS B 449 ASN B 916 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 21448 Z= 0.414 Angle : 0.849 7.837 29212 Z= 0.439 Chirality : 0.042 0.485 3266 Planarity : 0.008 0.098 3888 Dihedral : 10.042 119.852 3137 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.33 % Favored : 94.56 % Rotamer: Outliers : 2.49 % Allowed : 10.21 % Favored : 87.30 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.15 (0.15), residues: 2721 helix: -1.24 (0.14), residues: 1121 sheet: -1.93 (0.23), residues: 441 loop : -1.19 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 535 HIS 0.009 0.002 HIS B 340 PHE 0.026 0.002 PHE B 560 TYR 0.027 0.003 TYR A 114 ARG 0.008 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 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. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 136 time to evaluate : 3.533 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: A 783 LEU cc_start: 0.8847 (tt) cc_final: 0.8551 (mm) REVERT: A 1248 ARG cc_start: 0.8149 (mmp80) cc_final: 0.7214 (ptt90) REVERT: B 381 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.7106 (mp) REVERT: B 471 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8324 (tt) REVERT: B 1000 MET cc_start: 0.4342 (tmm) cc_final: 0.3012 (ppp) outliers start: 52 outliers final: 40 residues processed: 181 average time/residue: 0.9902 time to fit residues: 260.5466 Evaluate side-chains 150 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 108 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1117 GLU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1373 ARG Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 GLN Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1261 ASP Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 268 optimal weight: 9.9990 chunk 221 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 199 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 ASN B 905 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21448 Z= 0.281 Angle : 0.706 7.086 29212 Z= 0.364 Chirality : 0.040 0.456 3266 Planarity : 0.006 0.054 3888 Dihedral : 8.885 109.539 3122 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.77 % Favored : 94.19 % Rotamer: Outliers : 2.21 % Allowed : 11.22 % Favored : 86.58 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.50 (0.16), residues: 2721 helix: -0.52 (0.15), residues: 1105 sheet: -1.83 (0.23), residues: 434 loop : -0.95 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 535 HIS 0.007 0.002 HIS A 711 PHE 0.022 0.002 PHE B 372 TYR 0.020 0.002 TYR A 290 ARG 0.005 0.001 ARG B1196 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 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. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 122 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 783 LEU cc_start: 0.8917 (tt) cc_final: 0.8604 (mm) REVERT: A 1248 ARG cc_start: 0.8504 (mmp80) cc_final: 0.7343 (ptt90) REVERT: B 1000 MET cc_start: 0.4401 (tmm) cc_final: 0.3268 (ppp) REVERT: B 1095 TRP cc_start: 0.4228 (OUTLIER) cc_final: 0.4019 (m-10) REVERT: B 1231 LEU cc_start: 0.1202 (OUTLIER) cc_final: 0.0976 (mt) outliers start: 46 outliers final: 38 residues processed: 159 average time/residue: 0.9300 time to fit residues: 220.4977 Evaluate side-chains 143 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 103 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1373 ARG Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1085 GLN Chi-restraints excluded: chain B residue 1095 TRP Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1231 LEU Chi-restraints excluded: chain B residue 1261 ASP Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 20.0000 chunk 186 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 118 optimal weight: 30.0000 chunk 166 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 263 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 236 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 21448 Z= 0.347 Angle : 0.694 6.660 29212 Z= 0.356 Chirality : 0.039 0.446 3266 Planarity : 0.006 0.055 3888 Dihedral : 8.357 117.161 3110 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.06 % Favored : 93.90 % Rotamer: Outliers : 2.64 % Allowed : 11.74 % Favored : 85.62 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % 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: -1.39 (0.16), residues: 2721 helix: -0.25 (0.15), residues: 1108 sheet: -1.95 (0.23), residues: 444 loop : -0.99 (0.19), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 535 HIS 0.007 0.002 HIS B 340 PHE 0.021 0.002 PHE B 560 TYR 0.016 0.002 TYR A 290 ARG 0.005 0.001 ARG B1196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 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. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 112 time to evaluate : 3.166 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 398 MET cc_start: 0.7052 (mmt) cc_final: 0.6634 (mmp) REVERT: A 1248 ARG cc_start: 0.8540 (mmp80) cc_final: 0.7379 (ptt90) REVERT: B 1231 LEU cc_start: 0.1376 (OUTLIER) cc_final: 0.1144 (mt) outliers start: 55 outliers final: 43 residues processed: 158 average time/residue: 0.8708 time to fit residues: 208.3207 Evaluate side-chains 142 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 98 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1117 GLU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1373 ARG Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1085 GLN Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1231 LEU Chi-restraints excluded: chain B residue 1261 ASP Chi-restraints excluded: chain B residue 1267 LEU Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 225 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1204 HIS ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21448 Z= 0.283 Angle : 0.653 6.654 29212 Z= 0.334 Chirality : 0.039 0.432 3266 Planarity : 0.005 0.052 3888 Dihedral : 7.920 116.786 3107 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.99 % Favored : 93.97 % Rotamer: Outliers : 2.11 % Allowed : 12.70 % Favored : 85.19 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.16), residues: 2721 helix: 0.02 (0.15), residues: 1099 sheet: -1.92 (0.23), residues: 446 loop : -0.86 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 14 HIS 0.007 0.002 HIS A 481 PHE 0.019 0.002 PHE B 560 TYR 0.018 0.002 TYR A 290 ARG 0.005 0.000 ARG B1196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 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. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 112 time to evaluate : 3.367 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 1248 ARG cc_start: 0.8544 (mmp80) cc_final: 0.7385 (ptt90) REVERT: A 1267 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7428 (mt) REVERT: B 1109 ARG cc_start: 0.7535 (ttm170) cc_final: 0.7212 (tpt90) REVERT: B 1231 LEU cc_start: 0.1383 (OUTLIER) cc_final: 0.1130 (mt) outliers start: 44 outliers final: 36 residues processed: 149 average time/residue: 0.8565 time to fit residues: 192.8892 Evaluate side-chains 141 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 103 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1085 GLN Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1231 LEU Chi-restraints excluded: chain B residue 1267 LEU Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 7.9990 chunk 237 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 219 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21448 Z= 0.226 Angle : 0.619 6.376 29212 Z= 0.313 Chirality : 0.038 0.423 3266 Planarity : 0.005 0.054 3888 Dihedral : 7.704 112.224 3107 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.25 % Allowed : 13.28 % Favored : 84.47 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % 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: -0.88 (0.16), residues: 2721 helix: 0.30 (0.16), residues: 1095 sheet: -1.86 (0.23), residues: 434 loop : -0.77 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 535 HIS 0.007 0.001 HIS A 481 PHE 0.019 0.002 PHE A 560 TYR 0.019 0.002 TYR A 290 ARG 0.006 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 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. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 121 time to evaluate : 3.134 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: A 162 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7332 (ptp-110) REVERT: A 783 LEU cc_start: 0.8889 (tt) cc_final: 0.8291 (mp) REVERT: A 1246 ASP cc_start: 0.8238 (t0) cc_final: 0.7317 (t0) REVERT: A 1248 ARG cc_start: 0.8585 (mmp80) cc_final: 0.7441 (ptt90) REVERT: A 1267 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7453 (mt) REVERT: B 1231 LEU cc_start: 0.1441 (OUTLIER) cc_final: 0.1207 (mt) outliers start: 47 outliers final: 36 residues processed: 160 average time/residue: 0.9034 time to fit residues: 218.0779 Evaluate side-chains 149 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 110 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1085 GLN Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1231 LEU Chi-restraints excluded: chain B residue 1267 LEU Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 263 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 160 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21448 Z= 0.359 Angle : 0.673 6.669 29212 Z= 0.345 Chirality : 0.039 0.432 3266 Planarity : 0.005 0.054 3888 Dihedral : 7.776 116.534 3105 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.59 % Allowed : 13.47 % Favored : 83.94 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % 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: -1.05 (0.16), residues: 2721 helix: 0.19 (0.15), residues: 1102 sheet: -2.18 (0.23), residues: 444 loop : -0.79 (0.19), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 535 HIS 0.006 0.002 HIS B 340 PHE 0.019 0.002 PHE B 560 TYR 0.015 0.002 TYR B 874 ARG 0.011 0.001 ARG B1020 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 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. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 109 time to evaluate : 3.192 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: A 162 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7326 (ptp-110) REVERT: A 1246 ASP cc_start: 0.8285 (t0) cc_final: 0.7350 (t0) REVERT: A 1248 ARG cc_start: 0.8605 (mmp80) cc_final: 0.7425 (ptt90) REVERT: A 1267 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7523 (mt) REVERT: B 1020 ARG cc_start: 0.5180 (OUTLIER) cc_final: 0.4597 (ttp-170) REVERT: B 1231 LEU cc_start: 0.1638 (OUTLIER) cc_final: 0.1378 (mt) outliers start: 54 outliers final: 42 residues processed: 153 average time/residue: 0.8872 time to fit residues: 202.8575 Evaluate side-chains 151 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 105 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1020 ARG Chi-restraints excluded: chain B residue 1080 LEU Chi-restraints excluded: chain B residue 1085 GLN Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1231 LEU Chi-restraints excluded: chain B residue 1267 LEU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21448 Z= 0.263 Angle : 0.624 6.488 29212 Z= 0.317 Chirality : 0.038 0.420 3266 Planarity : 0.005 0.055 3888 Dihedral : 7.504 111.973 3102 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.30 % Allowed : 14.05 % Favored : 83.65 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % 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: -0.88 (0.17), residues: 2721 helix: 0.36 (0.16), residues: 1094 sheet: -2.13 (0.23), residues: 441 loop : -0.72 (0.19), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 14 HIS 0.005 0.001 HIS B 340 PHE 0.019 0.002 PHE B 560 TYR 0.018 0.002 TYR A 290 ARG 0.006 0.000 ARG A1402 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 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. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 115 time to evaluate : 3.407 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: A 162 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7316 (ptp-110) REVERT: A 311 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7567 (pp20) REVERT: A 1246 ASP cc_start: 0.8236 (t0) cc_final: 0.7263 (t0) REVERT: A 1248 ARG cc_start: 0.8587 (mmp80) cc_final: 0.7432 (ptt90) REVERT: A 1267 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7517 (mt) REVERT: B 988 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7141 (mm) REVERT: B 1231 LEU cc_start: 0.1614 (OUTLIER) cc_final: 0.1358 (mt) outliers start: 48 outliers final: 40 residues processed: 156 average time/residue: 0.8959 time to fit residues: 209.9013 Evaluate side-chains 156 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 111 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 983 SER Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1080 LEU Chi-restraints excluded: chain B residue 1085 GLN Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1231 LEU Chi-restraints excluded: chain B residue 1267 LEU Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 10.0000 chunk 252 optimal weight: 20.0000 chunk 229 optimal weight: 20.0000 chunk 245 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 192 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 231 optimal weight: 0.7980 chunk 244 optimal weight: 9.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21448 Z= 0.368 Angle : 0.672 6.719 29212 Z= 0.345 Chirality : 0.039 0.424 3266 Planarity : 0.006 0.057 3888 Dihedral : 7.602 117.460 3102 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.92 % Allowed : 13.71 % Favored : 83.37 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % 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: -1.12 (0.16), residues: 2721 helix: 0.21 (0.15), residues: 1097 sheet: -2.29 (0.22), residues: 461 loop : -0.83 (0.19), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 14 HIS 0.006 0.002 HIS B 340 PHE 0.029 0.002 PHE A 216 TYR 0.014 0.002 TYR B 51 ARG 0.005 0.001 ARG B 901 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 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. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 107 time to evaluate : 3.454 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: A 311 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7583 (pp20) REVERT: A 1246 ASP cc_start: 0.8291 (t0) cc_final: 0.7336 (t0) REVERT: A 1248 ARG cc_start: 0.8612 (mmp80) cc_final: 0.7427 (ptt90) REVERT: A 1267 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7536 (mt) REVERT: B 988 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7206 (mm) REVERT: B 1231 LEU cc_start: 0.1645 (OUTLIER) cc_final: 0.1382 (mt) outliers start: 61 outliers final: 49 residues processed: 156 average time/residue: 0.8664 time to fit residues: 204.5288 Evaluate side-chains 160 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 107 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 983 SER Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1006 GLN Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1020 ARG Chi-restraints excluded: chain B residue 1080 LEU Chi-restraints excluded: chain B residue 1085 GLN Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1231 LEU Chi-restraints excluded: chain B residue 1267 LEU Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 3.9990 chunk 259 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 271 optimal weight: 20.0000 chunk 250 optimal weight: 10.0000 chunk 216 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 167 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21448 Z= 0.276 Angle : 0.629 6.350 29212 Z= 0.320 Chirality : 0.038 0.419 3266 Planarity : 0.005 0.055 3888 Dihedral : 7.451 116.449 3102 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.44 % Allowed : 13.95 % Favored : 83.60 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % 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: -0.92 (0.17), residues: 2721 helix: 0.39 (0.16), residues: 1093 sheet: -2.20 (0.23), residues: 450 loop : -0.76 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 14 HIS 0.005 0.001 HIS B 340 PHE 0.020 0.002 PHE B 560 TYR 0.018 0.002 TYR A 290 ARG 0.005 0.000 ARG A1402 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 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. Residue SER 1385 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 114 time to evaluate : 3.361 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: A 311 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7559 (pp20) REVERT: A 1246 ASP cc_start: 0.8229 (t0) cc_final: 0.7264 (t0) REVERT: A 1248 ARG cc_start: 0.8590 (mmp80) cc_final: 0.7418 (ptt90) REVERT: A 1267 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7549 (mt) REVERT: B 470 MET cc_start: 0.8398 (ttt) cc_final: 0.8092 (ttt) REVERT: B 988 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7235 (mm) REVERT: B 1231 LEU cc_start: 0.1501 (OUTLIER) cc_final: 0.1253 (mt) outliers start: 51 outliers final: 45 residues processed: 156 average time/residue: 0.8813 time to fit residues: 208.7650 Evaluate side-chains 161 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 112 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 917 ASP Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 983 SER Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1276 GLU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 757 SER Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 988 LEU Chi-restraints excluded: chain B residue 1080 LEU Chi-restraints excluded: chain B residue 1085 GLN Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1231 LEU Chi-restraints excluded: chain B residue 1267 LEU Chi-restraints excluded: chain B residue 1282 GLU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain B residue 1335 MET Chi-restraints excluded: chain B residue 1385 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 6.9990 chunk 230 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 199 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 216 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 27 optimal weight: 0.1980 chunk 39 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.078799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.060051 restraints weight = 300434.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.061528 restraints weight = 125410.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.062502 restraints weight = 76224.582| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21448 Z= 0.166 Angle : 0.590 5.902 29212 Z= 0.293 Chirality : 0.038 0.404 3266 Planarity : 0.005 0.049 3888 Dihedral : 7.052 102.861 3102 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.73 % Allowed : 14.62 % Favored : 83.65 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.16 % 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: -0.44 (0.17), residues: 2721 helix: 0.80 (0.16), residues: 1096 sheet: -2.13 (0.24), residues: 421 loop : -0.48 (0.20), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 14 HIS 0.004 0.001 HIS B 421 PHE 0.024 0.002 PHE A 216 TYR 0.042 0.002 TYR B 874 ARG 0.006 0.000 ARG A1419 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7063.29 seconds wall clock time: 127 minutes 0.82 seconds (7620.82 seconds total)