Starting phenix.real_space_refine (version: dev) on Wed Dec 21 05:51:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/12_2022/7en2_31200_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/12_2022/7en2_31200.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/12_2022/7en2_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_31200/12_2022/7en2_31200_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/12_2022/7en2_31200_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/12_2022/7en2_31200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/12_2022/7en2_31200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/12_2022/7en2_31200_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7en2_31200/12_2022/7en2_31200_neut_trim_updated.pdb" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 18.04, per 1000 atoms: 0.43 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: 35.78 Conformation dependent library (CDL) restraints added in 3.3 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: 4.94 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: 22.87 Time building geometry restraints manager: 37.32 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: 15914 26.79 - 53.59: 590 53.59 - 80.38: 284 80.38 - 107.18: 18 107.18 - 133.97: 2 Dihedral angle restraints: 16808 sinusoidal: 7998 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 16805 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 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. 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: 0.890 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: 0.630 Extract box with map and model: 7.360 Check model and map are aligned: 0.570 Convert atoms to be neutral: 0.360 Process input model: 134.840 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 : 15.843 133.971 7921 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.17 % Favored : 92.32 % Rotamer Outliers : 2.21 % 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 *********************** 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 : 3.382 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 outliers start: 46 outliers final: 21 residues processed: 279 average time/residue: 0.9348 time to fit residues: 376.9994 Evaluate side-chains 154 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 3.375 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 4 residues processed: 21 average time/residue: 0.7695 time to fit residues: 28.6758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 139 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 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: 5.5990 ------------------------------------------------------------------------------- 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 449 ASN B 482 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 21448 Z= 0.405 Angle : 0.847 8.074 29212 Z= 0.436 Chirality : 0.043 0.508 3266 Planarity : 0.008 0.083 3888 Dihedral : 9.002 119.319 3075 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.33 % Favored : 94.56 % Rotamer Outliers : 1.97 % 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: -2.14 (0.15), residues: 2721 helix: -1.23 (0.14), residues: 1119 sheet: -1.91 (0.23), residues: 438 loop : -1.21 (0.18), residues: 1164 *********************** 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 177 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 136 time to evaluate : 3.588 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 outliers start: 41 outliers final: 31 residues processed: 171 average time/residue: 0.8632 time to fit residues: 221.6423 Evaluate side-chains 139 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 3.417 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 4 residues processed: 31 average time/residue: 0.6201 time to fit residues: 36.1147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 168 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 268 optimal weight: 30.0000 chunk 221 optimal weight: 5.9990 chunk 246 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 ASN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 21448 Z= 0.315 Angle : 0.721 6.888 29212 Z= 0.373 Chirality : 0.041 0.458 3266 Planarity : 0.006 0.050 3888 Dihedral : 7.773 110.759 3075 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.28 % Favored : 93.68 % Rotamer Outliers : 0.86 % 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: -1.64 (0.15), residues: 2721 helix: -0.58 (0.15), residues: 1108 sheet: -1.78 (0.23), residues: 433 loop : -1.15 (0.18), residues: 1180 *********************** 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 134 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 3.305 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 outliers start: 18 outliers final: 11 residues processed: 131 average time/residue: 0.8671 time to fit residues: 172.5877 Evaluate side-chains 111 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 3.291 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 11 average time/residue: 0.6552 time to fit residues: 15.7831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 128 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 166 optimal weight: 4.9990 chunk 249 optimal weight: 30.0000 chunk 263 optimal weight: 0.5980 chunk 130 optimal weight: 8.9990 chunk 236 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 GLN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.097 21448 Z= 0.323 Angle : 0.685 7.039 29212 Z= 0.350 Chirality : 0.039 0.452 3266 Planarity : 0.005 0.051 3888 Dihedral : 7.497 116.841 3075 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.99 % Favored : 93.97 % Rotamer Outliers : 1.01 % 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: -1.50 (0.16), residues: 2721 helix: -0.28 (0.15), residues: 1104 sheet: -2.01 (0.22), residues: 459 loop : -1.09 (0.18), residues: 1158 *********************** 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 131 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 129 average time/residue: 0.8875 time to fit residues: 177.6532 Evaluate side-chains 110 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 3.459 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 13 average time/residue: 0.6519 time to fit residues: 18.4876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 3 optimal weight: 6.9990 chunk 196 optimal weight: 0.0050 chunk 108 optimal weight: 10.0000 chunk 225 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 236 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 overall best weight: 1.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7238 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 21448 Z= 0.201 Angle : 0.625 6.450 29212 Z= 0.315 Chirality : 0.039 0.443 3266 Planarity : 0.005 0.048 3888 Dihedral : 7.021 109.459 3075 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.66 % Favored : 94.30 % Rotamer Outliers : 0.48 % 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: -0.98 (0.16), residues: 2721 helix: 0.21 (0.15), residues: 1103 sheet: -1.74 (0.24), residues: 431 loop : -0.91 (0.19), residues: 1187 *********************** 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 136 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 3.453 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 outliers start: 10 outliers final: 7 residues processed: 135 average time/residue: 0.9012 time to fit residues: 185.8006 Evaluate side-chains 117 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 3.358 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 7 average time/residue: 0.7280 time to fit residues: 12.5116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 9.9990 chunk 237 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 264 optimal weight: 9.9990 chunk 219 optimal weight: 3.9990 chunk 122 optimal weight: 0.0470 chunk 21 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 overall best weight: 3.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3780 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= 0.277 Angle : 0.634 6.537 29212 Z= 0.322 Chirality : 0.038 0.445 3266 Planarity : 0.005 0.078 3888 Dihedral : 6.895 111.063 3075 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.06 % Favored : 93.90 % Rotamer Outliers : 0.72 % 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: -0.93 (0.16), residues: 2721 helix: 0.31 (0.15), residues: 1111 sheet: -1.86 (0.24), residues: 440 loop : -0.89 (0.19), residues: 1170 *********************** 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 134 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 3.243 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 outliers start: 15 outliers final: 10 residues processed: 132 average time/residue: 0.8844 time to fit residues: 178.0403 Evaluate side-chains 114 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 3.704 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 10 average time/residue: 0.6720 time to fit residues: 15.2122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 30.0000 chunk 29 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 263 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 GLN ** 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** B1179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.4050 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= 0.409 Angle : 0.697 6.786 29212 Z= 0.359 Chirality : 0.040 0.448 3266 Planarity : 0.006 0.050 3888 Dihedral : 7.088 118.335 3075 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.64 % Favored : 92.32 % Rotamer Outliers : 0.91 % 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: -1.23 (0.16), residues: 2721 helix: 0.13 (0.16), residues: 1095 sheet: -2.13 (0.23), residues: 456 loop : -1.04 (0.19), residues: 1170 *********************** 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 126 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 3.360 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 outliers start: 19 outliers final: 16 residues processed: 121 average time/residue: 0.8583 time to fit residues: 160.4097 Evaluate side-chains 118 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 3.157 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 16 average time/residue: 0.5802 time to fit residues: 20.8335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 157 optimal weight: 0.0980 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 21448 Z= 0.227 Angle : 0.616 6.254 29212 Z= 0.311 Chirality : 0.038 0.442 3266 Planarity : 0.005 0.051 3888 Dihedral : 6.715 109.074 3075 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.03 % Favored : 93.94 % Rotamer Outliers : 0.53 % 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: -0.83 (0.17), residues: 2721 helix: 0.46 (0.16), residues: 1094 sheet: -2.03 (0.24), residues: 427 loop : -0.80 (0.19), residues: 1200 *********************** 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 131 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 3.456 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 outliers start: 11 outliers final: 7 residues processed: 129 average time/residue: 0.8837 time to fit residues: 171.9547 Evaluate side-chains 116 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 3.044 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 7 average time/residue: 0.7079 time to fit residues: 11.5981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 229 optimal weight: 30.0000 chunk 245 optimal weight: 20.0000 chunk 147 optimal weight: 0.9980 chunk 106 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1204 HIS ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 21448 Z= 0.327 Angle : 0.649 6.623 29212 Z= 0.331 Chirality : 0.039 0.444 3266 Planarity : 0.005 0.048 3888 Dihedral : 6.756 108.943 3075 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.17 % Favored : 92.80 % Rotamer Outliers : 0.38 % 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: -0.94 (0.16), residues: 2721 helix: 0.40 (0.16), residues: 1096 sheet: -2.13 (0.23), residues: 453 loop : -0.84 (0.19), residues: 1172 *********************** 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 116 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 3.510 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 outliers start: 8 outliers final: 7 residues processed: 116 average time/residue: 0.8945 time to fit residues: 159.0574 Evaluate side-chains 113 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 3.348 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 7 average time/residue: 0.7356 time to fit residues: 12.7736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 158 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 271 optimal weight: 20.0000 chunk 250 optimal weight: 30.0000 chunk 216 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 21448 Z= 0.312 Angle : 0.643 6.492 29212 Z= 0.328 Chirality : 0.039 0.443 3266 Planarity : 0.005 0.050 3888 Dihedral : 6.734 107.792 3075 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.09 % Favored : 92.87 % Rotamer Outliers : 0.48 % 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: -0.95 (0.17), residues: 2721 helix: 0.37 (0.16), residues: 1103 sheet: -2.23 (0.23), residues: 447 loop : -0.80 (0.19), residues: 1171 ********************** 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 123 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 3.281 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 outliers start: 10 outliers final: 6 residues processed: 123 average time/residue: 0.8747 time to fit residues: 165.3542 Evaluate side-chains 116 residues out of total 2086 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 3.564 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 6 average time/residue: 0.9570 time to fit residues: 12.7705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 199 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 216 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.077965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.059250 restraints weight = 302721.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.060888 restraints weight = 131421.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.061709 restraints weight = 81940.502| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 21448 Z= 0.226 Angle : 0.607 6.267 29212 Z= 0.305 Chirality : 0.038 0.442 3266 Planarity : 0.005 0.045 3888 Dihedral : 6.518 98.819 3075 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer Outliers : 0.34 % 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: -0.68 (0.17), residues: 2721 helix: 0.65 (0.16), residues: 1102 sheet: -2.24 (0.23), residues: 435 loop : -0.65 (0.20), residues: 1184 =============================================================================== Job complete usr+sys time: 6683.13 seconds wall clock time: 119 minutes 24.05 seconds (7164.05 seconds total)