Starting phenix.real_space_refine on Sun Jul 21 01:24:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlh_36397/07_2024/8jlh_36397.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlh_36397/07_2024/8jlh_36397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlh_36397/07_2024/8jlh_36397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlh_36397/07_2024/8jlh_36397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlh_36397/07_2024/8jlh_36397.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlh_36397/07_2024/8jlh_36397.cif" } resolution = 2.9 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= 0.031 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 8117 2.51 5 N 2099 2.21 5 O 2332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 153": "OE1" <-> "OE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 514": "OD1" <-> "OD2" Residue "A PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 890": "OD1" <-> "OD2" Residue "B TYR 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 920": "OE1" <-> "OE2" Residue "B GLU 925": "OE1" <-> "OE2" Residue "B GLU 961": "OE1" <-> "OE2" Residue "B TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1058": "OD1" <-> "OD2" Residue "B ASP 1076": "OD1" <-> "OD2" Residue "B GLU 1081": "OE1" <-> "OE2" Residue "B ASP 1086": "OD1" <-> "OD2" Residue "B TYR 1112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1210": "OE1" <-> "OE2" Residue "C GLU 490": "OE1" <-> "OE2" Residue "C TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 528": "OD1" <-> "OD2" Residue "C GLU 533": "OE1" <-> "OE2" Residue "C ASP 560": "OD1" <-> "OD2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 563": "OE1" <-> "OE2" Residue "C GLU 581": "OE1" <-> "OE2" Residue "D TYR 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 907": "OD1" <-> "OD2" Residue "D GLU 961": "OE1" <-> "OE2" Residue "D TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 982": "OE1" <-> "OE2" Residue "D ASP 1009": "OD1" <-> "OD2" Residue "D TYR 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1037": "OD1" <-> "OD2" Residue "D GLU 1081": "OE1" <-> "OE2" Residue "D TYR 1104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1156": "OE1" <-> "OE2" Residue "D GLU 1210": "OE1" <-> "OE2" Residue "D ASP 1213": "OD1" <-> "OD2" Residue "D TYR 1255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1289": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12610 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4674 Classifications: {'peptide': 592} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 576} Chain breaks: 1 Chain: "B" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3437 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411} Chain: "C" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 918 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "D" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3437 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'UKX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.84, per 1000 atoms: 0.62 Number of scatterers: 12610 At special positions: 0 Unit cell: (92.13, 151.89, 142.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2332 8.00 N 2099 7.00 C 8117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 3 " NAG-ASN " NAG A 802 " - " ASN A 498 " " NAG A 803 " - " ASN A 548 " " NAG C 900 " - " ASN C 498 " " NAG C 901 " - " ASN C 548 " " NAG E 1 " - " ASN A 573 " " NAG F 1 " - " ASN C 573 " Time building additional restraints: 5.07 Conformation dependent library (CDL) restraints added in 2.2 seconds 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2866 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 20 sheets defined 31.4% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 137 through 160 Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.618A pdb=" N ASP A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 198 Proline residue: A 191 - end of helix removed outlier: 4.285A pdb=" N LYS A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 4.599A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TYR A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 220 " --> pdb=" O MET A 216 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 252 removed outlier: 3.527A pdb=" N SER A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 271 removed outlier: 4.295A pdb=" N GLY A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.717A pdb=" N ILE A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 297 through 315 removed outlier: 4.064A pdb=" N MET A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.821A pdb=" N VAL A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.566A pdb=" N PHE A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 386 Processing helix chain 'A' and resid 419 through 439 removed outlier: 3.644A pdb=" N PHE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 483 Proline residue: A 469 - end of helix Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 591 through 619 removed outlier: 4.250A pdb=" N TYR A 595 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 609 " --> pdb=" O THR A 605 " (cutoff:3.500A) Proline residue: A 610 - end of helix removed outlier: 3.593A pdb=" N ILE A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 641 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 647 through 676 removed outlier: 3.788A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 707 Processing helix chain 'A' and resid 713 through 731 Processing helix chain 'B' and resid 954 through 958 Processing helix chain 'B' and resid 1080 through 1092 Processing helix chain 'B' and resid 1265 through 1273 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 562 through 564 No H-bonds generated for 'chain 'C' and resid 562 through 564' Processing helix chain 'D' and resid 929 through 933 removed outlier: 3.800A pdb=" N VAL D 933 " --> pdb=" O ASN D 930 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 958 Processing helix chain 'D' and resid 1080 through 1092 Processing helix chain 'D' and resid 1210 through 1215 removed outlier: 4.225A pdb=" N VAL D1214 " --> pdb=" O ILE D1211 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY D1215 " --> pdb=" O PRO D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1265 through 1273 Processing sheet with id=AA1, first strand: chain 'A' and resid 540 through 542 removed outlier: 7.088A pdb=" N LEU A 521 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU A 502 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER A 523 " --> pdb=" O GLU A 502 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 566 through 567 removed outlier: 5.916A pdb=" N PHE A 546 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 521 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU A 502 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER A 523 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLY A 509 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG A 491 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TYR A 511 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLU A 493 " --> pdb=" O TYR A 511 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 497 Processing sheet with id=AA4, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.649A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B1074 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER B 880 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE B1072 " --> pdb=" O SER B 880 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N VAL B 882 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 10.570A pdb=" N LYS B1070 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 16.798A pdb=" N LYS B 884 " --> pdb=" O MET B1068 " (cutoff:3.500A) removed outlier: 18.501A pdb=" N MET B1068 " --> pdb=" O LYS B 884 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.649A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B1074 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER B 880 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE B1072 " --> pdb=" O SER B 880 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N VAL B 882 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 10.570A pdb=" N LYS B1070 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 16.798A pdb=" N LYS B 884 " --> pdb=" O MET B1068 " (cutoff:3.500A) removed outlier: 18.501A pdb=" N MET B1068 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE B1069 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS B 948 " --> pdb=" O ILE B1069 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR B1071 " --> pdb=" O TRP B 946 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TRP B 946 " --> pdb=" O TYR B1071 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B1037 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 897 through 900 Processing sheet with id=AA7, first strand: chain 'B' and resid 962 through 968 removed outlier: 6.856A pdb=" N VAL B 976 " --> pdb=" O ILE B 964 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASN B 966 " --> pdb=" O TRP B 974 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N TRP B 974 " --> pdb=" O ASN B 966 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1112 through 1115 Processing sheet with id=AA9, first strand: chain 'B' and resid 1122 through 1125 Processing sheet with id=AB1, first strand: chain 'B' and resid 1159 through 1164 removed outlier: 3.920A pdb=" N LYS B1159 " --> pdb=" O VAL B1185 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP B1178 " --> pdb=" O MET B1223 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B1220 " --> pdb=" O GLN B1240 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LYS B1226 " --> pdb=" O LYS B1234 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N LYS B1234 " --> pdb=" O LYS B1226 " (cutoff:3.500A) removed outlier: 27.316A pdb=" N ASN B1233 " --> pdb=" O LEU B1254 " (cutoff:3.500A) removed outlier: 23.531A pdb=" N LEU B1254 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 16.017A pdb=" N CYS B1235 " --> pdb=" O PHE B1252 " (cutoff:3.500A) removed outlier: 11.347A pdb=" N PHE B1252 " --> pdb=" O CYS B1235 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N MET B1237 " --> pdb=" O ILE B1250 " (cutoff:3.500A) removed outlier: 16.795A pdb=" N ALA B1259 " --> pdb=" O ALA B1208 " (cutoff:3.500A) removed outlier: 12.520A pdb=" N ALA B1208 " --> pdb=" O ALA B1259 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU B1261 " --> pdb=" O LEU B1206 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS B1204 " --> pdb=" O ALA B1263 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE B1182 " --> pdb=" O LEU B1193 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N THR B1195 " --> pdb=" O VAL B1180 " (cutoff:3.500A) removed outlier: 15.168A pdb=" N VAL B1180 " --> pdb=" O THR B1195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 485 through 488 removed outlier: 9.277A pdb=" N THR C 500 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N SER C 523 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU C 502 " --> pdb=" O SER C 523 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N SER C 525 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN C 504 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU C 527 " --> pdb=" O GLN C 504 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N HIS C 506 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 485 through 488 removed outlier: 9.277A pdb=" N THR C 500 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N SER C 523 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU C 502 " --> pdb=" O SER C 523 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N SER C 525 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN C 504 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU C 527 " --> pdb=" O GLN C 504 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N HIS C 506 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE C 546 " --> pdb=" O VAL C 567 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 496 through 497 removed outlier: 5.619A pdb=" N PHE C 497 " --> pdb=" O ILE C 517 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE C 536 " --> pdb=" O TYR C 557 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 887 through 890 removed outlier: 3.532A pdb=" N ASP D 887 " --> pdb=" O LYS D 884 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU D1074 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER D 880 " --> pdb=" O PHE D1072 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE D1072 " --> pdb=" O SER D 880 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N VAL D 882 " --> pdb=" O LYS D1070 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N LYS D1070 " --> pdb=" O VAL D 882 " (cutoff:3.500A) removed outlier: 16.743A pdb=" N LYS D 884 " --> pdb=" O MET D1068 " (cutoff:3.500A) removed outlier: 18.366A pdb=" N MET D1068 " --> pdb=" O LYS D 884 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR D 905 " --> pdb=" O LYS D 915 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 887 through 890 removed outlier: 3.532A pdb=" N ASP D 887 " --> pdb=" O LYS D 884 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU D1074 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER D 880 " --> pdb=" O PHE D1072 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE D1072 " --> pdb=" O SER D 880 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N VAL D 882 " --> pdb=" O LYS D1070 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N LYS D1070 " --> pdb=" O VAL D 882 " (cutoff:3.500A) removed outlier: 16.743A pdb=" N LYS D 884 " --> pdb=" O MET D1068 " (cutoff:3.500A) removed outlier: 18.366A pdb=" N MET D1068 " --> pdb=" O LYS D 884 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE D1069 " --> pdb=" O LYS D 948 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS D 948 " --> pdb=" O ILE D1069 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR D1071 " --> pdb=" O TRP D 946 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TRP D 946 " --> pdb=" O TYR D1071 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP D1037 " --> pdb=" O ILE D1029 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE D1031 " --> pdb=" O LEU D1035 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU D1035 " --> pdb=" O ILE D1031 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 897 through 900 removed outlier: 7.933A pdb=" N MET D1054 " --> pdb=" O CYS D 967 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N CYS D 967 " --> pdb=" O MET D1054 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LYS D1056 " --> pdb=" O ILE D 965 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE D 965 " --> pdb=" O LYS D1056 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N THR D 963 " --> pdb=" O LEU D 978 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU D 978 " --> pdb=" O THR D 963 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TRP D 974 " --> pdb=" O CYS D 967 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1112 through 1115 Processing sheet with id=AB9, first strand: chain 'D' and resid 1122 through 1125 Processing sheet with id=AC1, first strand: chain 'D' and resid 1159 through 1164 removed outlier: 4.062A pdb=" N LYS D1159 " --> pdb=" O VAL D1185 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LYS D1226 " --> pdb=" O LYS D1234 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N LYS D1234 " --> pdb=" O LYS D1226 " (cutoff:3.500A) removed outlier: 27.430A pdb=" N ASN D1233 " --> pdb=" O LEU D1254 " (cutoff:3.500A) removed outlier: 23.467A pdb=" N LEU D1254 " --> pdb=" O ASN D1233 " (cutoff:3.500A) removed outlier: 16.107A pdb=" N CYS D1235 " --> pdb=" O PHE D1252 " (cutoff:3.500A) removed outlier: 11.462A pdb=" N PHE D1252 " --> pdb=" O CYS D1235 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N MET D1237 " --> pdb=" O ILE D1250 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D1263 " --> pdb=" O LYS D1204 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS D1204 " --> pdb=" O ALA D1263 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1159 through 1164 removed outlier: 4.062A pdb=" N LYS D1159 " --> pdb=" O VAL D1185 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE D1182 " --> pdb=" O LEU D1193 " (cutoff:3.500A) 609 hydrogen bonds defined for protein. 1689 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: 5.08 Time building geometry restraints manager: 5.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3624 1.33 - 1.46: 2901 1.46 - 1.58: 6273 1.58 - 1.70: 0 1.70 - 1.83: 99 Bond restraints: 12897 Sorted by residual: bond pdb=" C5 UKX A 801 " pdb=" N2 UKX A 801 " ideal model delta sigma weight residual 1.340 1.387 -0.047 2.00e-02 2.50e+03 5.46e+00 bond pdb=" C1 UKX A 801 " pdb=" N1 UKX A 801 " ideal model delta sigma weight residual 1.353 1.391 -0.038 2.00e-02 2.50e+03 3.58e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" CA ILE D1211 " pdb=" CB ILE D1211 " ideal model delta sigma weight residual 1.534 1.545 -0.011 6.80e-03 2.16e+04 2.45e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.44e+00 ... (remaining 12892 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.77: 147 105.77 - 112.84: 6744 112.84 - 119.91: 4290 119.91 - 126.98: 6135 126.98 - 134.05: 118 Bond angle restraints: 17434 Sorted by residual: angle pdb=" CB MET B 937 " pdb=" CG MET B 937 " pdb=" SD MET B 937 " ideal model delta sigma weight residual 112.70 127.07 -14.37 3.00e+00 1.11e-01 2.29e+01 angle pdb=" N VAL D1202 " pdb=" CA VAL D1202 " pdb=" C VAL D1202 " ideal model delta sigma weight residual 111.81 108.12 3.69 8.60e-01 1.35e+00 1.84e+01 angle pdb=" CB MET A 206 " pdb=" CG MET A 206 " pdb=" SD MET A 206 " ideal model delta sigma weight residual 112.70 125.25 -12.55 3.00e+00 1.11e-01 1.75e+01 angle pdb=" CA GLN D 992 " pdb=" CB GLN D 992 " pdb=" CG GLN D 992 " ideal model delta sigma weight residual 114.10 121.70 -7.60 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CA GLN A 430 " pdb=" CB GLN A 430 " pdb=" CG GLN A 430 " ideal model delta sigma weight residual 114.10 121.48 -7.38 2.00e+00 2.50e-01 1.36e+01 ... (remaining 17429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6820 17.97 - 35.93: 666 35.93 - 53.90: 176 53.90 - 71.86: 37 71.86 - 89.83: 9 Dihedral angle restraints: 7708 sinusoidal: 3223 harmonic: 4485 Sorted by residual: dihedral pdb=" CA PHE C 497 " pdb=" C PHE C 497 " pdb=" N ASN C 498 " pdb=" CA ASN C 498 " ideal model delta harmonic sigma weight residual 180.00 147.21 32.79 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CA PHE A 497 " pdb=" C PHE A 497 " pdb=" N ASN A 498 " pdb=" CA ASN A 498 " ideal model delta harmonic sigma weight residual 180.00 149.30 30.70 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA VAL B1144 " pdb=" C VAL B1144 " pdb=" N THR B1145 " pdb=" CA THR B1145 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 7705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1554 0.055 - 0.109: 315 0.109 - 0.164: 43 0.164 - 0.218: 1 0.218 - 0.273: 3 Chirality restraints: 1916 Sorted by residual: chirality pdb=" C1 NAG A 803 " pdb=" ND2 ASN A 548 " pdb=" C2 NAG A 803 " pdb=" O5 NAG A 803 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C6 UKX A 801 " pdb=" C5 UKX A 801 " pdb=" C7 UKX A 801 " pdb=" N1 UKX A 801 " both_signs ideal model delta sigma weight residual False 2.45 2.67 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C1 NAG C 901 " pdb=" ND2 ASN C 548 " pdb=" C2 NAG C 901 " pdb=" O5 NAG C 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1913 not shown) Planarity restraints: 2209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 487 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.83e+00 pdb=" N PRO C 488 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 488 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 488 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 992 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C GLN D 992 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN D 992 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN D 993 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B1213 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C ASP B1213 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP B1213 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B1214 " -0.011 2.00e-02 2.50e+03 ... (remaining 2206 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 395 2.71 - 3.26: 12213 3.26 - 3.80: 20202 3.80 - 4.35: 26699 4.35 - 4.90: 45152 Nonbonded interactions: 104661 Sorted by model distance: nonbonded pdb=" OH TYR A 279 " pdb=" O PRO A 355 " model vdw 2.162 2.440 nonbonded pdb=" OG1 THR D 943 " pdb=" O ASN D1073 " model vdw 2.214 2.440 nonbonded pdb=" NE2 GLN A 323 " pdb=" O GLY A 325 " model vdw 2.225 2.520 nonbonded pdb=" O PHE A 546 " pdb=" OG SER A 569 " model vdw 2.228 2.440 nonbonded pdb=" O GLY D1132 " pdb=" OG SER D1207 " model vdw 2.232 2.440 ... (remaining 104656 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 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.350 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 38.160 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:13.110 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.004 0.047 12897 Z= 0.231 Angle : 0.635 14.367 17434 Z= 0.353 Chirality : 0.045 0.273 1916 Planarity : 0.004 0.065 2203 Dihedral : 15.498 89.830 4842 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.39 % Allowed : 18.23 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1532 helix: 1.71 (0.24), residues: 432 sheet: 0.24 (0.28), residues: 332 loop : -1.08 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 333 HIS 0.003 0.001 HIS A 367 PHE 0.012 0.001 PHE A 497 TYR 0.025 0.001 TYR A 169 ARG 0.007 0.000 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6907 (tm-30) REVERT: A 324 MET cc_start: 0.5335 (tpp) cc_final: 0.5046 (tpt) REVERT: A 712 LYS cc_start: 0.6670 (mtpm) cc_final: 0.6114 (ttpp) REVERT: B 1086 ASP cc_start: 0.7278 (t0) cc_final: 0.6995 (t70) REVERT: D 1203 GLU cc_start: 0.4058 (mm-30) cc_final: 0.3774 (mm-30) outliers start: 19 outliers final: 12 residues processed: 178 average time/residue: 1.1870 time to fit residues: 231.2176 Evaluate side-chains 165 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 971 ASN Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain D residue 1236 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS A 354 GLN A 367 HIS A 434 ASN A 568 ASN B 899 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN B1003 GLN B1046 ASN B1091 GLN B1176 ASN ** B1265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 ASN D 912 ASN D 913 GLN D 960 ASN D1003 GLN D1093 ASN D1106 GLN D1177 ASN ** D1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12897 Z= 0.382 Angle : 0.628 7.976 17434 Z= 0.335 Chirality : 0.048 0.320 1916 Planarity : 0.004 0.057 2203 Dihedral : 6.502 74.430 1931 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.05 % Allowed : 15.96 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.15 (0.21), residues: 1532 helix: 1.70 (0.24), residues: 440 sheet: 0.17 (0.28), residues: 353 loop : -1.39 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 333 HIS 0.004 0.001 HIS A 494 PHE 0.024 0.002 PHE B1100 TYR 0.020 0.002 TYR A 306 ARG 0.007 0.001 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 165 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8126 (mttm) REVERT: B 1086 ASP cc_start: 0.7385 (t70) cc_final: 0.7084 (t0) REVERT: B 1187 LYS cc_start: 0.8289 (mmpt) cc_final: 0.7963 (mppt) outliers start: 69 outliers final: 31 residues processed: 212 average time/residue: 1.0994 time to fit residues: 255.9822 Evaluate side-chains 186 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 971 ASN Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1000 LYS Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 937 MET Chi-restraints excluded: chain D residue 956 ILE Chi-restraints excluded: chain D residue 960 ASN Chi-restraints excluded: chain D residue 961 GLU Chi-restraints excluded: chain D residue 1003 GLN Chi-restraints excluded: chain D residue 1161 ILE Chi-restraints excluded: chain D residue 1188 ASN Chi-restraints excluded: chain D residue 1236 LYS Chi-restraints excluded: chain D residue 1294 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 0.0050 chunk 116 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 47 optimal weight: 0.3980 chunk 112 optimal weight: 0.6980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN B1046 ASN B1115 ASN ** B1265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 ASN ** D 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1003 GLN D1177 ASN D1199 GLN ** D1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12897 Z= 0.161 Angle : 0.516 7.816 17434 Z= 0.278 Chirality : 0.044 0.265 1916 Planarity : 0.003 0.055 2203 Dihedral : 5.694 56.767 1922 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.37 % Allowed : 17.72 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.16 (0.21), residues: 1532 helix: 2.06 (0.24), residues: 440 sheet: 0.32 (0.29), residues: 336 loop : -1.22 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.002 0.000 HIS A 378 PHE 0.009 0.001 PHE A 497 TYR 0.023 0.001 TYR A 169 ARG 0.007 0.000 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 160 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 515 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8102 (mttm) REVERT: A 568 ASN cc_start: 0.8458 (t0) cc_final: 0.8046 (t160) REVERT: A 583 CYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6496 (m) REVERT: A 712 LYS cc_start: 0.6822 (OUTLIER) cc_final: 0.6245 (ttpp) REVERT: B 1085 LYS cc_start: 0.6288 (OUTLIER) cc_final: 0.6084 (mptt) REVERT: B 1086 ASP cc_start: 0.7380 (t70) cc_final: 0.7094 (t0) REVERT: B 1187 LYS cc_start: 0.8232 (mmpt) cc_final: 0.7904 (mppt) REVERT: B 1219 GLN cc_start: 0.7615 (pt0) cc_final: 0.7182 (pt0) REVERT: D 906 TYR cc_start: 0.6478 (m-80) cc_final: 0.6233 (m-80) REVERT: D 1058 ASP cc_start: 0.7166 (t70) cc_final: 0.6663 (p0) REVERT: D 1203 GLU cc_start: 0.4036 (mm-30) cc_final: 0.3822 (mm-30) outliers start: 46 outliers final: 23 residues processed: 190 average time/residue: 1.2297 time to fit residues: 255.4387 Evaluate side-chains 168 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 971 ASN Chi-restraints excluded: chain B residue 1000 LYS Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1085 LYS Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain D residue 1003 GLN Chi-restraints excluded: chain D residue 1156 GLU Chi-restraints excluded: chain D residue 1177 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 0.9990 chunk 105 optimal weight: 0.3980 chunk 72 optimal weight: 0.0070 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 133 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN B1046 ASN B1091 GLN B1093 ASN B1265 ASN B1268 ASN C 568 ASN D 960 ASN D1003 GLN D1106 GLN ** D1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12897 Z= 0.205 Angle : 0.526 9.414 17434 Z= 0.282 Chirality : 0.044 0.265 1916 Planarity : 0.003 0.050 2203 Dihedral : 5.501 55.811 1918 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.66 % Allowed : 18.16 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1532 helix: 2.09 (0.24), residues: 440 sheet: 0.44 (0.31), residues: 299 loop : -1.14 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.002 0.001 HIS A 161 PHE 0.014 0.001 PHE D1072 TYR 0.014 0.001 TYR B1149 ARG 0.008 0.000 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 149 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 515 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8079 (mttm) REVERT: A 583 CYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6511 (m) REVERT: A 647 SER cc_start: 0.7134 (p) cc_final: 0.6838 (t) REVERT: A 712 LYS cc_start: 0.6865 (mtpm) cc_final: 0.6281 (ttpp) REVERT: B 1086 ASP cc_start: 0.7423 (t70) cc_final: 0.7144 (t0) REVERT: B 1187 LYS cc_start: 0.8236 (mmpt) cc_final: 0.7890 (mppt) REVERT: D 961 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7189 (tm-30) REVERT: D 1054 MET cc_start: 0.6180 (tpt) cc_final: 0.5968 (tmm) REVERT: D 1058 ASP cc_start: 0.7025 (t70) cc_final: 0.6513 (p0) REVERT: D 1081 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6949 (tm-30) outliers start: 50 outliers final: 26 residues processed: 187 average time/residue: 1.1914 time to fit residues: 244.2382 Evaluate side-chains 175 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 971 ASN Chi-restraints excluded: chain B residue 1000 LYS Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1005 VAL Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain D residue 961 GLU Chi-restraints excluded: chain D residue 1003 GLN Chi-restraints excluded: chain D residue 1156 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN B1046 ASN B1091 GLN C 568 ASN D 960 ASN ** D1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 12897 Z= 0.419 Angle : 0.630 9.077 17434 Z= 0.333 Chirality : 0.048 0.295 1916 Planarity : 0.004 0.048 2203 Dihedral : 5.837 57.503 1917 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.90 % Allowed : 18.08 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.09 (0.21), residues: 1532 helix: 1.77 (0.24), residues: 439 sheet: 0.21 (0.29), residues: 323 loop : -1.30 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 333 HIS 0.004 0.001 HIS A 494 PHE 0.025 0.002 PHE B1100 TYR 0.021 0.002 TYR A 306 ARG 0.007 0.001 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 150 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6870 (tm-30) REVERT: A 310 MET cc_start: 0.6152 (mmt) cc_final: 0.5849 (mmt) REVERT: A 444 ARG cc_start: 0.4795 (OUTLIER) cc_final: 0.4473 (ttt-90) REVERT: A 515 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8150 (mttm) REVERT: A 583 CYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6644 (m) REVERT: A 627 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.7003 (ttt) REVERT: A 712 LYS cc_start: 0.6806 (OUTLIER) cc_final: 0.6133 (ttpp) REVERT: B 940 ASN cc_start: 0.6948 (OUTLIER) cc_final: 0.6688 (p0) REVERT: B 1003 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8220 (mt0) REVERT: B 1064 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.6068 (mtp85) REVERT: B 1086 ASP cc_start: 0.7447 (t70) cc_final: 0.7204 (t0) REVERT: B 1187 LYS cc_start: 0.8269 (mmpt) cc_final: 0.7941 (mppt) REVERT: B 1219 GLN cc_start: 0.7797 (pt0) cc_final: 0.7302 (pt0) REVERT: C 583 CYS cc_start: 0.6003 (OUTLIER) cc_final: 0.5737 (t) REVERT: D 1054 MET cc_start: 0.6208 (tpt) cc_final: 0.5983 (tmm) outliers start: 67 outliers final: 34 residues processed: 200 average time/residue: 1.1686 time to fit residues: 256.4410 Evaluate side-chains 190 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 146 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 444 ARG Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain B residue 940 ASN Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 971 ASN Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1000 LYS Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1280 CYS Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain C residue 583 CYS Chi-restraints excluded: chain D residue 961 GLU Chi-restraints excluded: chain D residue 1143 VAL Chi-restraints excluded: chain D residue 1161 ILE Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain D residue 1214 VAL Chi-restraints excluded: chain D residue 1236 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 149 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN B1046 ASN B1091 GLN C 568 ASN D 960 ASN D1003 GLN D1177 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12897 Z= 0.208 Angle : 0.546 10.836 17434 Z= 0.290 Chirality : 0.045 0.268 1916 Planarity : 0.003 0.051 2203 Dihedral : 5.562 57.767 1917 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.47 % Allowed : 19.03 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.10 (0.21), residues: 1532 helix: 2.00 (0.24), residues: 440 sheet: 0.16 (0.30), residues: 312 loop : -1.15 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.002 0.000 HIS A 161 PHE 0.011 0.001 PHE A 497 TYR 0.020 0.001 TYR A 169 ARG 0.009 0.000 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 156 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8071 (mttm) REVERT: A 583 CYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6539 (m) REVERT: A 712 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6250 (ttpp) REVERT: B 1064 ARG cc_start: 0.6298 (OUTLIER) cc_final: 0.5944 (mtp85) REVERT: B 1086 ASP cc_start: 0.7399 (t70) cc_final: 0.7185 (t70) REVERT: B 1187 LYS cc_start: 0.8299 (mmpt) cc_final: 0.7941 (mppt) REVERT: B 1219 GLN cc_start: 0.7794 (pt0) cc_final: 0.7298 (pt0) REVERT: C 583 CYS cc_start: 0.6008 (OUTLIER) cc_final: 0.5704 (t) REVERT: D 961 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: D 1054 MET cc_start: 0.6246 (tpt) cc_final: 0.6033 (tmm) outliers start: 61 outliers final: 31 residues processed: 200 average time/residue: 1.2132 time to fit residues: 267.1554 Evaluate side-chains 185 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 971 ASN Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1085 LYS Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1280 CYS Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain C residue 583 CYS Chi-restraints excluded: chain D residue 961 GLU Chi-restraints excluded: chain D residue 1003 GLN Chi-restraints excluded: chain D residue 1058 ASP Chi-restraints excluded: chain D residue 1214 VAL Chi-restraints excluded: chain D residue 1236 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 91 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN B1046 ASN C 568 ASN D 960 ASN D1003 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12897 Z= 0.181 Angle : 0.538 11.545 17434 Z= 0.284 Chirality : 0.045 0.339 1916 Planarity : 0.003 0.047 2203 Dihedral : 5.457 58.953 1917 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.95 % Allowed : 19.40 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1532 helix: 2.10 (0.24), residues: 440 sheet: 0.09 (0.29), residues: 331 loop : -1.03 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.002 0.000 HIS A 161 PHE 0.010 0.001 PHE A 497 TYR 0.019 0.001 TYR A 169 ARG 0.009 0.000 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 147 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.6031 (mmt) cc_final: 0.5804 (mmt) REVERT: A 515 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8046 (mttm) REVERT: A 583 CYS cc_start: 0.7017 (OUTLIER) cc_final: 0.6515 (m) REVERT: A 712 LYS cc_start: 0.6884 (OUTLIER) cc_final: 0.6340 (ttpp) REVERT: B 940 ASN cc_start: 0.6809 (OUTLIER) cc_final: 0.6556 (p0) REVERT: B 1064 ARG cc_start: 0.6268 (OUTLIER) cc_final: 0.5909 (mtp85) REVERT: B 1187 LYS cc_start: 0.8253 (mmpt) cc_final: 0.7894 (mppt) REVERT: B 1219 GLN cc_start: 0.7781 (pt0) cc_final: 0.7262 (pt0) REVERT: C 583 CYS cc_start: 0.6005 (OUTLIER) cc_final: 0.5697 (t) REVERT: D 961 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: D 1054 MET cc_start: 0.6261 (tpt) cc_final: 0.6043 (tmm) REVERT: D 1143 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.7900 (p) outliers start: 54 outliers final: 29 residues processed: 186 average time/residue: 1.1729 time to fit residues: 239.9297 Evaluate side-chains 181 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 144 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 940 ASN Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 971 ASN Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 547 ARG Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain C residue 583 CYS Chi-restraints excluded: chain D residue 961 GLU Chi-restraints excluded: chain D residue 1003 GLN Chi-restraints excluded: chain D residue 1058 ASP Chi-restraints excluded: chain D residue 1143 VAL Chi-restraints excluded: chain D residue 1161 ILE Chi-restraints excluded: chain D residue 1214 VAL Chi-restraints excluded: chain D residue 1236 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 94 optimal weight: 0.0000 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 0.0970 chunk 116 optimal weight: 10.0000 chunk 135 optimal weight: 0.6980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN B1091 GLN C 568 ASN D 912 ASN D 960 ASN D1003 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12897 Z= 0.166 Angle : 0.535 12.231 17434 Z= 0.282 Chirality : 0.044 0.284 1916 Planarity : 0.003 0.047 2203 Dihedral : 5.332 58.480 1917 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.00 % Allowed : 20.57 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.29 (0.21), residues: 1532 helix: 2.12 (0.24), residues: 441 sheet: 0.14 (0.30), residues: 310 loop : -0.94 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.002 0.000 HIS A 161 PHE 0.010 0.001 PHE D1117 TYR 0.018 0.001 TYR A 169 ARG 0.009 0.000 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 147 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8040 (mttm) REVERT: A 583 CYS cc_start: 0.6978 (OUTLIER) cc_final: 0.6492 (m) REVERT: A 712 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6387 (ttpp) REVERT: B 1003 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8210 (mt0) REVERT: B 1064 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5955 (mtp85) REVERT: B 1065 ARG cc_start: 0.7760 (tpp-160) cc_final: 0.7471 (tpp-160) REVERT: B 1187 LYS cc_start: 0.8235 (mmpt) cc_final: 0.7885 (mppt) REVERT: B 1219 GLN cc_start: 0.7719 (pt0) cc_final: 0.7186 (pt0) REVERT: C 583 CYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5616 (t) REVERT: D 961 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7127 (tm-30) REVERT: D 1058 ASP cc_start: 0.6779 (OUTLIER) cc_final: 0.6361 (p0) REVERT: D 1143 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.7839 (p) outliers start: 41 outliers final: 22 residues processed: 177 average time/residue: 1.2008 time to fit residues: 232.3125 Evaluate side-chains 172 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 966 ASN Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain C residue 583 CYS Chi-restraints excluded: chain D residue 961 GLU Chi-restraints excluded: chain D residue 1003 GLN Chi-restraints excluded: chain D residue 1058 ASP Chi-restraints excluded: chain D residue 1143 VAL Chi-restraints excluded: chain D residue 1161 ILE Chi-restraints excluded: chain D residue 1214 VAL Chi-restraints excluded: chain D residue 1236 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 138 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 912 ASN D 960 ASN D1003 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12897 Z= 0.228 Angle : 0.562 13.507 17434 Z= 0.293 Chirality : 0.045 0.269 1916 Planarity : 0.003 0.045 2203 Dihedral : 5.348 56.921 1913 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.37 % Allowed : 20.35 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1532 helix: 2.07 (0.24), residues: 440 sheet: 0.10 (0.29), residues: 331 loop : -1.01 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.002 0.001 HIS A 161 PHE 0.011 0.001 PHE A 497 TYR 0.015 0.001 TYR A 169 ARG 0.009 0.000 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 142 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8067 (mttm) REVERT: A 583 CYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6531 (m) REVERT: A 712 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6384 (ttpp) REVERT: B 940 ASN cc_start: 0.6780 (OUTLIER) cc_final: 0.6559 (p0) REVERT: B 1003 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8368 (mt0) REVERT: B 1064 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5944 (mtp85) REVERT: B 1187 LYS cc_start: 0.8232 (mmpt) cc_final: 0.7880 (mppt) REVERT: B 1219 GLN cc_start: 0.7726 (pt0) cc_final: 0.7184 (pt0) REVERT: C 583 CYS cc_start: 0.5928 (OUTLIER) cc_final: 0.5607 (t) REVERT: D 961 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7133 (tm-30) REVERT: D 1143 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.7889 (p) outliers start: 46 outliers final: 27 residues processed: 176 average time/residue: 1.1109 time to fit residues: 215.4048 Evaluate side-chains 174 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain B residue 940 ASN Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain C residue 583 CYS Chi-restraints excluded: chain D residue 961 GLU Chi-restraints excluded: chain D residue 1003 GLN Chi-restraints excluded: chain D residue 1058 ASP Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain D residue 1143 VAL Chi-restraints excluded: chain D residue 1161 ILE Chi-restraints excluded: chain D residue 1214 VAL Chi-restraints excluded: chain D residue 1236 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 9.9990 chunk 89 optimal weight: 0.0370 chunk 69 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 0.0370 chunk 74 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 960 ASN D1003 GLN ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12897 Z= 0.225 Angle : 0.562 12.882 17434 Z= 0.294 Chirality : 0.045 0.263 1916 Planarity : 0.003 0.046 2203 Dihedral : 5.353 54.892 1913 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.93 % Allowed : 21.01 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.21 (0.21), residues: 1532 helix: 2.01 (0.24), residues: 441 sheet: 0.10 (0.29), residues: 331 loop : -0.99 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 333 HIS 0.002 0.000 HIS A 161 PHE 0.012 0.001 PHE D1117 TYR 0.016 0.001 TYR A 169 ARG 0.009 0.000 ARG A 737 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8062 (mttm) REVERT: A 583 CYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6540 (m) REVERT: A 712 LYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6342 (ttpp) REVERT: B 940 ASN cc_start: 0.6827 (OUTLIER) cc_final: 0.6576 (p0) REVERT: B 1064 ARG cc_start: 0.6326 (OUTLIER) cc_final: 0.5959 (mtp85) REVERT: B 1084 ILE cc_start: 0.6313 (mm) cc_final: 0.6055 (mt) REVERT: B 1187 LYS cc_start: 0.8251 (mmpt) cc_final: 0.7899 (mppt) REVERT: B 1219 GLN cc_start: 0.7711 (pt0) cc_final: 0.7175 (pt0) REVERT: C 583 CYS cc_start: 0.5932 (OUTLIER) cc_final: 0.5603 (t) REVERT: D 961 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: D 1143 VAL cc_start: 0.8715 (OUTLIER) cc_final: 0.7902 (p) outliers start: 40 outliers final: 28 residues processed: 171 average time/residue: 1.1155 time to fit residues: 209.8144 Evaluate side-chains 176 residues out of total 1366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 140 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 563 GLU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain B residue 940 ASN Chi-restraints excluded: chain B residue 956 ILE Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1214 VAL Chi-restraints excluded: chain B residue 1254 LEU Chi-restraints excluded: chain B residue 1283 GLU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 528 ASP Chi-restraints excluded: chain C residue 540 THR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 575 THR Chi-restraints excluded: chain C residue 583 CYS Chi-restraints excluded: chain D residue 961 GLU Chi-restraints excluded: chain D residue 1003 GLN Chi-restraints excluded: chain D residue 1058 ASP Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain D residue 1143 VAL Chi-restraints excluded: chain D residue 1161 ILE Chi-restraints excluded: chain D residue 1214 VAL Chi-restraints excluded: chain D residue 1236 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS B 899 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 960 ASN D1003 GLN ** D1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.223782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.153266 restraints weight = 12997.484| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.19 r_work: 0.3426 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12897 Z= 0.208 Angle : 0.559 14.394 17434 Z= 0.292 Chirality : 0.044 0.253 1916 Planarity : 0.003 0.046 2203 Dihedral : 5.307 54.758 1913 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.22 % Allowed : 20.79 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.24 (0.21), residues: 1532 helix: 2.05 (0.24), residues: 441 sheet: 0.11 (0.29), residues: 331 loop : -0.98 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 985 HIS 0.002 0.000 HIS A 161 PHE 0.013 0.001 PHE D1117 TYR 0.016 0.001 TYR A 169 ARG 0.009 0.000 ARG A 737 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4921.87 seconds wall clock time: 86 minutes 47.96 seconds (5207.96 seconds total)