Starting phenix.real_space_refine on Mon Jul 22 20:28:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppt_17815/07_2024/8ppt_17815_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppt_17815/07_2024/8ppt_17815.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/8ppt_17815/07_2024/8ppt_17815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppt_17815/07_2024/8ppt_17815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppt_17815/07_2024/8ppt_17815_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppt_17815/07_2024/8ppt_17815_neut.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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 34 5.49 5 Mg 3 5.21 5 S 75 5.16 5 C 12460 2.51 5 N 3284 2.21 5 O 3761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "A TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "D PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 42": "OD1" <-> "OD2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D ASP 188": "OD1" <-> "OD2" Residue "D ASP 235": "OD1" <-> "OD2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E GLU 33": "OE1" <-> "OE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B ASP 495": "OD1" <-> "OD2" Residue "B ASP 584": "OD1" <-> "OD2" Residue "B ASP 600": "OD1" <-> "OD2" Residue "B GLU 641": "OE1" <-> "OE2" Residue "B TYR 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 776": "OE1" <-> "OE2" Residue "B ASP 1187": "OD1" <-> "OD2" Residue "B GLU 1196": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 19620 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3565 Classifications: {'peptide': 447} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 415} Chain: "C" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1939 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain: "D" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1939 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain: "E" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1939 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain: "P" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 369 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "T" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "B" Number of atoms: 9535 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1191, 9528 Classifications: {'peptide': 1191} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1123} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 1191, 9528 Classifications: {'peptide': 1191} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1123} Chain breaks: 1 bond proxies already assigned to first conformer: 9723 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15521 SG CYS B 706 17.290 104.259 62.511 1.00 54.10 S ATOM 15543 SG CYS B 709 17.403 105.381 58.905 1.00100.89 S ATOM 15608 SG CYS B 718 20.610 105.185 60.749 1.00 64.77 S ATOM 15629 SG CYS B 721 18.158 107.910 61.682 1.00 75.38 S ATOM 15712 SG CYS B 731 15.107 79.734 61.311 1.00 85.25 S ATOM 15736 SG CYS B 734 13.188 81.340 58.312 1.00 95.21 S ATOM 15864 SG CYS B 750 11.595 81.073 61.795 1.00 97.06 S ATOM 15886 SG CYS B 753 11.995 77.991 59.934 1.00124.80 S ATOM 18877 SG CYS B1123 49.506 74.372 52.322 1.00 70.79 S ATOM 18899 SG CYS B1126 45.772 75.042 52.835 1.00 76.08 S ATOM 19005 SG CYS B1139 47.292 71.696 51.155 1.00 96.74 S ATOM 19025 SG CYS B1142 46.485 75.243 49.687 1.00107.69 S Time building chain proxies: 15.83, per 1000 atoms: 0.81 Number of scatterers: 19620 At special positions: 0 Unit cell: (116.96, 145.34, 148.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 75 16.00 P 34 15.00 Mg 3 11.99 O 3761 8.00 N 3284 7.00 C 12460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.90 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 709 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 718 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 721 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 706 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 750 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 753 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 731 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 734 " pdb=" ZN B1303 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1126 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1142 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1139 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1123 " Number of angles added : 18 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4436 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 20 sheets defined 34.5% alpha, 20.4% beta 14 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 6.86 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.623A pdb=" N VAL A 206 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 removed outlier: 4.084A pdb=" N ILE A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.601A pdb=" N ASN A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 removed outlier: 3.921A pdb=" N LYS A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 415 through 419 removed outlier: 3.651A pdb=" N LEU A 419 " --> pdb=" O TYR A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 436 Processing helix chain 'A' and resid 464 through 473 Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.661A pdb=" N VAL A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 527 Processing helix chain 'A' and resid 584 through 590 Processing helix chain 'C' and resid 9 through 22 removed outlier: 3.614A pdb=" N PHE C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 81 Processing helix chain 'C' and resid 138 through 152 removed outlier: 3.784A pdb=" N LEU C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 209 Processing helix chain 'D' and resid 9 through 22 removed outlier: 3.613A pdb=" N PHE D 13 " --> pdb=" O GLY D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 138 through 152 Processing helix chain 'D' and resid 201 through 209 Processing helix chain 'E' and resid 9 through 21 removed outlier: 3.627A pdb=" N PHE E 13 " --> pdb=" O GLY E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 138 through 152 removed outlier: 4.110A pdb=" N LEU E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER E 152 " --> pdb=" O ALA E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 209 Processing helix chain 'B' and resid 6 through 30 removed outlier: 3.784A pdb=" N ILE B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 59 through 71 removed outlier: 4.376A pdb=" N ARG B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 87 Processing helix chain 'B' and resid 94 through 112 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 145 through 150 removed outlier: 3.513A pdb=" N SER B 150 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 169 removed outlier: 3.762A pdb=" N GLN B 155 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 195 removed outlier: 3.570A pdb=" N HIS B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 213 Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 272 through 283 Processing helix chain 'B' and resid 311 through 324 Processing helix chain 'B' and resid 328 through 332 removed outlier: 3.781A pdb=" N LYS B 332 " --> pdb=" O LYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 374 Processing helix chain 'B' and resid 419 through 427 removed outlier: 3.557A pdb=" N ALA B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.612A pdb=" N PHE B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 486 through 498 Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 517 through 529 Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 539 through 543 removed outlier: 3.765A pdb=" N VAL B 543 " --> pdb=" O TRP B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 558 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 585 through 592 Processing helix chain 'B' and resid 607 through 615 removed outlier: 4.053A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 612 " --> pdb=" O PRO B 608 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 613 " --> pdb=" O TRP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 Processing helix chain 'B' and resid 631 through 640 Processing helix chain 'B' and resid 686 through 693 Processing helix chain 'B' and resid 740 through 746 removed outlier: 3.902A pdb=" N GLY B 745 " --> pdb=" O SER B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 779 removed outlier: 3.783A pdb=" N LEU B 770 " --> pdb=" O ARG B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 812 removed outlier: 3.787A pdb=" N GLY B 805 " --> pdb=" O PRO B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 849 Processing helix chain 'B' and resid 876 through 897 removed outlier: 3.650A pdb=" N LYS B 885 " --> pdb=" O ARG B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 913 removed outlier: 3.916A pdb=" N ILE B 913 " --> pdb=" O GLU B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 950 Processing helix chain 'B' and resid 965 through 972 Processing helix chain 'B' and resid 996 through 1000 removed outlier: 3.794A pdb=" N VAL B1000 " --> pdb=" O PRO B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1007 removed outlier: 3.597A pdb=" N ASN B1006 " --> pdb=" O GLU B1003 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET B1007 " --> pdb=" O VAL B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1022 removed outlier: 3.769A pdb=" N TYR B1018 " --> pdb=" O PRO B1014 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B1022 " --> pdb=" O TYR B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1031 removed outlier: 3.580A pdb=" N VAL B1031 " --> pdb=" O LYS B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1040 Processing helix chain 'B' and resid 1066 through 1071 removed outlier: 3.877A pdb=" N LEU B1071 " --> pdb=" O TYR B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1088 Processing helix chain 'B' and resid 1092 through 1117 removed outlier: 4.049A pdb=" N VAL B1096 " --> pdb=" O ASP B1092 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU B1098 " --> pdb=" O HIS B1094 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N HIS B1104 " --> pdb=" O ILE B1100 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B1105 " --> pdb=" O LEU B1101 " (cutoff:3.500A) Proline residue: B1107 - end of helix removed outlier: 4.006A pdb=" N THR B1117 " --> pdb=" O LEU B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1155 Processing helix chain 'B' and resid 1158 through 1169 removed outlier: 3.666A pdb=" N TYR B1169 " --> pdb=" O LEU B1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 1172 through 1190 removed outlier: 4.007A pdb=" N PHE B1190 " --> pdb=" O ILE B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1208 through 1215 Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 201 removed outlier: 6.089A pdb=" N VAL A 485 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL A 556 " --> pdb=" O VAL A 575 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 567 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 565 " --> pdb=" O ASN A 576 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 272 removed outlier: 3.774A pdb=" N VAL A 267 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA A 318 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE A 334 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS A 320 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE A 297 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LYS A 333 " --> pdb=" O PHE A 297 " (cutoff:3.500A) removed outlier: 12.119A pdb=" N TYR A 335 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 284 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 289 Processing sheet with id=AA4, first strand: chain 'A' and resid 477 through 479 removed outlier: 6.312A pdb=" N MET A 444 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR A 354 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ILE A 400 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 356 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 357 " --> pdb=" O PRO A 600 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL A 599 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL A 612 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL A 601 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 608 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 62 removed outlier: 3.774A pdb=" N LYS C 60 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE C 3 " --> pdb=" O LYS C 93 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS C 93 " --> pdb=" O PHE C 3 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR C 108 " --> pdb=" O LYS D 178 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS D 178 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU D 169 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N SER D 154 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 72 removed outlier: 3.578A pdb=" N VAL C 31 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 71 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA C 27 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLU C 26 " --> pdb=" O MET C 41 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET C 41 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA C 28 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG C 39 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN C 52 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG C 238 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 239 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR C 231 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS C 133 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE C 189 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL C 135 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 195 through 200 removed outlier: 6.538A pdb=" N SER C 154 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLU C 169 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 179 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU C 174 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 178 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR E 108 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS E 60 " --> pdb=" O VAL E 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 61 through 62 removed outlier: 4.856A pdb=" N THR D 108 " --> pdb=" O LYS E 178 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS E 178 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU E 174 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU E 169 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N SER E 154 " --> pdb=" O GLU E 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 67 through 72 removed outlier: 3.763A pdb=" N VAL D 71 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA D 27 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU D 26 " --> pdb=" O MET D 41 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N MET D 41 " --> pdb=" O GLU D 26 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ALA D 28 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG D 39 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR D 232 " --> pdb=" O GLU D 216 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU D 216 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP D 188 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU D 137 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU D 186 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 72 removed outlier: 3.673A pdb=" N VAL E 71 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA E 27 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLU E 26 " --> pdb=" O MET E 41 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N MET E 41 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ALA E 28 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ARG E 39 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS E 30 " --> pdb=" O SER E 37 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE E 49 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 239 " --> pdb=" O TYR E 231 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR E 231 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR E 232 " --> pdb=" O GLU E 216 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU E 216 " --> pdb=" O TYR E 232 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP E 188 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU E 137 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU E 186 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 43 through 44 removed outlier: 7.633A pdb=" N GLY B 941 " --> pdb=" O ASP B 824 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR B 826 " --> pdb=" O GLY B 941 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA B 943 " --> pdb=" O THR B 826 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA B 828 " --> pdb=" O ALA B 943 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU B 875 " --> pdb=" O ILE B 933 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE B 935 " --> pdb=" O LEU B 875 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 122 through 129 removed outlier: 6.944A pdb=" N TYR B 142 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL B 125 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA B 140 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ILE B 127 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR B 138 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 437 through 441 removed outlier: 6.008A pdb=" N ARG B 351 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE B 441 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ARG B 353 " --> pdb=" O ILE B 441 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 365 through 367 Processing sheet with id=AB6, first strand: chain 'B' and resid 414 through 416 removed outlier: 6.442A pdb=" N ILE B 406 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 560 through 563 removed outlier: 6.867A pdb=" N GLU B 560 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 575 " --> pdb=" O GLU B 560 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU B 562 " --> pdb=" O LYS B 573 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 697 through 701 removed outlier: 3.616A pdb=" N ILE B 701 " --> pdb=" O ALA B 761 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 761 " --> pdb=" O ILE B 701 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AC1, first strand: chain 'B' and resid 832 through 833 Processing sheet with id=AC2, first strand: chain 'B' and resid 1129 through 1130 811 hydrogen bonds defined for protein. 2235 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 9.20 Time building geometry restraints manager: 8.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4647 1.33 - 1.45: 3930 1.45 - 1.58: 11289 1.58 - 1.70: 66 1.70 - 1.82: 132 Bond restraints: 20064 Sorted by residual: bond pdb=" C PRO A 210 " pdb=" O PRO A 210 " ideal model delta sigma weight residual 1.240 1.210 0.031 1.12e-02 7.97e+03 7.55e+00 bond pdb=" N VAL A 508 " pdb=" CA VAL A 508 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.23e-02 6.61e+03 6.00e+00 bond pdb=" N PHE A 507 " pdb=" CA PHE A 507 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.67e+00 bond pdb=" C PRO A 509 " pdb=" O PRO A 509 " ideal model delta sigma weight residual 1.235 1.207 0.028 1.30e-02 5.92e+03 4.53e+00 bond pdb=" N GLY A 510 " pdb=" CA GLY A 510 " ideal model delta sigma weight residual 1.450 1.478 -0.028 1.33e-02 5.65e+03 4.45e+00 ... (remaining 20059 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.24: 699 106.24 - 113.19: 10822 113.19 - 120.14: 7084 120.14 - 127.09: 8410 127.09 - 134.04: 232 Bond angle restraints: 27247 Sorted by residual: angle pdb=" N VAL B1141 " pdb=" CA VAL B1141 " pdb=" C VAL B1141 " ideal model delta sigma weight residual 111.77 107.22 4.55 1.04e+00 9.25e-01 1.92e+01 angle pdb=" N PRO A 211 " pdb=" CA PRO A 211 " pdb=" CB PRO A 211 " ideal model delta sigma weight residual 103.15 99.29 3.86 9.70e-01 1.06e+00 1.58e+01 angle pdb=" N PRO A 211 " pdb=" CA PRO A 211 " pdb=" C PRO A 211 " ideal model delta sigma weight residual 111.68 117.55 -5.87 1.67e+00 3.59e-01 1.23e+01 angle pdb=" CA PRO A 211 " pdb=" C PRO A 211 " pdb=" O PRO A 211 " ideal model delta sigma weight residual 121.86 117.88 3.98 1.22e+00 6.72e-01 1.07e+01 angle pdb=" C GLY A 559 " pdb=" N HIS A 560 " pdb=" CA HIS A 560 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.12e+00 ... (remaining 27242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 11545 35.73 - 71.46: 605 71.46 - 107.20: 29 107.20 - 142.93: 0 142.93 - 178.66: 2 Dihedral angle restraints: 12181 sinusoidal: 5288 harmonic: 6893 Sorted by residual: dihedral pdb=" CA LYS B 668 " pdb=" C LYS B 668 " pdb=" N PRO B 669 " pdb=" CA PRO B 669 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA GLU B1093 " pdb=" C GLU B1093 " pdb=" N HIS B1094 " pdb=" CA HIS B1094 " ideal model delta harmonic sigma weight residual 180.00 -158.48 -21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA TYR B1047 " pdb=" C TYR B1047 " pdb=" N TYR B1048 " pdb=" CA TYR B1048 " ideal model delta harmonic sigma weight residual 180.00 -160.10 -19.90 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 12178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2502 0.054 - 0.107: 467 0.107 - 0.161: 83 0.161 - 0.215: 0 0.215 - 0.268: 1 Chirality restraints: 3053 Sorted by residual: chirality pdb=" CB VAL B1141 " pdb=" CA VAL B1141 " pdb=" CG1 VAL B1141 " pdb=" CG2 VAL B1141 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA ASP B 600 " pdb=" N ASP B 600 " pdb=" C ASP B 600 " pdb=" CB ASP B 600 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 3050 not shown) Planarity restraints: 3393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 208 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.67e+00 pdb=" C LEU A 208 " 0.054 2.00e-02 2.50e+03 pdb=" O LEU A 208 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG A 209 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 235 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" CG ASP C 235 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP C 235 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP C 235 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 145 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO B 146 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " 0.030 5.00e-02 4.00e+02 ... (remaining 3390 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 100 2.54 - 3.13: 13606 3.13 - 3.72: 28254 3.72 - 4.31: 40354 4.31 - 4.90: 70334 Nonbonded interactions: 152648 Sorted by model distance: nonbonded pdb=" OD1 ASN A 450 " pdb="MG MG A 701 " model vdw 1.950 2.170 nonbonded pdb=" OD2 ASP A 404 " pdb="MG MG A 701 " model vdw 2.124 2.170 nonbonded pdb=" ND1 HIS A 560 " pdb="MG MG A 701 " model vdw 2.166 2.250 nonbonded pdb=" O SER B 149 " pdb=" OG SER B 149 " model vdw 2.182 2.440 nonbonded pdb=" O THR A 595 " pdb=" OG1 THR A 595 " model vdw 2.196 2.440 ... (remaining 152643 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 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 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: 3.810 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: 0.970 Check model and map are aligned: 0.140 Set scattering table: 0.210 Process input model: 71.200 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 : 0.003 0.039 20064 Z= 0.193 Angle : 0.554 6.114 27247 Z= 0.300 Chirality : 0.043 0.268 3053 Planarity : 0.004 0.054 3393 Dihedral : 19.224 178.659 7745 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.82 % Allowed : 30.71 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2366 helix: 1.04 (0.20), residues: 700 sheet: 0.24 (0.23), residues: 523 loop : -1.04 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 552 HIS 0.003 0.001 HIS B 944 PHE 0.011 0.001 PHE A 463 TYR 0.016 0.001 TYR B 138 ARG 0.008 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 217 time to evaluate : 2.123 Fit side-chains REVERT: A 351 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6746 (pt0) REVERT: C 190 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6938 (mt-10) REVERT: D 127 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7471 (mp0) REVERT: B 667 MET cc_start: 0.8716 (mtt) cc_final: 0.8210 (mtt) outliers start: 58 outliers final: 55 residues processed: 274 average time/residue: 1.2483 time to fit residues: 388.9405 Evaluate side-chains 265 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 210 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 104 GLN Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 768 SER Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1045 GLU Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1149 THR Chi-restraints excluded: chain B residue 1181 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 121 optimal weight: 0.0170 chunk 95 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN E 223 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** B 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20064 Z= 0.280 Angle : 0.592 7.408 27247 Z= 0.307 Chirality : 0.046 0.153 3053 Planarity : 0.005 0.059 3393 Dihedral : 13.192 179.275 3005 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 5.25 % Allowed : 27.41 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2366 helix: 0.96 (0.19), residues: 724 sheet: 0.11 (0.22), residues: 559 loop : -1.05 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 552 HIS 0.004 0.001 HIS B 944 PHE 0.015 0.002 PHE A 463 TYR 0.017 0.002 TYR D 231 ARG 0.007 0.000 ARG E 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 230 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7524 (mptt) REVERT: A 351 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6727 (pt0) REVERT: C 64 ASP cc_start: 0.5774 (OUTLIER) cc_final: 0.5420 (m-30) REVERT: C 181 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6863 (mm) REVERT: C 190 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7139 (mt-10) REVERT: D 127 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7459 (mp0) REVERT: D 225 MET cc_start: 0.7411 (ptt) cc_final: 0.6374 (pp-130) REVERT: B 254 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7394 (mp) REVERT: B 617 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7940 (mp) REVERT: B 1212 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7184 (mp) outliers start: 108 outliers final: 48 residues processed: 307 average time/residue: 1.2356 time to fit residues: 430.3899 Evaluate side-chains 270 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 216 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1045 GLU Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1161 THR Chi-restraints excluded: chain B residue 1170 ASN Chi-restraints excluded: chain B residue 1200 THR Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 59 optimal weight: 0.0010 chunk 215 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 172 optimal weight: 4.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS E 52 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20064 Z= 0.201 Angle : 0.536 6.936 27247 Z= 0.280 Chirality : 0.044 0.147 3053 Planarity : 0.004 0.049 3393 Dihedral : 12.742 179.224 2953 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.76 % Allowed : 28.13 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2366 helix: 1.20 (0.20), residues: 712 sheet: 0.14 (0.22), residues: 556 loop : -0.98 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 622 HIS 0.003 0.001 HIS B 944 PHE 0.013 0.001 PHE A 463 TYR 0.014 0.001 TYR B 138 ARG 0.005 0.000 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 221 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7550 (mptt) REVERT: A 390 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7308 (mm-30) REVERT: C 64 ASP cc_start: 0.5591 (OUTLIER) cc_final: 0.5291 (m-30) REVERT: C 162 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7160 (t0) REVERT: C 190 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7158 (mt-10) REVERT: D 73 MET cc_start: 0.7925 (mmp) cc_final: 0.7670 (mmp) REVERT: D 127 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7438 (mp0) REVERT: D 143 GLU cc_start: 0.7519 (mp0) cc_final: 0.7152 (mp0) REVERT: D 225 MET cc_start: 0.7438 (ptt) cc_final: 0.6475 (pp-130) REVERT: E 233 ILE cc_start: 0.6435 (mm) cc_final: 0.5822 (pt) REVERT: B 186 GLU cc_start: 0.5618 (pt0) cc_final: 0.5413 (pt0) REVERT: B 254 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7167 (mp) REVERT: B 580 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: B 617 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7909 (mp) REVERT: B 625 MET cc_start: 0.7732 (mmp) cc_final: 0.7299 (mtp) REVERT: B 663 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8211 (tttm) REVERT: B 667 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8254 (mtt) REVERT: B 1212 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7151 (mp) outliers start: 98 outliers final: 43 residues processed: 292 average time/residue: 1.2905 time to fit residues: 426.3039 Evaluate side-chains 266 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 213 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1200 THR Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 0.0980 chunk 162 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 229 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 205 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20064 Z= 0.300 Angle : 0.600 7.766 27247 Z= 0.310 Chirality : 0.046 0.163 3053 Planarity : 0.005 0.051 3393 Dihedral : 12.759 179.521 2941 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.54 % Allowed : 27.94 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.17), residues: 2366 helix: 1.00 (0.19), residues: 718 sheet: 0.07 (0.22), residues: 559 loop : -1.09 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 622 HIS 0.005 0.001 HIS B 944 PHE 0.015 0.002 PHE B 467 TYR 0.017 0.002 TYR D 231 ARG 0.005 0.000 ARG E 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 221 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7610 (mptt) REVERT: C 64 ASP cc_start: 0.5744 (OUTLIER) cc_final: 0.5400 (m-30) REVERT: C 162 ASN cc_start: 0.7404 (OUTLIER) cc_final: 0.7066 (t0) REVERT: C 190 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7287 (mt-10) REVERT: D 73 MET cc_start: 0.7998 (mmp) cc_final: 0.7665 (mmp) REVERT: D 74 ASP cc_start: 0.7954 (t0) cc_final: 0.7715 (t0) REVERT: D 127 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7455 (mp0) REVERT: D 143 GLU cc_start: 0.7587 (mp0) cc_final: 0.7262 (mp0) REVERT: D 169 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7051 (tp30) REVERT: D 227 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7802 (ptm) REVERT: E 167 ARG cc_start: 0.8237 (mtp-110) cc_final: 0.7926 (mtp-110) REVERT: E 233 ILE cc_start: 0.6460 (mm) cc_final: 0.5838 (pt) REVERT: B 110 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7888 (mp) REVERT: B 254 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7265 (mp) REVERT: B 353 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8661 (mtt180) REVERT: B 580 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: B 625 MET cc_start: 0.7738 (mmp) cc_final: 0.7329 (mtp) REVERT: B 663 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8207 (tttt) REVERT: B 737 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7522 (mt-10) REVERT: B 1187 ASP cc_start: 0.7987 (t0) cc_final: 0.7533 (m-30) REVERT: B 1212 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7137 (mp) outliers start: 114 outliers final: 65 residues processed: 309 average time/residue: 1.2597 time to fit residues: 441.0473 Evaluate side-chains 290 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 214 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 223 ASN Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1161 THR Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1200 THR Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 170 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20064 Z= 0.215 Angle : 0.548 7.391 27247 Z= 0.285 Chirality : 0.044 0.149 3053 Planarity : 0.004 0.051 3393 Dihedral : 12.642 179.387 2938 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.25 % Allowed : 28.57 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2366 helix: 1.10 (0.19), residues: 718 sheet: 0.11 (0.22), residues: 559 loop : -1.04 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 622 HIS 0.003 0.001 HIS B 533 PHE 0.013 0.001 PHE A 463 TYR 0.014 0.001 TYR B 138 ARG 0.005 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 228 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7591 (mptt) REVERT: A 306 ARG cc_start: 0.7459 (ppt90) cc_final: 0.7206 (tpm170) REVERT: A 351 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6231 (mt-10) REVERT: C 64 ASP cc_start: 0.5642 (OUTLIER) cc_final: 0.5333 (m-30) REVERT: C 162 ASN cc_start: 0.7475 (OUTLIER) cc_final: 0.7121 (t0) REVERT: C 190 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: C 235 ASP cc_start: 0.8241 (m-30) cc_final: 0.7919 (t0) REVERT: D 73 MET cc_start: 0.7972 (mmp) cc_final: 0.7634 (mmp) REVERT: D 74 ASP cc_start: 0.7938 (t0) cc_final: 0.7652 (t0) REVERT: D 121 ILE cc_start: 0.6430 (OUTLIER) cc_final: 0.6226 (mm) REVERT: D 127 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: D 143 GLU cc_start: 0.7545 (mp0) cc_final: 0.7268 (mp0) REVERT: D 155 MET cc_start: 0.8288 (ttt) cc_final: 0.8017 (ttm) REVERT: D 169 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7036 (tp30) REVERT: D 227 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7875 (ptm) REVERT: E 233 ILE cc_start: 0.6506 (mm) cc_final: 0.5890 (pt) REVERT: B 110 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7747 (mp) REVERT: B 254 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7120 (mp) REVERT: B 321 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7215 (ttmt) REVERT: B 353 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8640 (mtt180) REVERT: B 617 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7838 (mp) REVERT: B 625 MET cc_start: 0.7742 (mmp) cc_final: 0.7329 (mtp) REVERT: B 663 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8216 (tttm) REVERT: B 737 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7528 (mt-10) REVERT: B 1212 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7115 (mp) outliers start: 108 outliers final: 65 residues processed: 310 average time/residue: 1.2770 time to fit residues: 448.4264 Evaluate side-chains 294 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 215 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 223 ASN Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 958 ASP Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1161 THR Chi-restraints excluded: chain B residue 1170 ASN Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1200 THR Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 5.9990 chunk 206 optimal weight: 0.0970 chunk 45 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 229 optimal weight: 0.7980 chunk 190 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20064 Z= 0.164 Angle : 0.517 7.455 27247 Z= 0.269 Chirality : 0.043 0.164 3053 Planarity : 0.004 0.050 3393 Dihedral : 12.499 179.639 2937 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.32 % Allowed : 29.98 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2366 helix: 1.35 (0.20), residues: 711 sheet: 0.24 (0.22), residues: 551 loop : -0.94 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.002 0.001 HIS B 533 PHE 0.011 0.001 PHE B 443 TYR 0.016 0.001 TYR A 197 ARG 0.007 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 229 time to evaluate : 2.273 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7566 (mptt) REVERT: A 306 ARG cc_start: 0.7404 (ppt90) cc_final: 0.7067 (tpm170) REVERT: C 64 ASP cc_start: 0.5523 (OUTLIER) cc_final: 0.5263 (m-30) REVERT: C 190 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: C 235 ASP cc_start: 0.8250 (m-30) cc_final: 0.7939 (t0) REVERT: D 74 ASP cc_start: 0.7885 (t0) cc_final: 0.7623 (t0) REVERT: D 127 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7406 (mp0) REVERT: D 143 GLU cc_start: 0.7485 (mp0) cc_final: 0.7282 (mp0) REVERT: D 155 MET cc_start: 0.8210 (ttt) cc_final: 0.7974 (ttm) REVERT: D 169 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7019 (tp30) REVERT: D 227 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7799 (ptm) REVERT: D 236 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: E 143 GLU cc_start: 0.6777 (pt0) cc_final: 0.6494 (pp20) REVERT: E 167 ARG cc_start: 0.8201 (mtp-110) cc_final: 0.7717 (mtp180) REVERT: E 169 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: E 233 ILE cc_start: 0.6536 (mm) cc_final: 0.5924 (pt) REVERT: B 111 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.7825 (m) REVERT: B 321 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7201 (ttmt) REVERT: B 617 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7787 (mp) REVERT: B 625 MET cc_start: 0.7708 (mmp) cc_final: 0.7319 (mtp) REVERT: B 663 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8233 (tttt) REVERT: B 667 MET cc_start: 0.8693 (mtt) cc_final: 0.8187 (mtt) REVERT: B 1187 ASP cc_start: 0.7848 (t0) cc_final: 0.7413 (m-30) REVERT: B 1212 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7099 (mp) outliers start: 89 outliers final: 47 residues processed: 300 average time/residue: 1.2953 time to fit residues: 440.4387 Evaluate side-chains 279 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 221 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1161 THR Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1200 THR Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 167 optimal weight: 0.0970 chunk 129 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 228 optimal weight: 0.6980 chunk 142 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN E 52 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20064 Z= 0.172 Angle : 0.526 7.879 27247 Z= 0.271 Chirality : 0.043 0.175 3053 Planarity : 0.004 0.049 3393 Dihedral : 12.476 179.822 2935 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.18 % Allowed : 30.42 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2366 helix: 1.42 (0.20), residues: 711 sheet: 0.24 (0.22), residues: 553 loop : -0.87 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 379 HIS 0.002 0.001 HIS B 944 PHE 0.011 0.001 PHE A 463 TYR 0.015 0.001 TYR A 197 ARG 0.006 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 220 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7558 (mptt) REVERT: C 62 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6593 (tm-30) REVERT: C 64 ASP cc_start: 0.5503 (OUTLIER) cc_final: 0.5260 (m-30) REVERT: C 190 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: C 235 ASP cc_start: 0.8202 (m-30) cc_final: 0.7919 (t0) REVERT: D 74 ASP cc_start: 0.7894 (t0) cc_final: 0.7640 (t0) REVERT: D 127 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: D 155 MET cc_start: 0.8198 (ttt) cc_final: 0.7942 (ttm) REVERT: D 169 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7064 (tp30) REVERT: D 227 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7862 (ptm) REVERT: D 236 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: E 143 GLU cc_start: 0.6801 (pt0) cc_final: 0.6545 (pp20) REVERT: E 233 ILE cc_start: 0.6563 (mm) cc_final: 0.5985 (pt) REVERT: B 110 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7599 (mp) REVERT: B 111 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.7837 (m) REVERT: B 254 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7076 (mp) REVERT: B 321 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7214 (ttmt) REVERT: B 617 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7801 (mp) REVERT: B 625 MET cc_start: 0.7686 (mmp) cc_final: 0.7359 (mpp) REVERT: B 663 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8223 (tttt) REVERT: B 1187 ASP cc_start: 0.7848 (t0) cc_final: 0.7419 (m-30) REVERT: B 1212 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7078 (mp) outliers start: 86 outliers final: 56 residues processed: 289 average time/residue: 1.3145 time to fit residues: 429.9320 Evaluate side-chains 284 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 215 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1196 GLU Chi-restraints excluded: chain B residue 1200 THR Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 0.0060 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN E 52 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20064 Z= 0.284 Angle : 0.604 12.294 27247 Z= 0.308 Chirality : 0.046 0.239 3053 Planarity : 0.005 0.050 3393 Dihedral : 12.655 179.982 2935 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.76 % Allowed : 29.74 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2366 helix: 1.15 (0.19), residues: 718 sheet: 0.13 (0.22), residues: 559 loop : -0.99 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 379 HIS 0.004 0.001 HIS B 944 PHE 0.015 0.001 PHE B 467 TYR 0.016 0.002 TYR A 197 ARG 0.008 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 222 time to evaluate : 2.325 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7586 (mptt) REVERT: C 62 GLU cc_start: 0.6914 (tm-30) cc_final: 0.6559 (tm-30) REVERT: C 64 ASP cc_start: 0.5583 (OUTLIER) cc_final: 0.5298 (m-30) REVERT: C 165 THR cc_start: 0.7969 (OUTLIER) cc_final: 0.7742 (m) REVERT: C 190 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7305 (mt-10) REVERT: C 235 ASP cc_start: 0.8218 (m-30) cc_final: 0.7937 (t0) REVERT: D 74 ASP cc_start: 0.7937 (t0) cc_final: 0.7665 (t0) REVERT: D 127 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: D 155 MET cc_start: 0.8225 (ttt) cc_final: 0.7900 (ttm) REVERT: D 169 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7123 (tp30) REVERT: D 236 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: E 233 ILE cc_start: 0.6567 (mm) cc_final: 0.6017 (pt) REVERT: B 254 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7249 (mp) REVERT: B 321 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7233 (ttmt) REVERT: B 625 MET cc_start: 0.7689 (mmp) cc_final: 0.7316 (mtp) REVERT: B 663 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8222 (tttt) REVERT: B 1212 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7088 (mp) outliers start: 98 outliers final: 67 residues processed: 294 average time/residue: 1.2526 time to fit residues: 419.1504 Evaluate side-chains 295 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 218 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1196 GLU Chi-restraints excluded: chain B residue 1200 THR Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 0.0030 chunk 199 optimal weight: 1.9990 chunk 212 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 192 optimal weight: 0.8980 chunk 201 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 225 optimal weight: 0.8980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN E 223 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN B1198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20064 Z= 0.168 Angle : 0.543 17.579 27247 Z= 0.276 Chirality : 0.043 0.173 3053 Planarity : 0.004 0.049 3393 Dihedral : 12.530 179.759 2935 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.50 % Allowed : 31.20 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2366 helix: 1.40 (0.20), residues: 711 sheet: 0.25 (0.22), residues: 551 loop : -0.90 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 379 HIS 0.002 0.001 HIS A 362 PHE 0.011 0.001 PHE B 443 TYR 0.020 0.001 TYR A 197 ARG 0.014 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 218 time to evaluate : 2.211 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7560 (mptt) REVERT: C 62 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6603 (tm-30) REVERT: C 190 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: C 235 ASP cc_start: 0.8251 (m-30) cc_final: 0.7983 (t0) REVERT: D 74 ASP cc_start: 0.7901 (t0) cc_final: 0.7654 (t0) REVERT: D 127 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: D 155 MET cc_start: 0.8209 (ttt) cc_final: 0.7965 (ttm) REVERT: D 169 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7108 (tp30) REVERT: D 236 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: E 39 ARG cc_start: 0.7216 (ttm110) cc_final: 0.6721 (ttm110) REVERT: E 143 GLU cc_start: 0.6830 (pt0) cc_final: 0.6526 (pp20) REVERT: E 167 ARG cc_start: 0.8179 (mtp-110) cc_final: 0.7948 (mtp180) REVERT: E 233 ILE cc_start: 0.6492 (mm) cc_final: 0.6023 (pt) REVERT: B 111 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7757 (m) REVERT: B 254 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.7001 (mp) REVERT: B 625 MET cc_start: 0.7699 (mmp) cc_final: 0.7382 (mpp) REVERT: B 663 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8238 (tttm) REVERT: B 1187 ASP cc_start: 0.7883 (t0) cc_final: 0.7382 (m-30) REVERT: B 1212 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7120 (mp) outliers start: 72 outliers final: 53 residues processed: 275 average time/residue: 1.3177 time to fit residues: 410.5846 Evaluate side-chains 276 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 215 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1196 GLU Chi-restraints excluded: chain B residue 1200 THR Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 236 optimal weight: 0.0060 chunk 217 optimal weight: 0.8980 chunk 188 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 149 optimal weight: 0.4980 chunk 200 optimal weight: 0.0030 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN B1198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20064 Z= 0.149 Angle : 0.527 16.959 27247 Z= 0.267 Chirality : 0.043 0.165 3053 Planarity : 0.004 0.049 3393 Dihedral : 12.457 179.942 2935 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.82 % Allowed : 31.92 % Favored : 65.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2366 helix: 1.53 (0.20), residues: 717 sheet: 0.28 (0.22), residues: 551 loop : -0.80 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 379 HIS 0.002 0.000 HIS B 180 PHE 0.012 0.001 PHE B 443 TYR 0.020 0.001 TYR A 197 ARG 0.013 0.000 ARG D 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 224 time to evaluate : 2.013 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7501 (mptt) REVERT: A 351 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6421 (mm-30) REVERT: A 390 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7318 (mm-30) REVERT: C 143 GLU cc_start: 0.7064 (pt0) cc_final: 0.6801 (mp0) REVERT: C 190 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: C 235 ASP cc_start: 0.8180 (m-30) cc_final: 0.7945 (t0) REVERT: D 73 MET cc_start: 0.7949 (mmp) cc_final: 0.7642 (mmp) REVERT: D 74 ASP cc_start: 0.7833 (t0) cc_final: 0.7616 (t0) REVERT: D 127 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: D 155 MET cc_start: 0.8184 (ttt) cc_final: 0.7929 (ttm) REVERT: D 169 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7079 (tp30) REVERT: D 236 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: E 39 ARG cc_start: 0.7262 (ttm110) cc_final: 0.6785 (ttm110) REVERT: E 167 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7845 (mtp180) REVERT: E 233 ILE cc_start: 0.6527 (mm) cc_final: 0.6046 (pt) REVERT: B 111 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7892 (m) REVERT: B 254 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7044 (mp) REVERT: B 625 MET cc_start: 0.7636 (mmp) cc_final: 0.7334 (mpp) REVERT: B 667 MET cc_start: 0.8613 (mtt) cc_final: 0.8041 (mtt) REVERT: B 1187 ASP cc_start: 0.7895 (t0) cc_final: 0.7402 (m-30) REVERT: B 1212 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6997 (mp) outliers start: 58 outliers final: 46 residues processed: 274 average time/residue: 1.3054 time to fit residues: 404.8441 Evaluate side-chains 270 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 217 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 78 optimal weight: 0.0050 chunk 193 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.0470 chunk 165 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.5492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.199158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.160757 restraints weight = 34959.387| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 4.64 r_work: 0.3437 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20064 Z= 0.159 Angle : 0.529 15.844 27247 Z= 0.268 Chirality : 0.043 0.165 3053 Planarity : 0.004 0.048 3393 Dihedral : 12.468 179.827 2933 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.67 % Allowed : 32.26 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2366 helix: 1.56 (0.20), residues: 717 sheet: 0.31 (0.22), residues: 551 loop : -0.77 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 379 HIS 0.002 0.001 HIS B 944 PHE 0.013 0.001 PHE D 164 TYR 0.018 0.001 TYR A 197 ARG 0.009 0.000 ARG D 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7298.29 seconds wall clock time: 127 minutes 41.00 seconds (7661.00 seconds total)