Starting phenix.real_space_refine on Thu Mar 21 10:59:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urw_42502/03_2024/8urw_42502_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urw_42502/03_2024/8urw_42502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urw_42502/03_2024/8urw_42502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urw_42502/03_2024/8urw_42502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urw_42502/03_2024/8urw_42502_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urw_42502/03_2024/8urw_42502_updated.pdb" } resolution = 2.79 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= 0.035 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 2 6.06 5 P 97 5.49 5 Mg 1 5.21 5 S 85 5.16 5 C 18400 2.51 5 N 5353 2.21 5 O 5958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 112": "OD1" <-> "OD2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 166": "OD1" <-> "OD2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "C ASP 45": "OD1" <-> "OD2" Residue "C ASP 105": "OD1" <-> "OD2" Residue "C ASP 307": "OD1" <-> "OD2" Residue "C GLU 695": "OE1" <-> "OE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C ASP 846": "OD1" <-> "OD2" Residue "C ASP 1013": "OD1" <-> "OD2" Residue "C TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 5": "OE1" <-> "OE2" Residue "D PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D ASP 164": "OD1" <-> "OD2" Residue "D ASP 231": "OD1" <-> "OD2" Residue "D PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "D ASP 416": "OD1" <-> "OD2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "D GLU 566": "OE1" <-> "OE2" Residue "D GLU 571": "OE1" <-> "OE2" Residue "D ASP 580": "OD1" <-> "OD2" Residue "E ASP 6": "OD1" <-> "OD2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E ASP 66": "OD1" <-> "OD2" Residue "E GLU 67": "OE1" <-> "OE2" Residue "Z GLU 74": "OE1" <-> "OE2" Residue "Z ASP 199": "OD1" <-> "OD2" Residue "Z GLU 266": "OE1" <-> "OE2" Residue "Z GLU 427": "OE1" <-> "OE2" Residue "Z TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 560": "OE1" <-> "OE2" Residue "Z TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 1031": "OD1" <-> "OD2" Residue "Z ASP 1120": "OD1" <-> "OD2" Residue "G GLU 132": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29896 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1738 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 216} Chain: "B" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1738 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 216} Chain: "C" Number of atoms: 8529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8529 Classifications: {'peptide': 1080} Link IDs: {'PTRANS': 61, 'TRANS': 1018} Chain: "D" Number of atoms: 4961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4961 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 32, 'TRANS': 587} Chain: "E" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 529 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "Z" Number of atoms: 9461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1235, 9461 Classifications: {'peptide': 1235} Link IDs: {'PTRANS': 46, 'TRANS': 1188} Chain: "G" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 957 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain: "N" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 825 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "T" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 815 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "R" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 311 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 9, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CTP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12545 SG CYS D 70 93.293 111.943 114.118 1.00128.39 S ATOM 12561 SG CYS D 72 92.762 114.242 116.793 1.00123.83 S ATOM 12670 SG CYS D 85 96.125 112.281 116.665 1.00129.15 S ATOM 12696 SG CYS D 88 92.929 110.499 117.687 1.00131.04 S ATOM 19221 SG CYS Z 221 97.479 47.868 86.292 1.00 73.95 S ATOM 19777 SG CYS Z 295 94.501 49.797 87.703 1.00 59.75 S ATOM 19826 SG CYS Z 302 95.949 50.640 84.234 1.00 54.28 S ATOM 19850 SG CYS Z 305 93.943 47.566 84.704 1.00 63.60 S Time building chain proxies: 16.42, per 1000 atoms: 0.55 Number of scatterers: 29896 At special positions: 0 Unit cell: (126.54, 152.19, 231.705, 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 2 29.99 S 85 16.00 P 97 15.00 Mg 1 11.99 O 5958 8.00 N 5353 7.00 C 18400 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: 11.82 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 70 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 72 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 85 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 88 " pdb=" ZN Z1401 " pdb="ZN ZN Z1401 " - pdb=" SG CYS Z 302 " pdb="ZN ZN Z1401 " - pdb=" SG CYS Z 305 " pdb="ZN ZN Z1401 " - pdb=" SG CYS Z 221 " pdb="ZN ZN Z1401 " - pdb=" SG CYS Z 295 " Number of angles added : 12 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6580 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 97 helices and 40 sheets defined 27.0% alpha, 13.0% beta 36 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 12.33 Creating SS restraints... Processing helix chain 'A' and resid 31 through 45 removed outlier: 3.632A pdb=" N ALA A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 82 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 205 through 223 Proline residue: A 222 - end of helix Processing helix chain 'B' and resid 31 through 45 removed outlier: 3.581A pdb=" N SER B 45 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 83 removed outlier: 3.969A pdb=" N GLU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 205 through 223 Proline residue: B 222 - end of helix Processing helix chain 'C' and resid 19 through 37 removed outlier: 5.234A pdb=" N LEU C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 73 Processing helix chain 'C' and resid 182 through 188 Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 203 through 213 removed outlier: 3.525A pdb=" N GLN C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 229 Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 257 through 268 Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 309 through 311 No H-bonds generated for 'chain 'C' and resid 309 through 311' Processing helix chain 'C' and resid 317 through 342 removed outlier: 3.729A pdb=" N ASN C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG C 334 " --> pdb=" O ASN C 330 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE C 335 " --> pdb=" O ARG C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 353 Processing helix chain 'C' and resid 358 through 368 Processing helix chain 'C' and resid 381 through 389 removed outlier: 3.639A pdb=" N LYS C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 527 through 530 removed outlier: 3.503A pdb=" N LEU C 530 " --> pdb=" O ALA C 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 527 through 530' Processing helix chain 'C' and resid 534 through 536 No H-bonds generated for 'chain 'C' and resid 534 through 536' Processing helix chain 'C' and resid 539 through 551 removed outlier: 3.886A pdb=" N ARG C 550 " --> pdb=" O SER C 546 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN C 551 " --> pdb=" O ASN C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 575 removed outlier: 4.102A pdb=" N SER C 575 " --> pdb=" O ALA C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 680 No H-bonds generated for 'chain 'C' and resid 677 through 680' Processing helix chain 'C' and resid 715 through 717 No H-bonds generated for 'chain 'C' and resid 715 through 717' Processing helix chain 'C' and resid 753 through 762 Processing helix chain 'C' and resid 856 through 862 Proline residue: C 860 - end of helix Processing helix chain 'C' and resid 866 through 880 removed outlier: 3.699A pdb=" N ALA C 876 " --> pdb=" O MET C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 893 removed outlier: 3.679A pdb=" N TYR C 893 " --> pdb=" O ASP C 890 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 890 through 893' Processing helix chain 'C' and resid 897 through 913 Processing helix chain 'C' and resid 916 through 918 No H-bonds generated for 'chain 'C' and resid 916 through 918' Processing helix chain 'C' and resid 956 through 958 No H-bonds generated for 'chain 'C' and resid 956 through 958' Processing helix chain 'C' and resid 979 through 981 No H-bonds generated for 'chain 'C' and resid 979 through 981' Processing helix chain 'C' and resid 989 through 998 Processing helix chain 'C' and resid 1001 through 1008 Processing helix chain 'C' and resid 1017 through 1027 Processing helix chain 'C' and resid 1038 through 1050 removed outlier: 3.709A pdb=" N LEU C1050 " --> pdb=" O GLU C1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 24 Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 132 through 138 Processing helix chain 'D' and resid 163 through 175 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 201 through 213 removed outlier: 4.172A pdb=" N ALA D 213 " --> pdb=" O ARG D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 235 removed outlier: 3.632A pdb=" N LEU D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 243 removed outlier: 3.690A pdb=" N MET D 243 " --> pdb=" O PRO D 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 240 through 243' Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 270 through 290 Processing helix chain 'D' and resid 298 through 313 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 343 through 347 Processing helix chain 'D' and resid 376 through 382 removed outlier: 3.748A pdb=" N GLU D 381 " --> pdb=" O GLU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 393 Processing helix chain 'D' and resid 400 through 409 Processing helix chain 'D' and resid 412 through 421 removed outlier: 3.595A pdb=" N GLU D 419 " --> pdb=" O ASP D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 439 No H-bonds generated for 'chain 'D' and resid 437 through 439' Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.600A pdb=" N CYS D 460 " --> pdb=" O PRO D 457 " (cutoff:3.500A) Proline residue: D 461 - end of helix No H-bonds generated for 'chain 'D' and resid 457 through 463' Processing helix chain 'D' and resid 480 through 489 Processing helix chain 'D' and resid 511 through 519 Processing helix chain 'D' and resid 538 through 545 Processing helix chain 'D' and resid 609 through 622 Processing helix chain 'E' and resid 9 through 21 Processing helix chain 'E' and resid 26 through 46 Processing helix chain 'E' and resid 56 through 68 removed outlier: 3.633A pdb=" N LEU E 68 " --> pdb=" O MET E 64 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 30 Processing helix chain 'Z' and resid 35 through 54 removed outlier: 3.968A pdb=" N THR Z 52 " --> pdb=" O PHE Z 48 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG Z 53 " --> pdb=" O ARG Z 49 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA Z 54 " --> pdb=" O TYR Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 69 through 89 Processing helix chain 'Z' and resid 94 through 123 Processing helix chain 'Z' and resid 128 through 134 Processing helix chain 'Z' and resid 141 through 148 removed outlier: 3.791A pdb=" N GLN Z 146 " --> pdb=" O SER Z 142 " (cutoff:3.500A) Processing helix chain 'Z' and resid 176 through 193 removed outlier: 3.920A pdb=" N TYR Z 184 " --> pdb=" O ILE Z 180 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY Z 185 " --> pdb=" O ILE Z 181 " (cutoff:3.500A) Processing helix chain 'Z' and resid 197 through 210 Processing helix chain 'Z' and resid 242 through 245 No H-bonds generated for 'chain 'Z' and resid 242 through 245' Processing helix chain 'Z' and resid 273 through 281 Processing helix chain 'Z' and resid 292 through 294 No H-bonds generated for 'chain 'Z' and resid 292 through 294' Processing helix chain 'Z' and resid 303 through 306 No H-bonds generated for 'chain 'Z' and resid 303 through 306' Processing helix chain 'Z' and resid 322 through 344 removed outlier: 3.810A pdb=" N GLU Z 332 " --> pdb=" O GLN Z 328 " (cutoff:3.500A) Proline residue: Z 333 - end of helix removed outlier: 3.630A pdb=" N MET Z 339 " --> pdb=" O THR Z 335 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG Z 340 " --> pdb=" O GLN Z 336 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR Z 341 " --> pdb=" O LEU Z 337 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N PHE Z 342 " --> pdb=" O THR Z 338 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS Z 343 " --> pdb=" O MET Z 339 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR Z 344 " --> pdb=" O ARG Z 340 " (cutoff:3.500A) Processing helix chain 'Z' and resid 991 through 993 No H-bonds generated for 'chain 'Z' and resid 991 through 993' Processing helix chain 'Z' and resid 995 through 1003 Processing helix chain 'Z' and resid 1026 through 1028 No H-bonds generated for 'chain 'Z' and resid 1026 through 1028' Processing helix chain 'Z' and resid 1073 through 1087 removed outlier: 3.723A pdb=" N LEU Z1077 " --> pdb=" O PRO Z1073 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU Z1078 " --> pdb=" O HIS Z1074 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1092 through 1116 Processing helix chain 'Z' and resid 1123 through 1133 removed outlier: 3.881A pdb=" N GLN Z1132 " --> pdb=" O VAL Z1128 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N MET Z1133 " --> pdb=" O ILE Z1129 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1155 through 1167 removed outlier: 3.712A pdb=" N LEU Z1167 " --> pdb=" O ASN Z1163 " (cutoff:3.500A) Processing helix chain 'Z' and resid 1182 through 1186 removed outlier: 3.792A pdb=" N SER Z1186 " --> pdb=" O ILE Z1182 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 1182 through 1186' Processing helix chain 'Z' and resid 1192 through 1196 Processing helix chain 'Z' and resid 1201 through 1211 Processing helix chain 'Z' and resid 1223 through 1226 No H-bonds generated for 'chain 'Z' and resid 1223 through 1226' Processing helix chain 'Z' and resid 1233 through 1235 No H-bonds generated for 'chain 'Z' and resid 1233 through 1235' Processing helix chain 'G' and resid 33 through 46 Processing helix chain 'G' and resid 92 through 99 Processing helix chain 'G' and resid 130 through 136 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 12 removed outlier: 6.840A pdb=" N ARG A 21 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER A 10 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TYR A 19 " --> pdb=" O SER A 10 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 86 through 88 Processing sheet with id= C, first strand: chain 'A' and resid 94 through 101 removed outlier: 3.923A pdb=" N GLN A 94 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 141 " --> pdb=" O GLN A 94 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 54 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU A 142 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL A 52 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY A 144 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR A 50 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 146 through 148 Processing sheet with id= E, first strand: chain 'A' and resid 104 through 107 Processing sheet with id= F, first strand: chain 'B' and resid 4 through 7 Processing sheet with id= G, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.509A pdb=" N ARG B 11 " --> pdb=" O TYR B 19 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 95 through 101 removed outlier: 4.705A pdb=" N GLU B 136 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 54 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU B 142 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL B 52 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY B 144 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N THR B 50 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 146 through 148 Processing sheet with id= J, first strand: chain 'B' and resid 105 through 107 removed outlier: 3.829A pdb=" N ALA B 127 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 52 through 54 Processing sheet with id= L, first strand: chain 'C' and resid 115 through 117 Processing sheet with id= M, first strand: chain 'C' and resid 127 through 130 Processing sheet with id= N, first strand: chain 'C' and resid 133 through 139 removed outlier: 4.616A pdb=" N HIS C 148 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 390 through 392 Processing sheet with id= P, first strand: chain 'C' and resid 467 through 469 Processing sheet with id= Q, first strand: chain 'C' and resid 497 through 501 Processing sheet with id= R, first strand: chain 'C' and resid 604 through 608 removed outlier: 3.779A pdb=" N TYR C 589 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR C 598 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE C 587 " --> pdb=" O THR C 598 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 943 through 949 removed outlier: 4.316A pdb=" N THR C 943 " --> pdb=" O TYR C 660 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE C 852 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 743 through 745 Processing sheet with id= U, first strand: chain 'C' and resid 821 through 823 removed outlier: 7.753A pdb=" N ILE C 674 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE C 835 " --> pdb=" O ILE C 674 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 79 through 85 removed outlier: 4.031A pdb=" N GLY C 104 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL C 84 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE C 102 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 686 through 697 removed outlier: 3.658A pdb=" N MET C 804 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP C 786 " --> pdb=" O TYR C 809 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA C 811 " --> pdb=" O VAL C 784 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL C 784 " --> pdb=" O ALA C 811 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= Y, first strand: chain 'D' and resid 356 through 360 Processing sheet with id= Z, first strand: chain 'D' and resid 361 through 363 removed outlier: 6.023A pdb=" N ILE D 453 " --> pdb=" O VAL D 362 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'D' and resid 555 through 558 removed outlier: 6.833A pdb=" N ARG D 593 " --> pdb=" O LEU D 601 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN D 603 " --> pdb=" O ARG D 591 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG D 591 " --> pdb=" O GLN D 603 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR D 582 " --> pdb=" O ALA D 578 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 227 through 229 Processing sheet with id= AC, first strand: chain 'Z' and resid 372 through 376 Processing sheet with id= AD, first strand: chain 'Z' and resid 390 through 395 Processing sheet with id= AE, first strand: chain 'Z' and resid 451 through 455 Processing sheet with id= AF, first strand: chain 'Z' and resid 486 through 489 Processing sheet with id= AG, first strand: chain 'Z' and resid 903 through 906 removed outlier: 3.648A pdb=" N ALA Z 942 " --> pdb=" O GLN Z 949 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG Z 951 " --> pdb=" O VAL Z 940 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL Z 940 " --> pdb=" O ARG Z 951 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'Z' and resid 1152 through 1154 Processing sheet with id= AI, first strand: chain 'Z' and resid 232 through 234 removed outlier: 6.466A pdb=" N ASP Z 234 " --> pdb=" O ILE Z 238 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILE Z 238 " --> pdb=" O ASP Z 234 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Z' and resid 354 through 357 removed outlier: 3.615A pdb=" N ALA Z 426 " --> pdb=" O LEU Z 356 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'Z' and resid 441 through 446 removed outlier: 3.709A pdb=" N VAL Z 979 " --> pdb=" O VAL Z 445 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'Z' and resid 459 through 464 removed outlier: 3.533A pdb=" N ARG Z 476 " --> pdb=" O VAL Z 459 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU Z 461 " --> pdb=" O ALA Z 474 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ALA Z 474 " --> pdb=" O GLU Z 461 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS Z 463 " --> pdb=" O ARG Z 472 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ARG Z 472 " --> pdb=" O LYS Z 463 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 104 through 107 removed outlier: 7.110A pdb=" N GLN G 27 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N PHE G 107 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA G 25 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN G 55 " --> pdb=" O ARG G 87 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 60 through 63 799 hydrogen bonds defined for protein. 2250 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 11.33 Time building geometry restraints manager: 12.81 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: 8816 1.33 - 1.45: 4895 1.45 - 1.57: 16553 1.57 - 1.70: 190 1.70 - 1.82: 142 Bond restraints: 30596 Sorted by residual: bond pdb=" C5 CTP R 101 " pdb=" C6 CTP R 101 " ideal model delta sigma weight residual 1.390 1.340 0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" C4 CTP R 101 " pdb=" N3 CTP R 101 " ideal model delta sigma weight residual 1.380 1.337 0.043 2.00e-02 2.50e+03 4.71e+00 bond pdb=" C4' CTP R 101 " pdb=" O4' CTP R 101 " ideal model delta sigma weight residual 1.410 1.452 -0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" C5' CTP R 101 " pdb=" O5' CTP R 101 " ideal model delta sigma weight residual 1.410 1.446 -0.036 2.00e-02 2.50e+03 3.21e+00 bond pdb=" CB GLU D 571 " pdb=" CG GLU D 571 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.26e+00 ... (remaining 30591 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.85: 1085 105.85 - 112.89: 16581 112.89 - 119.94: 10432 119.94 - 126.98: 13257 126.98 - 134.03: 521 Bond angle restraints: 41876 Sorted by residual: angle pdb=" N VAL Z 588 " pdb=" CA VAL Z 588 " pdb=" C VAL Z 588 " ideal model delta sigma weight residual 113.71 108.95 4.76 9.50e-01 1.11e+00 2.51e+01 angle pdb=" PB CTP R 101 " pdb=" O3B CTP R 101 " pdb=" PG CTP R 101 " ideal model delta sigma weight residual 120.50 132.67 -12.17 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CA GLU D 571 " pdb=" CB GLU D 571 " pdb=" CG GLU D 571 " ideal model delta sigma weight residual 114.10 121.44 -7.34 2.00e+00 2.50e-01 1.35e+01 angle pdb=" PA CTP R 101 " pdb=" O3A CTP R 101 " pdb=" PB CTP R 101 " ideal model delta sigma weight residual 120.50 131.29 -10.79 3.00e+00 1.11e-01 1.29e+01 angle pdb=" CA TYR C 59 " pdb=" CB TYR C 59 " pdb=" CG TYR C 59 " ideal model delta sigma weight residual 113.90 120.28 -6.38 1.80e+00 3.09e-01 1.26e+01 ... (remaining 41871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.80: 16875 32.80 - 65.60: 1449 65.60 - 98.40: 95 98.40 - 131.19: 2 131.19 - 163.99: 4 Dihedral angle restraints: 18425 sinusoidal: 8185 harmonic: 10240 Sorted by residual: dihedral pdb=" O3B CTP R 101 " pdb=" O3A CTP R 101 " pdb=" PB CTP R 101 " pdb=" PA CTP R 101 " ideal model delta sinusoidal sigma weight residual -39.29 124.70 -163.99 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O1G CTP R 101 " pdb=" O3B CTP R 101 " pdb=" PG CTP R 101 " pdb=" PB CTP R 101 " ideal model delta sinusoidal sigma weight residual 82.72 -136.16 -141.12 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" CA ILE D 120 " pdb=" C ILE D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual 180.00 153.06 26.94 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 18422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3557 0.042 - 0.084: 814 0.084 - 0.126: 364 0.126 - 0.168: 25 0.168 - 0.210: 4 Chirality restraints: 4764 Sorted by residual: chirality pdb=" C2' CTP R 101 " pdb=" C1' CTP R 101 " pdb=" C3' CTP R 101 " pdb=" O2' CTP R 101 " both_signs ideal model delta sigma weight residual False -2.47 -2.68 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO Z1017 " pdb=" N PRO Z1017 " pdb=" C PRO Z1017 " pdb=" CB PRO Z1017 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" C3' CTP R 101 " pdb=" C2' CTP R 101 " pdb=" C4' CTP R 101 " pdb=" O3' CTP R 101 " both_signs ideal model delta sigma weight residual False -2.47 -2.65 0.18 2.00e-01 2.50e+01 8.30e-01 ... (remaining 4761 not shown) Planarity restraints: 5181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG Z1016 " -0.056 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO Z1017 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO Z1017 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO Z1017 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 571 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.47e+00 pdb=" CD GLU D 571 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU D 571 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU D 571 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 580 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" CG ASP D 580 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP D 580 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP D 580 " -0.013 2.00e-02 2.50e+03 ... (remaining 5178 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4271 2.76 - 3.30: 25329 3.30 - 3.83: 46574 3.83 - 4.37: 53626 4.37 - 4.90: 95099 Nonbonded interactions: 224899 Sorted by model distance: nonbonded pdb="MG MG D 701 " pdb=" O1A CTP R 101 " model vdw 2.226 2.170 nonbonded pdb=" O SER C 131 " pdb=" OH TYR C 135 " model vdw 2.235 2.440 nonbonded pdb=" NH2 ARG A 41 " pdb=" OD1 ASP C 840 " model vdw 2.236 2.520 nonbonded pdb=" OE2 GLU C 333 " pdb=" NH2 ARG C 337 " model vdw 2.244 2.520 nonbonded pdb=" NH1 ARG C 614 " pdb=" OD1 ASP C 618 " model vdw 2.246 2.520 ... (remaining 224894 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 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: 0.030 Extract box with map and model: 14.970 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 89.910 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 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 0.062 30596 Z= 0.171 Angle : 0.562 12.175 41876 Z= 0.297 Chirality : 0.042 0.210 4764 Planarity : 0.004 0.085 5181 Dihedral : 20.954 163.992 11845 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.12 % Favored : 93.54 % Rotamer: Outliers : 4.41 % Allowed : 31.97 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.96 (0.14), residues: 3560 helix: 1.63 (0.17), residues: 951 sheet: 0.16 (0.22), residues: 536 loop : -2.10 (0.12), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 875 HIS 0.003 0.000 HIS A 62 PHE 0.014 0.001 PHE A 169 TYR 0.016 0.001 TYR B 125 ARG 0.010 0.000 ARG C 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 227 time to evaluate : 3.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7387 (ttm170) cc_final: 0.6838 (ttm170) REVERT: C 45 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7700 (p0) REVERT: C 63 ARG cc_start: 0.5901 (tpt170) cc_final: 0.5446 (mmp-170) REVERT: C 99 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: C 302 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8739 (mp0) REVERT: C 333 GLU cc_start: 0.8678 (tt0) cc_final: 0.8396 (tm-30) REVERT: C 403 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.7979 (ttt90) REVERT: Z 466 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7802 (ptt90) REVERT: Z 633 TRP cc_start: 0.1701 (OUTLIER) cc_final: 0.0291 (t-100) REVERT: G 42 GLN cc_start: 0.9290 (tm-30) cc_final: 0.9085 (tm-30) REVERT: G 46 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8832 (t) outliers start: 133 outliers final: 97 residues processed: 354 average time/residue: 1.3325 time to fit residues: 557.4471 Evaluate side-chains 298 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 196 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 1012 SER Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 168 THR Chi-restraints excluded: chain Z residue 200 SER Chi-restraints excluded: chain Z residue 270 ASP Chi-restraints excluded: chain Z residue 300 SER Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 341 THR Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain Z residue 389 ASN Chi-restraints excluded: chain Z residue 410 THR Chi-restraints excluded: chain Z residue 437 THR Chi-restraints excluded: chain Z residue 448 ASP Chi-restraints excluded: chain Z residue 498 VAL Chi-restraints excluded: chain Z residue 533 THR Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 633 TRP Chi-restraints excluded: chain Z residue 645 ILE Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 684 ARG Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 717 VAL Chi-restraints excluded: chain Z residue 756 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 797 THR Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 1028 ASP Chi-restraints excluded: chain Z residue 1040 THR Chi-restraints excluded: chain Z residue 1055 SER Chi-restraints excluded: chain Z residue 1091 ASP Chi-restraints excluded: chain Z residue 1098 SER Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1123 ASP Chi-restraints excluded: chain Z residue 1145 THR Chi-restraints excluded: chain Z residue 1161 SER Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1183 THR Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 116 TYR Chi-restraints excluded: chain G residue 129 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 10.0000 chunk 275 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 94 optimal weight: 0.0970 chunk 186 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 285 optimal weight: 50.0000 chunk 110 optimal weight: 0.0970 chunk 173 optimal weight: 0.0370 chunk 212 optimal weight: 3.9990 chunk 330 optimal weight: 2.9990 overall best weight: 0.8456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN C 712 ASN C 826 HIS D 260 GLN D 398 ASN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN Z1199 GLN G 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30596 Z= 0.164 Angle : 0.517 7.697 41876 Z= 0.270 Chirality : 0.042 0.182 4764 Planarity : 0.004 0.090 5181 Dihedral : 16.162 161.804 5143 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.35 % Favored : 93.31 % Rotamer: Outliers : 5.17 % Allowed : 30.38 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.74 (0.14), residues: 3560 helix: 1.91 (0.17), residues: 959 sheet: 0.14 (0.22), residues: 564 loop : -2.01 (0.12), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 875 HIS 0.007 0.001 HIS Z 852 PHE 0.011 0.001 PHE D 266 TYR 0.011 0.001 TYR C 680 ARG 0.011 0.000 ARG Z 535 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 204 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8101 (tpp-160) cc_final: 0.7711 (tpm170) REVERT: A 183 ARG cc_start: 0.7562 (ttm170) cc_final: 0.7144 (ttm170) REVERT: A 191 ASP cc_start: 0.8244 (m-30) cc_final: 0.7831 (m-30) REVERT: C 63 ARG cc_start: 0.5810 (tpt170) cc_final: 0.5296 (mmp-170) REVERT: C 302 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8747 (mp0) REVERT: C 778 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8550 (m-40) REVERT: D 580 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7276 (p0) REVERT: Z 466 ARG cc_start: 0.8377 (ttp80) cc_final: 0.7845 (ptt90) REVERT: Z 508 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8190 (m-30) REVERT: Z 990 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7734 (p0) REVERT: Z 1146 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8846 (pp) outliers start: 156 outliers final: 73 residues processed: 345 average time/residue: 1.2687 time to fit residues: 523.3078 Evaluate side-chains 270 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 192 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 712 ASN Chi-restraints excluded: chain C residue 727 ILE Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 778 ASN Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 168 THR Chi-restraints excluded: chain Z residue 199 ASP Chi-restraints excluded: chain Z residue 270 ASP Chi-restraints excluded: chain Z residue 389 ASN Chi-restraints excluded: chain Z residue 437 THR Chi-restraints excluded: chain Z residue 444 ASP Chi-restraints excluded: chain Z residue 498 VAL Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 508 ASP Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 645 ILE Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 717 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 906 LEU Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 990 ASP Chi-restraints excluded: chain Z residue 1040 THR Chi-restraints excluded: chain Z residue 1067 THR Chi-restraints excluded: chain Z residue 1091 ASP Chi-restraints excluded: chain Z residue 1098 SER Chi-restraints excluded: chain Z residue 1145 THR Chi-restraints excluded: chain Z residue 1146 ILE Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 90 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 7.9990 chunk 102 optimal weight: 0.2980 chunk 275 optimal weight: 0.2980 chunk 225 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 331 optimal weight: 0.9980 chunk 357 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 328 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 265 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 712 ASN D 398 ASN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 30596 Z= 0.153 Angle : 0.501 7.322 41876 Z= 0.261 Chirality : 0.041 0.177 4764 Planarity : 0.004 0.093 5181 Dihedral : 15.869 161.495 5054 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.29 % Favored : 93.40 % Rotamer: Outliers : 4.11 % Allowed : 31.41 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.62 (0.14), residues: 3560 helix: 2.05 (0.18), residues: 957 sheet: 0.24 (0.22), residues: 553 loop : -1.95 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 875 HIS 0.010 0.000 HIS D 80 PHE 0.011 0.001 PHE B 64 TYR 0.015 0.001 TYR E 42 ARG 0.007 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 201 time to evaluate : 3.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.8070 (tpp-160) cc_final: 0.7693 (tpm170) REVERT: A 183 ARG cc_start: 0.7567 (ttm170) cc_final: 0.7337 (ttm170) REVERT: A 191 ASP cc_start: 0.8194 (m-30) cc_final: 0.7804 (m-30) REVERT: B 73 ASP cc_start: 0.8646 (p0) cc_final: 0.8337 (p0) REVERT: C 63 ARG cc_start: 0.5478 (tpt170) cc_final: 0.4956 (mmp-170) REVERT: C 302 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8753 (mp0) REVERT: C 778 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8517 (m-40) REVERT: D 580 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7285 (p0) REVERT: Z 466 ARG cc_start: 0.8423 (ttp80) cc_final: 0.8071 (ptt90) REVERT: Z 467 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8510 (mm-40) REVERT: Z 809 GLN cc_start: 0.5869 (OUTLIER) cc_final: 0.5281 (pp30) REVERT: Z 990 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7831 (p0) outliers start: 124 outliers final: 71 residues processed: 309 average time/residue: 1.2390 time to fit residues: 461.3033 Evaluate side-chains 266 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 191 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 626 ILE Chi-restraints excluded: chain C residue 727 ILE Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 778 ASN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 16 ASP Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 168 THR Chi-restraints excluded: chain Z residue 270 ASP Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 320 GLU Chi-restraints excluded: chain Z residue 389 ASN Chi-restraints excluded: chain Z residue 437 THR Chi-restraints excluded: chain Z residue 448 ASP Chi-restraints excluded: chain Z residue 498 VAL Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 574 LEU Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 645 ILE Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 717 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 809 GLN Chi-restraints excluded: chain Z residue 906 LEU Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 990 ASP Chi-restraints excluded: chain Z residue 1040 THR Chi-restraints excluded: chain Z residue 1067 THR Chi-restraints excluded: chain Z residue 1091 ASP Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1189 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 57 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 36 optimal weight: 0.1980 chunk 158 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 332 optimal weight: 1.9990 chunk 351 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 chunk 314 optimal weight: 2.9990 chunk 94 optimal weight: 0.0270 overall best weight: 1.6444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 398 ASN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 GLN G 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30596 Z= 0.230 Angle : 0.523 7.427 41876 Z= 0.274 Chirality : 0.042 0.182 4764 Planarity : 0.004 0.093 5181 Dihedral : 15.808 161.483 5039 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.66 % Favored : 93.03 % Rotamer: Outliers : 4.57 % Allowed : 31.31 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.69 (0.14), residues: 3560 helix: 2.02 (0.18), residues: 957 sheet: 0.15 (0.21), residues: 566 loop : -2.00 (0.12), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 875 HIS 0.004 0.001 HIS D 80 PHE 0.015 0.001 PHE A 169 TYR 0.015 0.001 TYR C 680 ARG 0.007 0.000 ARG Z 535 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 199 time to evaluate : 3.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7217 (ttm170) REVERT: B 73 ASP cc_start: 0.8651 (p0) cc_final: 0.8331 (p0) REVERT: B 112 ASP cc_start: 0.7754 (p0) cc_final: 0.7333 (p0) REVERT: C 40 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7397 (p90) REVERT: C 63 ARG cc_start: 0.5324 (tpt170) cc_final: 0.4974 (mmp-170) REVERT: C 302 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8761 (mp0) REVERT: C 333 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8341 (tm-30) REVERT: C 746 LYS cc_start: 0.8336 (mttt) cc_final: 0.8120 (pttt) REVERT: D 210 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8850 (tm-30) REVERT: D 320 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7918 (ppt170) REVERT: D 419 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8413 (tm-30) REVERT: D 580 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7312 (p0) REVERT: Z 249 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.8148 (mmt180) REVERT: Z 466 ARG cc_start: 0.8442 (ttp80) cc_final: 0.8088 (ptt90) REVERT: Z 467 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8532 (mm-40) REVERT: Z 525 MET cc_start: 0.7109 (mmm) cc_final: 0.6785 (mpm) REVERT: Z 809 GLN cc_start: 0.5828 (OUTLIER) cc_final: 0.5205 (pp30) REVERT: Z 852 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.7562 (p90) REVERT: Z 990 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8010 (p0) REVERT: G 132 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8168 (mt-10) outliers start: 138 outliers final: 71 residues processed: 316 average time/residue: 1.2748 time to fit residues: 486.1843 Evaluate side-chains 271 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 190 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 727 ILE Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 249 ARG Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 320 GLU Chi-restraints excluded: chain Z residue 389 ASN Chi-restraints excluded: chain Z residue 437 THR Chi-restraints excluded: chain Z residue 444 ASP Chi-restraints excluded: chain Z residue 498 VAL Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 574 LEU Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 645 ILE Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 717 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 797 THR Chi-restraints excluded: chain Z residue 809 GLN Chi-restraints excluded: chain Z residue 852 HIS Chi-restraints excluded: chain Z residue 906 LEU Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 990 ASP Chi-restraints excluded: chain Z residue 1067 THR Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1144 ASP Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1189 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 57 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 8.9990 chunk 199 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 243 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 315 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 398 ASN Z1033 GLN Z1041 GLN G 45 GLN G 112 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 30596 Z= 0.421 Angle : 0.609 10.690 41876 Z= 0.320 Chirality : 0.046 0.192 4764 Planarity : 0.005 0.092 5181 Dihedral : 16.016 166.208 5029 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.36 % Favored : 92.36 % Rotamer: Outliers : 5.00 % Allowed : 30.95 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.96 (0.14), residues: 3560 helix: 1.77 (0.17), residues: 954 sheet: -0.01 (0.21), residues: 560 loop : -2.15 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 875 HIS 0.005 0.001 HIS D 100 PHE 0.023 0.002 PHE A 169 TYR 0.020 0.002 TYR C 680 ARG 0.026 0.000 ARG Z1016 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 191 time to evaluate : 3.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7274 (ttm170) REVERT: B 73 ASP cc_start: 0.8664 (p0) cc_final: 0.8431 (p0) REVERT: B 112 ASP cc_start: 0.7825 (p0) cc_final: 0.7416 (p0) REVERT: C 40 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7623 (p90) REVERT: C 63 ARG cc_start: 0.5272 (tpt170) cc_final: 0.4723 (mmp-170) REVERT: C 302 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8728 (mp0) REVERT: C 333 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: C 512 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7953 (mtm-85) REVERT: C 746 LYS cc_start: 0.8393 (mttt) cc_final: 0.8152 (pttt) REVERT: C 778 ASN cc_start: 0.8828 (m-40) cc_final: 0.8617 (m-40) REVERT: D 256 ARG cc_start: 0.9534 (OUTLIER) cc_final: 0.7927 (ptt90) REVERT: D 320 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7926 (ppt170) REVERT: D 419 GLU cc_start: 0.8754 (tt0) cc_final: 0.8440 (tm-30) REVERT: D 580 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7622 (p0) REVERT: Z 171 ARG cc_start: 0.9439 (OUTLIER) cc_final: 0.8637 (ttt180) REVERT: Z 249 ARG cc_start: 0.9380 (OUTLIER) cc_final: 0.8316 (mmt180) REVERT: Z 290 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8353 (mtt180) REVERT: Z 466 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8071 (ptt90) REVERT: Z 467 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8527 (mm-40) REVERT: Z 525 MET cc_start: 0.7197 (mmm) cc_final: 0.6831 (mpm) REVERT: Z 809 GLN cc_start: 0.5759 (OUTLIER) cc_final: 0.5206 (pp30) REVERT: Z 852 HIS cc_start: 0.8019 (OUTLIER) cc_final: 0.7644 (p90) REVERT: Z 864 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8694 (mppt) REVERT: Z 990 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8320 (p0) REVERT: Z 1146 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8869 (pp) outliers start: 151 outliers final: 77 residues processed: 321 average time/residue: 1.3641 time to fit residues: 521.0995 Evaluate side-chains 279 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 187 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 61 ASP Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 171 ARG Chi-restraints excluded: chain Z residue 249 ARG Chi-restraints excluded: chain Z residue 290 ARG Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 320 GLU Chi-restraints excluded: chain Z residue 389 ASN Chi-restraints excluded: chain Z residue 402 THR Chi-restraints excluded: chain Z residue 437 THR Chi-restraints excluded: chain Z residue 498 VAL Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 574 LEU Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 623 TYR Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 797 THR Chi-restraints excluded: chain Z residue 809 GLN Chi-restraints excluded: chain Z residue 852 HIS Chi-restraints excluded: chain Z residue 855 LEU Chi-restraints excluded: chain Z residue 864 LYS Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 990 ASP Chi-restraints excluded: chain Z residue 1067 THR Chi-restraints excluded: chain Z residue 1091 ASP Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1144 ASP Chi-restraints excluded: chain Z residue 1145 THR Chi-restraints excluded: chain Z residue 1146 ILE Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1183 THR Chi-restraints excluded: chain Z residue 1189 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 90 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 0.0980 chunk 316 optimal weight: 0.0570 chunk 69 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 352 optimal weight: 9.9990 chunk 292 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 398 ASN Z1033 GLN G 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30596 Z= 0.216 Angle : 0.539 9.965 41876 Z= 0.282 Chirality : 0.042 0.205 4764 Planarity : 0.004 0.084 5181 Dihedral : 15.885 177.839 5025 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.57 % Favored : 93.15 % Rotamer: Outliers : 4.21 % Allowed : 31.74 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.85 (0.14), residues: 3560 helix: 1.90 (0.17), residues: 952 sheet: -0.01 (0.21), residues: 576 loop : -2.09 (0.12), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 875 HIS 0.003 0.001 HIS D 80 PHE 0.017 0.001 PHE A 169 TYR 0.013 0.001 TYR B 125 ARG 0.015 0.000 ARG Z1016 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 192 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7775 (tpm170) cc_final: 0.7535 (tpm170) REVERT: A 73 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8434 (p0) REVERT: A 183 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7291 (ttm170) REVERT: B 73 ASP cc_start: 0.8619 (p0) cc_final: 0.8345 (p0) REVERT: B 112 ASP cc_start: 0.7842 (p0) cc_final: 0.7489 (p0) REVERT: C 63 ARG cc_start: 0.5258 (tpt170) cc_final: 0.4626 (mmp-170) REVERT: C 302 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8778 (mp0) REVERT: C 333 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8366 (tm-30) REVERT: C 778 ASN cc_start: 0.8804 (m-40) cc_final: 0.8587 (m-40) REVERT: D 210 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8877 (tm-30) REVERT: D 256 ARG cc_start: 0.9517 (OUTLIER) cc_final: 0.7781 (ptt90) REVERT: D 320 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7897 (ppt170) REVERT: D 419 GLU cc_start: 0.8741 (tt0) cc_final: 0.8409 (tm-30) REVERT: D 580 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7529 (p0) REVERT: Z 120 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8079 (t80) REVERT: Z 249 ARG cc_start: 0.9344 (OUTLIER) cc_final: 0.8270 (mmt180) REVERT: Z 466 ARG cc_start: 0.8431 (ttp80) cc_final: 0.8016 (ptt90) REVERT: Z 525 MET cc_start: 0.7189 (mmm) cc_final: 0.6842 (mpm) REVERT: Z 809 GLN cc_start: 0.5754 (OUTLIER) cc_final: 0.5201 (pp30) REVERT: Z 852 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.7664 (p90) REVERT: Z 864 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8672 (mppt) outliers start: 127 outliers final: 78 residues processed: 300 average time/residue: 1.3224 time to fit residues: 471.5984 Evaluate side-chains 275 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 185 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 727 ILE Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 61 ASP Chi-restraints excluded: chain Z residue 120 PHE Chi-restraints excluded: chain Z residue 168 THR Chi-restraints excluded: chain Z residue 249 ARG Chi-restraints excluded: chain Z residue 270 ASP Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 320 GLU Chi-restraints excluded: chain Z residue 389 ASN Chi-restraints excluded: chain Z residue 402 THR Chi-restraints excluded: chain Z residue 410 THR Chi-restraints excluded: chain Z residue 498 VAL Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 574 LEU Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 717 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 797 THR Chi-restraints excluded: chain Z residue 809 GLN Chi-restraints excluded: chain Z residue 852 HIS Chi-restraints excluded: chain Z residue 855 LEU Chi-restraints excluded: chain Z residue 864 LYS Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 1040 THR Chi-restraints excluded: chain Z residue 1067 THR Chi-restraints excluded: chain Z residue 1091 ASP Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1144 ASP Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1189 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 90 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 257 optimal weight: 0.7980 chunk 199 optimal weight: 4.9990 chunk 296 optimal weight: 50.0000 chunk 196 optimal weight: 0.9990 chunk 350 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 398 ASN ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 30596 Z= 0.191 Angle : 0.529 9.757 41876 Z= 0.276 Chirality : 0.042 0.199 4764 Planarity : 0.004 0.081 5181 Dihedral : 15.721 160.304 5024 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.46 % Favored : 93.26 % Rotamer: Outliers : 3.91 % Allowed : 32.21 % Favored : 63.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.75 (0.14), residues: 3560 helix: 1.97 (0.18), residues: 955 sheet: 0.04 (0.21), residues: 576 loop : -2.03 (0.12), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 875 HIS 0.002 0.000 HIS D 80 PHE 0.017 0.001 PHE A 169 TYR 0.016 0.001 TYR B 125 ARG 0.006 0.000 ARG Z 535 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 191 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8513 (p0) REVERT: A 183 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7248 (ttm170) REVERT: B 73 ASP cc_start: 0.8582 (p0) cc_final: 0.8316 (p0) REVERT: B 112 ASP cc_start: 0.7840 (p0) cc_final: 0.7452 (p0) REVERT: C 63 ARG cc_start: 0.5157 (tpt170) cc_final: 0.4596 (mmp-170) REVERT: D 210 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8875 (tm-30) REVERT: D 320 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7908 (ppt170) REVERT: D 419 GLU cc_start: 0.8736 (tt0) cc_final: 0.8398 (tm-30) REVERT: D 580 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7474 (p0) REVERT: Z 467 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8547 (mm-40) REVERT: Z 809 GLN cc_start: 0.5774 (OUTLIER) cc_final: 0.5220 (pp30) outliers start: 118 outliers final: 74 residues processed: 295 average time/residue: 1.3052 time to fit residues: 459.5291 Evaluate side-chains 267 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 187 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 727 ILE Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 168 THR Chi-restraints excluded: chain Z residue 270 ASP Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 320 GLU Chi-restraints excluded: chain Z residue 389 ASN Chi-restraints excluded: chain Z residue 402 THR Chi-restraints excluded: chain Z residue 410 THR Chi-restraints excluded: chain Z residue 444 ASP Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 574 LEU Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 682 ILE Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 717 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 797 THR Chi-restraints excluded: chain Z residue 809 GLN Chi-restraints excluded: chain Z residue 855 LEU Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 1040 THR Chi-restraints excluded: chain Z residue 1067 THR Chi-restraints excluded: chain Z residue 1091 ASP Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1144 ASP Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1189 THR Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 209 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 239 optimal weight: 0.7980 chunk 173 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 275 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 398 ASN ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1033 GLN G 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30596 Z= 0.239 Angle : 0.552 9.584 41876 Z= 0.288 Chirality : 0.043 0.202 4764 Planarity : 0.004 0.077 5181 Dihedral : 15.673 160.383 5021 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.69 % Favored : 93.06 % Rotamer: Outliers : 3.71 % Allowed : 32.74 % Favored : 63.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.79 (0.14), residues: 3560 helix: 1.95 (0.17), residues: 954 sheet: 0.03 (0.21), residues: 564 loop : -2.05 (0.12), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 875 HIS 0.003 0.001 HIS D 395 PHE 0.018 0.001 PHE A 169 TYR 0.017 0.001 TYR B 125 ARG 0.006 0.000 ARG Z 535 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 189 time to evaluate : 3.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8507 (p0) REVERT: A 183 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7236 (ttm170) REVERT: B 73 ASP cc_start: 0.8591 (p0) cc_final: 0.8329 (p0) REVERT: B 112 ASP cc_start: 0.7843 (p0) cc_final: 0.7458 (p0) REVERT: C 40 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7890 (p90) REVERT: C 63 ARG cc_start: 0.5194 (tpt170) cc_final: 0.4574 (mmp-170) REVERT: C 333 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8353 (tm-30) REVERT: C 512 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7945 (mtm-85) REVERT: D 210 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8887 (tm-30) REVERT: D 320 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7912 (ppt170) REVERT: D 419 GLU cc_start: 0.8739 (tt0) cc_final: 0.8408 (tm-30) REVERT: D 580 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7497 (p0) REVERT: Z 171 ARG cc_start: 0.9420 (OUTLIER) cc_final: 0.8544 (ttt180) REVERT: Z 249 ARG cc_start: 0.9350 (OUTLIER) cc_final: 0.8274 (mmt180) REVERT: Z 809 GLN cc_start: 0.5780 (OUTLIER) cc_final: 0.5230 (pp30) REVERT: Z 852 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7646 (p90) outliers start: 112 outliers final: 74 residues processed: 285 average time/residue: 1.3329 time to fit residues: 453.6174 Evaluate side-chains 273 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 187 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 727 ILE Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 168 THR Chi-restraints excluded: chain Z residue 171 ARG Chi-restraints excluded: chain Z residue 249 ARG Chi-restraints excluded: chain Z residue 270 ASP Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 320 GLU Chi-restraints excluded: chain Z residue 389 ASN Chi-restraints excluded: chain Z residue 402 THR Chi-restraints excluded: chain Z residue 410 THR Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 574 LEU Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 717 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 809 GLN Chi-restraints excluded: chain Z residue 852 HIS Chi-restraints excluded: chain Z residue 855 LEU Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 1040 THR Chi-restraints excluded: chain Z residue 1067 THR Chi-restraints excluded: chain Z residue 1091 ASP Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1145 THR Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1189 THR Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 2.9990 chunk 336 optimal weight: 5.9990 chunk 306 optimal weight: 5.9990 chunk 326 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 295 optimal weight: 20.0000 chunk 309 optimal weight: 0.9980 chunk 325 optimal weight: 0.9980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 398 ASN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1033 GLN G 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30596 Z= 0.269 Angle : 0.570 11.698 41876 Z= 0.297 Chirality : 0.043 0.203 4764 Planarity : 0.004 0.073 5181 Dihedral : 15.670 160.266 5020 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.94 % Favored : 92.78 % Rotamer: Outliers : 3.61 % Allowed : 32.80 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.84 (0.14), residues: 3560 helix: 1.90 (0.17), residues: 952 sheet: 0.00 (0.21), residues: 564 loop : -2.07 (0.12), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 875 HIS 0.003 0.001 HIS D 100 PHE 0.021 0.001 PHE A 169 TYR 0.016 0.001 TYR B 125 ARG 0.008 0.000 ARG Z 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 189 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8504 (p0) REVERT: A 183 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7193 (ttm170) REVERT: A 227 SER cc_start: 0.5986 (OUTLIER) cc_final: 0.5743 (m) REVERT: B 6 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7648 (pp20) REVERT: B 73 ASP cc_start: 0.8588 (p0) cc_final: 0.8338 (p0) REVERT: B 112 ASP cc_start: 0.7862 (p0) cc_final: 0.7507 (p0) REVERT: C 40 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7962 (p90) REVERT: C 63 ARG cc_start: 0.5252 (tpt170) cc_final: 0.4453 (mmp-170) REVERT: C 331 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8057 (mtp180) REVERT: C 333 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8354 (tm-30) REVERT: C 512 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7957 (mtm-85) REVERT: C 778 ASN cc_start: 0.8786 (m-40) cc_final: 0.8579 (m-40) REVERT: D 320 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7879 (ppt170) REVERT: D 419 GLU cc_start: 0.8749 (tt0) cc_final: 0.8424 (tm-30) REVERT: D 580 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7544 (p0) REVERT: Z 171 ARG cc_start: 0.9427 (OUTLIER) cc_final: 0.8683 (ttt180) REVERT: Z 249 ARG cc_start: 0.9355 (OUTLIER) cc_final: 0.8278 (mmt180) REVERT: Z 290 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8265 (mtt180) REVERT: Z 525 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6811 (mpm) REVERT: Z 809 GLN cc_start: 0.5800 (OUTLIER) cc_final: 0.5240 (pp30) REVERT: Z 852 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.7696 (p90) REVERT: Z 1146 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8919 (pp) REVERT: G 78 LYS cc_start: 0.8156 (mmtp) cc_final: 0.7893 (mttp) outliers start: 109 outliers final: 74 residues processed: 280 average time/residue: 1.4081 time to fit residues: 468.6756 Evaluate side-chains 276 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 185 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 727 ILE Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 168 THR Chi-restraints excluded: chain Z residue 171 ARG Chi-restraints excluded: chain Z residue 249 ARG Chi-restraints excluded: chain Z residue 270 ASP Chi-restraints excluded: chain Z residue 290 ARG Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 320 GLU Chi-restraints excluded: chain Z residue 389 ASN Chi-restraints excluded: chain Z residue 402 THR Chi-restraints excluded: chain Z residue 410 THR Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 525 MET Chi-restraints excluded: chain Z residue 574 LEU Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 682 ILE Chi-restraints excluded: chain Z residue 692 ASP Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 717 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 809 GLN Chi-restraints excluded: chain Z residue 852 HIS Chi-restraints excluded: chain Z residue 855 LEU Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 1040 THR Chi-restraints excluded: chain Z residue 1067 THR Chi-restraints excluded: chain Z residue 1091 ASP Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1146 ILE Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1189 THR Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 0.6980 chunk 345 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 240 optimal weight: 0.7980 chunk 362 optimal weight: 20.0000 chunk 333 optimal weight: 4.9990 chunk 288 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 398 ASN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z1033 GLN G 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30596 Z= 0.270 Angle : 0.582 12.944 41876 Z= 0.301 Chirality : 0.043 0.205 4764 Planarity : 0.004 0.069 5181 Dihedral : 15.644 160.007 5019 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.77 % Favored : 92.95 % Rotamer: Outliers : 3.31 % Allowed : 33.20 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.14), residues: 3560 helix: 1.88 (0.17), residues: 953 sheet: 0.00 (0.21), residues: 564 loop : -2.06 (0.12), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 875 HIS 0.003 0.001 HIS D 100 PHE 0.020 0.001 PHE A 169 TYR 0.016 0.001 TYR B 125 ARG 0.008 0.000 ARG Z 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 191 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8467 (p0) REVERT: A 183 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7191 (ttm170) REVERT: A 227 SER cc_start: 0.5799 (OUTLIER) cc_final: 0.5570 (m) REVERT: B 73 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8351 (p0) REVERT: B 112 ASP cc_start: 0.7859 (p0) cc_final: 0.7503 (p0) REVERT: C 40 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.8019 (p90) REVERT: C 63 ARG cc_start: 0.5189 (tpt170) cc_final: 0.4341 (mmp-170) REVERT: C 331 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8089 (mtp180) REVERT: C 333 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8353 (tm-30) REVERT: C 512 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7953 (mtm-85) REVERT: C 778 ASN cc_start: 0.8785 (m-40) cc_final: 0.8571 (m-40) REVERT: D 320 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7886 (ppt170) REVERT: D 419 GLU cc_start: 0.8747 (tt0) cc_final: 0.8424 (tm-30) REVERT: D 580 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7571 (p0) REVERT: Z 171 ARG cc_start: 0.9425 (OUTLIER) cc_final: 0.8649 (ttt180) REVERT: Z 249 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.8281 (mmt180) REVERT: Z 290 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8260 (mtt180) REVERT: Z 466 ARG cc_start: 0.8351 (ptm160) cc_final: 0.7942 (ptm-80) REVERT: Z 467 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8417 (mm-40) REVERT: Z 525 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.6885 (mpm) REVERT: Z 809 GLN cc_start: 0.5816 (OUTLIER) cc_final: 0.5243 (pp30) REVERT: Z 852 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7721 (p90) REVERT: Z 1146 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8908 (pp) REVERT: G 78 LYS cc_start: 0.8136 (mmtp) cc_final: 0.7815 (mttp) outliers start: 100 outliers final: 74 residues processed: 276 average time/residue: 1.4104 time to fit residues: 460.5324 Evaluate side-chains 278 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 187 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 6 GLU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 169 PHE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 727 ILE Chi-restraints excluded: chain C residue 771 ASP Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 828 ASN Chi-restraints excluded: chain C residue 881 ASP Chi-restraints excluded: chain C residue 950 LEU Chi-restraints excluded: chain C residue 953 VAL Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 156 GLN Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 300 ASN Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 536 ASN Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 584 THR Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 168 THR Chi-restraints excluded: chain Z residue 171 ARG Chi-restraints excluded: chain Z residue 249 ARG Chi-restraints excluded: chain Z residue 270 ASP Chi-restraints excluded: chain Z residue 290 ARG Chi-restraints excluded: chain Z residue 316 VAL Chi-restraints excluded: chain Z residue 320 GLU Chi-restraints excluded: chain Z residue 389 ASN Chi-restraints excluded: chain Z residue 402 THR Chi-restraints excluded: chain Z residue 410 THR Chi-restraints excluded: chain Z residue 444 ASP Chi-restraints excluded: chain Z residue 506 VAL Chi-restraints excluded: chain Z residue 525 MET Chi-restraints excluded: chain Z residue 574 LEU Chi-restraints excluded: chain Z residue 582 VAL Chi-restraints excluded: chain Z residue 609 VAL Chi-restraints excluded: chain Z residue 647 LEU Chi-restraints excluded: chain Z residue 692 ASP Chi-restraints excluded: chain Z residue 693 VAL Chi-restraints excluded: chain Z residue 695 VAL Chi-restraints excluded: chain Z residue 717 VAL Chi-restraints excluded: chain Z residue 749 VAL Chi-restraints excluded: chain Z residue 789 VAL Chi-restraints excluded: chain Z residue 797 THR Chi-restraints excluded: chain Z residue 809 GLN Chi-restraints excluded: chain Z residue 852 HIS Chi-restraints excluded: chain Z residue 855 LEU Chi-restraints excluded: chain Z residue 923 VAL Chi-restraints excluded: chain Z residue 928 LEU Chi-restraints excluded: chain Z residue 1040 THR Chi-restraints excluded: chain Z residue 1067 THR Chi-restraints excluded: chain Z residue 1091 ASP Chi-restraints excluded: chain Z residue 1112 SER Chi-restraints excluded: chain Z residue 1146 ILE Chi-restraints excluded: chain Z residue 1182 ILE Chi-restraints excluded: chain Z residue 1189 THR Chi-restraints excluded: chain G residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 3.9990 chunk 307 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 289 optimal weight: 50.0000 chunk 121 optimal weight: 5.9990 chunk 296 optimal weight: 50.0000 chunk 36 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 398 ASN ** D 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 915 GLN Z1033 GLN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.118002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.067888 restraints weight = 54860.075| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.92 r_work: 0.2696 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 30596 Z= 0.332 Angle : 0.605 12.584 41876 Z= 0.314 Chirality : 0.044 0.209 4764 Planarity : 0.004 0.066 5181 Dihedral : 15.685 159.853 5019 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.16 % Favored : 92.56 % Rotamer: Outliers : 3.45 % Allowed : 33.13 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.90 (0.14), residues: 3560 helix: 1.83 (0.17), residues: 949 sheet: -0.03 (0.21), residues: 574 loop : -2.10 (0.12), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 875 HIS 0.003 0.001 HIS A 62 PHE 0.025 0.001 PHE A 169 TYR 0.018 0.001 TYR B 125 ARG 0.007 0.000 ARG Z1016 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9854.92 seconds wall clock time: 174 minutes 44.04 seconds (10484.04 seconds total)